[Freesurfer] MNI to RAS conversion
External Email - Use Caution Dear Mailing List, I have a set of MNI coordinates (from SPM2) that I need to visualise relative to the Desikan-Killiany Atlas parcellation. However, I'm unsure how to convert these coordinates so that I can load up Freeview and visualise their location in RAS. I took at look at the 'Co-ordinate Systems' wiki ( [ https://secure-web.cisco.com/1sbzzg5doGPykSwEzV3LinGmIIvWDNkgsNwyHDKOFsZ45-q_53SrNbB7-C2BUJWcLPE5c_8TQCd-vj_zxMaCe8SBaYyvWyomDrijNzNyva47QMf3LynGDxdX3y0UUVa0trXtEqUe2FEKLiQk_UbjkEtJ-t1r8r-pbm4wcpnNmviVcnISFEp8WFr3Q7D6ISHQm63ghamGBKLRSWnMK2EX-StazzqOmNRXaGlJ2KQK4nyRfylwfU6yR3JN_m4STq96JajfTnSCcbfbAxEKXlZkztw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FCoordinateSystems | https://secure-web.cisco.com/1sbzzg5doGPykSwEzV3LinGmIIvWDNkgsNwyHDKOFsZ45-q_53SrNbB7-C2BUJWcLPE5c_8TQCd-vj_zxMaCe8SBaYyvWyomDrijNzNyva47QMf3LynGDxdX3y0UUVa0trXtEqUe2FEKLiQk_UbjkEtJ-t1r8r-pbm4wcpnNmviVcnISFEp8WFr3Q7D6ISHQm63ghamGBKLRSWnMK2EX-StazzqOmNRXaGlJ2KQK4nyRfylwfU6yR3JN_m4STq96JajfTnSCcbfbAxEKXlZkztw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FCoordinateSystems ] ), but was unable to determine how this could be done. The coordinates I need to convert are x = − 31, y = 25, z = − 7 and x = 41, y = 25, z = − 9 . Any assistance you can provide would be much appreciated. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://secure-web.cisco.com/1XfLgNltTMcAj2hlB2lDXpneNH0BEKa7I3JWAe0V_YjLyyldtEtKbepLJ52laS0iqDJvC16sqPzRsUsBCUL_IH7Bo2X_WFm4IkYBORS_iuKTCuqI-_2ccpM_cqcm6vEy4DcG0Y6_hDt-QTFiteouybhLPJf-abxc4JnNdUvOqjEWJ8b8FU29-GzlJi5DALiUXCc5NEx6RKomjQKwxNY4h60WzN24vnpo4Qteu4IlbNL_74nORG5WheiMxdTRANhuy8xEu_lzunHCprquq3Jrl5g/http%3A%2F%2Fneura.edu.au%2F | neura.edu.au ] [ https://secure-web.cisco.com/1-OSuRhzQFyIpveSl9n2IYWwim3153jvTfOp0oP1NoQ9i8s8prQsEa_7X4gQ6NcyirizVL0TtODDLfriunhl3S0biQDJ_s-wBDZcu507YVixnrLhTuuB8-G2aC6OXNzgMdkUvjHEGyAH1biXkAyjtcrYNQgKVnvQlFcLG7wN73P3GGolEGuYmz10p3zrPOJFN-rQBnyWmWiLOjeSC9K4JvlcGdsOCxG7c-l1S5yKUeWJJBlDGqCRxlpD33tH6k7djPkVFi3qh4e6uF1sFfujHDw/https%3A%2F%2Ftwitter.com%2Fneuraustralia | Twitter ] | [ https://secure-web.cisco.com/1zhTUDQgzdpMvHMPZJABMqxDyMdkh6R-Adj3u1S_KK6RNOEgi0CWnF8h26LuXKT_ItMZrmBZ-GMvqMElBq6R0nsBzBQgfguM1O64AwZz5O3YdSDMyuGqGJbDtviCk50qt4M7urjCy4LFt9WTYkGuBAr9Z05Fvg84XC2vWTPi1-WwHged-SjIYrEZr7uxwMOrKTRT1J6IrM412PC6CBV8B8dngepU6U4XowT1SXNNX3iCBhOrbHj4YARvdbJu5xk8lGnUjCylza7LNm4GiKy2Qng/https%3A%2F%2Fwww.facebook.com%2FNeuroscienceResearchAustralia | Facebook ] | [ http://secure-web.cisco.com/1eRxCu2OH0byg9xiwEv_GHTtEbivbUdVd52g3sB-lt6fa9Sd26P6J5K7kV8sIpit_gsQtJE1qNhjDAGhY_5zDyhlFMCBlHyOlJKS_MgSPRnOjKSJPrbfaepAh62aL7OYisQCn6wTcOj0eZVDfYtQoqJa61I1MNZ9LNoA3gR1uxPXgdoJxhdijEOpxJtyEj14nl3BZR2HeijZeLOZ_zmSbD2IE9j-fu8gSemPfdOElsvGD_Osc2P8WyOiCnQQpkgkrCNpvbgOIOaiicQcmXkBrow/http%3A%2F%2Fwww.neura.edu.au%2Fhelp-research%2Fsubscribe | Subscribe ] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Viewing labels in freeview
External Email - Use Caution Hi Ruopeng, Thank you for looking into this for me, changing the threshold as you suggested has solved my problem. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ] From: "Wang, Ruopeng" To: "Freesurfer support list" Sent: Monday, September 21, 2020 10:44:42 PM Subject: Re: [Freesurfer] Viewing labels in freeview Hi Bronwyn, All the values in your label are negative, while in freeview the default threshold is 0. If you change the threshold to a negative value from the GUI, you should see it. Best, Ruopeng On Sep 20, 2020, at 9:35 PM, Bronwyn Overs < [ mailto:b.ov...@neura.edu.au | b.ov...@neura.edu.au ] > wrote: External Email - Use Caution Hi Ruopeng, Thank you for your reply. I have since tried to open these problematic label files using freeview from FS 7.1.1, but I am still not able to see them on my surface. I now attach one of the two label files with this issue (the other was 6.6MB in size so was too large to send by email). Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ] From: "Wang, Ruopeng" < [ mailto:rwa...@mgh.harvard.edu | rwa...@mgh.harvard.edu ] > To: "Freesurfer support list" < [ mailto:freesurfer@nmr.mgh.harvard.edu | freesurfer@nmr.mgh.harvard.edu ] > Sent: Friday, September 18, 2020 10:28:45 PM Subject: Re: [Freesurfer] Viewing labels in freeview Hi Bronwyn, Would it be possible for you to send us the label file? You may also try the latest freeview from FS 7.1.1. A lot of changes and fixes have been made since version 5.3. Best, Ruopeng BQ_BEGIN On Sep 18, 2020, at 2:03 AM, Bronwyn Overs < [ mailto:b.ov...@neura.edu.au | b.ov...@neura.edu.au ] > wrote: External Email - Use Caution Dear freesurfer mailing list, I generated my own label file from a linear mixed effects model and now I want to view this label file on the surface of fsaverage using freeview. I am able to load the surface and label files successfully from the command line using the following: freeview -f $SUBJECTS_DIR/fsaverage_mod/surf/lh.inflated:label=lh.volume.stack.R3B.fwhm20.lmem.final.200817.gender.FDR-0001.label However, once freeview is open and the label file is loaded, I cannot see the label displayed on the surface (screenshot attached). I am currently using freesurfer version 5.3.0. Can someone please tell me how to make the label file visible on the surface of fsaverage? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ] ___ Freesurfer mailing list [ mailto:Freesurfer@nmr.mgh.harvard.edu | Freesurfer@nmr.mgh.harvard.edu ] [ https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer | https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ] ___ Freesurfer mailing list [ mailto:Freesurfer@nmr.mgh.harvard.edu | Freesurfer@nmr.mgh.harvard.edu ] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list [ mailto:Freesurfer@nmr.mgh.harvard.edu | Freesurfer@nmr.mgh.harvard.edu ] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer BQ_END ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Viewing labels in freeview
External Email - Use Caution Hi Ruopeng, Thank you for your reply. I have since tried to open these problematic label files using freeview from FS 7.1.1, but I am still not able to see them on my surface. I now attach one of the two label files with this issue (the other was 6.6MB in size so was too large to send by email). Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ] From: "Wang, Ruopeng" To: "Freesurfer support list" Sent: Friday, September 18, 2020 10:28:45 PM Subject: Re: [Freesurfer] Viewing labels in freeview Hi Bronwyn, Would it be possible for you to send us the label file? You may also try the latest freeview from FS 7.1.1. A lot of changes and fixes have been made since version 5.3. Best, Ruopeng On Sep 18, 2020, at 2:03 AM, Bronwyn Overs < [ mailto:b.ov...@neura.edu.au | b.ov...@neura.edu.au ] > wrote: External Email - Use Caution Dear freesurfer mailing list, I generated my own label file from a linear mixed effects model and now I want to view this label file on the surface of fsaverage using freeview. I am able to load the surface and label files successfully from the command line using the following: freeview -f $SUBJECTS_DIR/fsaverage_mod/surf/lh.inflated:label=lh.volume.stack.R3B.fwhm20.lmem.final.200817.gender.FDR-0001.label However, once freeview is open and the label file is loaded, I cannot see the label displayed on the surface (screenshot attached). I am currently using freesurfer version 5.3.0. Can someone please tell me how to make the label file visible on the surface of fsaverage? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ] ___ Freesurfer mailing list [ mailto:Freesurfer@nmr.mgh.harvard.edu | Freesurfer@nmr.mgh.harvard.edu ] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer rh.area.stack.R3B.fwhm20.lmem.final.200821.s.avg.dx.FDR-0003.label Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file
External Email - Use Caution Thank you very much Kersten! Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ] From: "Kersten Diers, DZNE" To: "Freesurfer support list" Sent: Monday, December 16, 2019 9:20:49 PM Subject: Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file External Email - Use Caution Hi Bronwyn, you can just add the two betas: it's the slope for the non-case group plus the difference in slopes between case and non-case group, so it should give the slope in the case group. Best regards, Kersten On Mi, 2019-12-11 at 12:53 +1100, Bronwyn Overs wrote: External Email - Use Caution Hi Kersten, Thank you for all of your help so far. I have now located the unstandardized beta values in lhstats(i).Bhat. Unfortunately one of the effects I was interested in was the slope for years within my case group, which required the use of the following contrast vector: 0 1 0 0 0 0 0 1 Do you know how I could estimate the effect size for this contrast given that it corresponds to two beta values (1 and 7)? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ] From: "Kersten Diers, DZNE" To: "Freesurfer support list" Sent: Saturday, November 30, 2019 6:50:26 AM Subject: Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file External Email - Use Caution Hi, please see my inline responses below. Best, Kersten On Fr, 2019-11-29 at 13:20 +1100, Bronwyn Overs wrote: BQ_BEGIN Hi Kersten, Thank you this is a good suggestion. Where can I get the unstandardized beta values for the lme I have already run? They are in e.g. lhstats(i).Bhat; see the tutorial webpage for some explanation. BQ_BEGIN Also, i'm not really sure how to interpret the unstandardized beta values for interaction effects like group X years, do you have any suggestions? BQ_END This would model a difference in slopes, right? So the beta value should reflect difference between the two particular groups of this contrast per year (if year is the unit of time). BQ_BEGIN Finally, do you know why the max vertex is listed as '-inf' for my largets cluster and is this a problem at all? BQ_END I can only speculate here, but it's probably worth checking: A sig value of 'Inf' would correspond to a p-value of (exactly) zero. So, one might investigate if any zeros are contained within the p-value arrays / maps, and if these zeros (if any) reflect the outcome of a statistical test (then it should be no problem) or if they were erroneously introduced. BQ_BEGIN Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ] From: "Kersten Diers, DZNE" To: "Bronwyn Overs" Cc: "Freesurfer support list" Sent: Friday, November 29, 2019 8:39:55 AM Subject: Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file Hello, and thanks for the explanation! Here's my first impression: I do not think that there is a really satisfying solution given these particular stats maps and the effect size measure you describe. I may be missing something, but I also have to admit that it is not immediately clear to me what motivates the choice of cohen's d (and the calculation you describe) in the current scenario - I've always thought of it as a measure of 'difference in means'. In a regression context, I would personally look for a measure of the "variance-explained" type. There seem to be at least two papers (Xu, 2003, Statistics in Medicine, and Selya, 2012, Frontiers) that cover these for mixed effects models. The calculation/implementation of these measures seems to be, however, not as straightforward as for classical multiple regression models; and as f
Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file
External Email - Use Caution
Hi Kersten,
Thank you for all of your help so far. I have now located the unstandardized
beta values in lhstats(i).Bhat. Unfortunately one of the effects I was
interested in was the slope for years within my case group, which required the
use of the following contrast vector:
0 1 0 0 0 0 0 1
Do you know how I could estimate the effect size for this contrast given that
it corresponds to two beta values (1 and 7)?
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1725
[ http://neura.edu.au/ | neura.edu.au ]
[ https://twitter.com/neuraustralia | Twitter ] | [
https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [
http://www.neura.edu.au/help-research/subscribe | Subscribe ]
From: "Kersten Diers, DZNE"
To: "Freesurfer support list"
Sent: Saturday, November 30, 2019 6:50:26 AM
Subject: Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary
file
External Email - Use Caution
Hi,
please see my inline responses below.
Best,
Kersten
On Fr, 2019-11-29 at 13:20 +1100, Bronwyn Overs wrote:
Hi Kersten,
Thank you this is a good suggestion. Where can I get the unstandardized beta
values for the lme I have already run?
They are in e.g. lhstats(i).Bhat; see the tutorial webpage for some
explanation.
BQ_BEGIN
Also, i'm not really sure how to interpret the unstandardized beta values for
interaction effects like group X years, do you have any suggestions?
BQ_END
This would model a difference in slopes, right? So the beta value should
reflect difference between the two particular groups of this contrast per year
(if year is the unit of time).
BQ_BEGIN
Finally, do you know why the max vertex is listed as '-inf' for my largets
cluster and is this a problem at all?
BQ_END
I can only speculate here, but it's probably worth checking: A sig value of
'Inf' would correspond to a p-value of (exactly) zero. So, one might
investigate if any zeros are contained within the p-value arrays / maps, and if
these zeros (if any) reflect the outcome of a statistical test (then it should
be no problem) or if they were erroneously introduced.
BQ_BEGIN
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1725
[ http://neura.edu.au/ | neura.edu.au ]
[ https://twitter.com/neuraustralia | Twitter ] | [
https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [
http://www.neura.edu.au/help-research/subscribe | Subscribe ]
From: "Kersten Diers, DZNE"
To: "Bronwyn Overs"
Cc: "Freesurfer support list"
Sent: Friday, November 29, 2019 8:39:55 AM
Subject: Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary
file
Hello,
and thanks for the explanation!
Here's my first impression:
I do not think that there is a really satisfying solution given these
particular stats maps and the effect size measure you describe.
I may be missing something, but I also have to admit that it is not immediately
clear to me what motivates the choice of cohen's d (and the calculation you
describe) in the current scenario - I've always thought of it as a measure of
'difference in means'.
In a regression context, I would personally look for a measure of the
"variance-explained" type. There seem to be at least two papers (Xu, 2003,
Statistics in Medicine, and Selya, 2012, Frontiers) that cover these for mixed
effects models. The calculation/implementation of these measures seems to be,
however, not as straightforward as for classical multiple regression models;
and as far as I can see, it would also involve fitting Null or reduced models,
and thus running analyses again.
By far the easiest and most straightforward way in my eyes is to report
unstandardized effect sizes, i.e. beta estimates, as you have clearly
interpretable main variables (group and time) with intuitive units that should
be comparable across studies from your field. So maybe this is an argument not
to standardize, and to state the effect size in terms of "change in thickness
per year" etc.?
Best regards,
Kersten
On Do, 2019-11-28 at 11:29 +1100, Bronwyn Overs wrote:
BQ_BEGIN
Hi Kersten,
No problem at al and thank you for your reply.
While running my correction for multiple comparisons I store the df associated
with each contrast vector using the following:
[~,~,dflh] = find(F_lhstats.df(2,:));
[~,~,dfrh] = find(F_rhstats.df(2,:));
dfmodelh = {floor(mode(dflh))};
dfmoderh = {floor(mode(dfrh))};
So far the dfmodelh and dfmoderh have been identical. I then calculate the
effect size for each
Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file
External Email - Use Caution
Hi Kersten,
Thank you this is a good suggestion. Where can I get the unstandardized beta
values for the lme I have already run? Also, i'm not really sure how to
interpret the unstandardized beta values for interaction effects like group X
years, do you have any suggestions? Finally, do you know why the max vertex is
listed as '-inf' for my largets cluster and is this a problem at all?
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1725
[ http://neura.edu.au/ | neura.edu.au ]
[ https://twitter.com/neuraustralia | Twitter ] | [
https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [
http://www.neura.edu.au/help-research/subscribe | Subscribe ]
From: "Kersten Diers, DZNE"
To: "Bronwyn Overs"
Cc: "Freesurfer support list"
Sent: Friday, November 29, 2019 8:39:55 AM
Subject: Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary
file
Hello,
and thanks for the explanation!
Here's my first impression:
I do not think that there is a really satisfying solution given these
particular stats maps and the effect size measure you describe.
I may be missing something, but I also have to admit that it is not immediately
clear to me what motivates the choice of cohen's d (and the calculation you
describe) in the current scenario - I've always thought of it as a measure of
'difference in means'.
In a regression context, I would personally look for a measure of the
"variance-explained" type. There seem to be at least two papers (Xu, 2003,
Statistics in Medicine, and Selya, 2012, Frontiers) that cover these for mixed
effects models. The calculation/implementation of these measures seems to be,
however, not as straightforward as for classical multiple regression models;
and as far as I can see, it would also involve fitting Null or reduced models,
and thus running analyses again.
By far the easiest and most straightforward way in my eyes is to report
unstandardized effect sizes, i.e. beta estimates, as you have clearly
interpretable main variables (group and time) with intuitive units that should
be comparable across studies from your field. So maybe this is an argument not
to standardize, and to state the effect size in terms of "change in thickness
per year" etc.?
Best regards,
Kersten
On Do, 2019-11-28 at 11:29 +1100, Bronwyn Overs wrote:
Hi Kersten,
No problem at al and thank you for your reply.
While running my correction for multiple comparisons I store the df associated
with each contrast vector using the following:
[~,~,dflh] = find(F_lhstats.df(2,:));
[~,~,dfrh] = find(F_rhstats.df(2,:));
dfmodelh = {floor(mode(dflh))};
dfmoderh = {floor(mode(dfrh))};
So far the dfmodelh and dfmoderh have been identical. I then calculate the
effect size for each cluster using the following steps:
1. Derive the p-value from the Max threshold ('Max'), where p = 10 to the power
of -abs(Max)
2. Calculate the t-value associated with this p-value, using the relevant df
for this contrast
3. Calculate cohen's d using 't' and 'df', where d = (t*2)/(sqrt(df))
When the Max threshold is listed as -inf I cannot complete these calculations.
Can you suggest an alternate method for generating effect sizes for these
clusters?
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1725
[ http://neura.edu.au/ | neura.edu.au ]
[ https://twitter.com/neuraustralia | Twitter ] | [
https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [
http://www.neura.edu.au/help-research/subscribe | Subscribe ]
From: "Kersten Diers, DZNE"
To: "Freesurfer support list"
Sent: Thursday, November 28, 2019 12:29:18 AM
Subject: Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary
file
External Email - Use Caution
Hi Bronwyn, Doug,
sorry - I missed the other mail from two weeks ago (and have been absent for a
few days), but I'm able to take a look now.
You mention that your goal is to calculate effect sizes. Could you briefly let
us know how you are planning to do it - this would help me to better understand
the issue.
Thanks,
Kersten
On Di, 2019-11-26 at 23:14 +, Greve, Douglas N.,Ph.D. wrote:
BQ_BEGIN
can you send the cluster summary file?
On 11/24/2019 7:09 PM, Bronwyn Overs wrote:
BQ_BEGIN
External Email - Use Caution
Hi Kersten,
Following on from Douglas's reply, you may remember my analysis as I forwarded
you some files in October (see [
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg64148.html |
https://www.mail-archive.com/freesurf
Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file
External Email - Use Caution
Hi Kersten,
No problem at al and thank you for your reply.
While running my correction for multiple comparisons I store the df associated
with each contrast vector using the following:
[~,~,dflh] = find(F_lhstats.df(2,:));
[~,~,dfrh] = find(F_rhstats.df(2,:));
dfmodelh = {floor(mode(dflh))};
dfmoderh = {floor(mode(dfrh))};
So far the dfmodelh and dfmoderh have been identical. I then calculate the
effect size for each cluster using the following steps:
1. Derive the p-value from the Max threshold ('Max'), where p = 10 to the power
of -abs(Max)
2. Calculate the t-value associated with this p-value, using the relevant df
for this contrast
3. Calculate cohen's d using 't' and 'df', where d = (t*2)/(sqrt(df))
When the Max threshold is listed as -inf I cannot complete these calculations.
Can you suggest an alternate method for generating effect sizes for these
clusters?
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1725
[ http://neura.edu.au/ | neura.edu.au ]
[ https://twitter.com/neuraustralia | Twitter ] | [
https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [
http://www.neura.edu.au/help-research/subscribe | Subscribe ]
From: "Kersten Diers, DZNE"
To: "Freesurfer support list"
Sent: Thursday, November 28, 2019 12:29:18 AM
Subject: Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary
file
External Email - Use Caution
Hi Bronwyn, Doug,
sorry - I missed the other mail from two weeks ago (and have been absent for a
few days), but I'm able to take a look now.
You mention that your goal is to calculate effect sizes. Could you briefly let
us know how you are planning to do it - this would help me to better understand
the issue.
Thanks,
Kersten
On Di, 2019-11-26 at 23:14 +, Greve, Douglas N.,Ph.D. wrote:
can you send the cluster summary file?
On 11/24/2019 7:09 PM, Bronwyn Overs wrote:
BQ_BEGIN
External Email - Use Caution
Hi Kersten,
Following on from Douglas's reply, you may remember my analysis as I forwarded
you some files in October (see [
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg64148.html |
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg64148.html ] ).
I followed your suggestions of removing the '--thmax 5' argument form
'mri_surfcluster', and now the labels generated by 'mri_label2label' overlap
perfectly with the significance maps from the LME. However, now my largest
clusters have a maximum threshold of '-inf' in my cluster summary files. Do you
have any idea how to get around this problem so that I can use my max threshold
values to calculate cluster-wise effect sizes?
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1725
[ http://neura.edu.au/ | neura.edu.au ]
[ https://twitter.com/neuraustralia | Twitter ] | [
https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [
http://www.neura.edu.au/help-research/subscribe | Subscribe ]
From: "Greve, Douglas N.,Ph.D." [ mailto:dgr...@mgh.harvard.edu |
]
To: "Freesurfer support list" [ mailto:freesurfer@nmr.mgh.harvard.edu |
] , "Kersten Diers, DZNE" [
mailto:kersten.di...@dzne.de |
]
Sent: Thursday, November 14, 2019 4:23:12 AM
Subject: Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary
file
I'll have to leave this one for Kersten as it appears that the LME stuff
is generating and inf value
On 11/12/19 7:05 PM, Bronwyn Overs wrote:
>
> External Email - Use Caution
>
> Hi Douglas,
>
> Yes I have looked at it in Freeview and I have attached a screenshot
> for your reference.
>
> The /fsdata/lme/thickness/rh.thickness.B1B7.mgh file was generated
> with a mass-univariate spatiotemporal model using
> 'lme_mass_fit_EMinit' and then FDR correction was applied across both
> hemispheres (lme_mass_FDR). I have provided analysis details and
> syntax below. The B1B7 contrast represents the affect of years in cases.
>
> Sample:
> Our sample includes 112 controls subjects, and 106 cases. All subjects
> are aged between 12 and 30 years. 153 or these subjects have 2
> time-points (77 control, 76 cases), while the remaining 65 individuals
> have only 1 MRI time-point. We also have mixed ethnicites - 165
> Caucasians, 23 Asians, and 30 mixed (Asians-Caucasians).
>
> The QDEC file contains the following 6 variables:
> 1. Y (years between scans)
> 2. A (baseline age)
> 3. G (group, 1=case, 0=control)
> 4. S (sex, 1=female, 0=male)
> 5. E1 (Ethnicity 1,
Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file
External Email - Use Caution
Hi Kersten,
Following on from Douglas's reply, you may remember my analysis as I forwarded
you some files in October (see [
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg64148.html |
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg64148.html ] ).
I followed your suggestions of removing the '--thmax 5' argument form
'mri_surfcluster', and now the labels generated by 'mri_label2label' overlap
perfectly with the significance maps from the LME. However, now my largest
clusters have a maximum threshold of '-inf' in my cluster summary files. Do you
have any idea how to get around this problem so that I can use my max threshold
values to calculate cluster-wise effect sizes?
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1725
[ http://neura.edu.au/ | neura.edu.au ]
[ https://twitter.com/neuraustralia | Twitter ] | [
https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [
http://www.neura.edu.au/help-research/subscribe | Subscribe ]
From: "Greve, Douglas N.,Ph.D."
To: "Freesurfer support list" , "Kersten Diers,
DZNE"
Sent: Thursday, November 14, 2019 4:23:12 AM
Subject: Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary
file
I'll have to leave this one for Kersten as it appears that the LME stuff
is generating and inf value
On 11/12/19 7:05 PM, Bronwyn Overs wrote:
>
> External Email - Use Caution
>
> Hi Douglas,
>
> Yes I have looked at it in Freeview and I have attached a screenshot
> for your reference.
>
> The /fsdata/lme/thickness/rh.thickness.B1B7.mgh file was generated
> with a mass-univariate spatiotemporal model using
> 'lme_mass_fit_EMinit' and then FDR correction was applied across both
> hemispheres (lme_mass_FDR). I have provided analysis details and
> syntax below. The B1B7 contrast represents the affect of years in cases.
>
> Sample:
> Our sample includes 112 controls subjects, and 106 cases. All subjects
> are aged between 12 and 30 years. 153 or these subjects have 2
> time-points (77 control, 76 cases), while the remaining 65 individuals
> have only 1 MRI time-point. We also have mixed ethnicites - 165
> Caucasians, 23 Asians, and 30 mixed (Asians-Caucasians).
>
> The QDEC file contains the following 6 variables:
> 1. Y (years between scans)
> 2. A (baseline age)
> 3. G (group, 1=case, 0=control)
> 4. S (sex, 1=female, 0=male)
> 5. E1 (Ethnicity 1, 1=asian, 0=other)
> 6. E2 (Ethnicity 1, 1=mixed-asian-caucasian, 0=other)
>
> Design matrix: [ones(length(M),1) M M(:,1).*M(:,3)]
> i.e. main effects for each of the qdec variables + an
> interaction term for years X group
>
> DVs: Cortical thickness, area and volume
>
> Model: Mass-univariate spatiotemporal model using
> 'lme_mass_fit_EMinit'
> CODE:
> % Read in surface files
> [Y,mri] = fs_read_Y(mgh);
> % Read in qdec file
> Qdec = fReadQdec(qdec);
> % Remove fsid from qdec
> Qdec = rmQdecCol(Qdec,1);
> % Store col 1 (fsid-base) in sID variable
> sID = Qdec(2:end,1);
> % Remove col 1 (fsid-base) from Qdec array
> Qdec = rmQdecCol(Qdec,1);
> % Convert Qdec to numeric matrix M
> M = Qdec2num(Qdec);
> % Sort data and evaluate design matrix
> [M,Y,ni] = sortData(M,1,Y,sID);
> X = eval([ones(length(M),1) M M(:,1).*M(:,3)])
> % Compute vertex-wise temporal covariance estimates.
> [Th0, Re] = lme_mass_fit_EMinit(X,[1],Y,ni,cortex,3);
> %Segmentation and model fitting.
> [Rgs, RgMeans, stats] = fit(Th0, Re, [1], sphere, cortex, X, Y,
> ni);
> %Check surfaces.
> surfcomp(Th0, RgMeans, sphere, fig1, fig2)
>
> Correction for multiple comparisons: FDR across both hemispheres
> CODE:
> P = [ F_lhstats.pval(lhcortex) F_rhstats.pval(rhcortex) ]; G = [
> F_lhstats.sgn(lhcortex)
> F_rhstats.sgn(rhcortex) ];
> [detvtx, sided_pval, pth] = lme_mass_FDR2(P,G,[],0.05,0);
> altfdr(r,2) = num2cell(abs(log10(lme_mass_FDR(P,0.05;
> pcor = -log10(pth);
> [~,~,dflh] = find(F_lhstats.df(2,:));
> [~,~,dfrh] = find(F_rhstats.df(2,:));
> dfmodelh(r,2) = {floor(mode(dflh))};
> dfmoderh(r,2) = {floor(mode(dfrh))};
> thrlh(r,2) = {pcor};
> thrrh(r,2) = {pcor};
> [~,dc] = size(detvtx);
> dvtx(r,2) = {dc};
>
> Kind regards,
>
>
> Bronwyn Overs
>
> Research Assistant
>
>
> Neuroscience Research Australia
> Margarete Ainsworth Building
> Barker Street Randwick Sydney NSW 2031 Australia
> *M* 0411 308 769 *T* +61 2 9399 1725
>
>
> neura.edu.au <http://neura.edu.au/>
>
> Twitt
[Freesurfer] Max threshold marked as '-inf' in cluster summary file
External Email - Use Caution
Dear Freesurfer Mailing List,
I have completed an LME analysis in matlab and have generated a number of
different cluster summary files for my various contrasts. In many of resulting
cluster summary files the 'Max' value for the largest cluster which encompasses
most of the brain surface is reported as infinity ('-inf'). Please find an
example file attached. As I was hoping to use these values to generate effect
size estimates, can you please tell me what alternate value I could substitute
here for 'Max'?
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1725
[ http://neura.edu.au/ | neura.edu.au ]
[ https://twitter.com/neuraustralia | Twitter ] | [
https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [
http://www.neura.edu.au/help-research/subscribe | Subscribe ]
# Cluster Growing Summary (mri_surfcluster)
# $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $
# $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
# CreationTime 2019/11/05-02:14:24-GMT
# cmdline mri_surfcluster --in /fsdata/lme/thickness/rh.thickness.B1B7.mgh
--subject fsaverage_mod --hemi rh --thmin 3 --thsign abs --olab
rh.thickness.B1B7.th001 --sum
/fsdata/lme/thickness/clustersummary/rh.thickness.B1B7.th001.ClusterSummary.txt
# cwd /fsdata/lme/thickness
# sysname Linux
# hostname work.server
# machine x86_64
# FixVertexAreaFlag 1
# FixSurfClusterArea 1
#
# Input /fsdata/lme/thickness/rh.thickness.B1B7.mgh
# Frame Number 0
# srcsubj fsaverage_mod
# hemi rh
# surface white
# SUBJECTS_DIR /fsdata
# SearchSpace_mm2 65020.8
# SearchSpace_vtx 163842
# Bonferroni 0
# Minimum Threshold 3
# Maximum Threshold infinity
# Threshold Signabs
# AdjustThreshWhenOneTail 1
# Area Threshold0 mm^2
# Overall max 2.04724 at vertex 113626
# Overall min -inf at vertex 41
# NClusters 7
# Total Cortical Surface Area 65020.8 (mm^2)
# FixMNI = 1
#
# ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZNVtxs
1 -inf 41 63036.28 60.9 -34.4 -10.2 122676
2 -3.189 89230 2.67 23.68.0 -13.6 7
3 -3.164 95874 0.45 46.6 -14.7 33.9 1
4 -3.039 161505 1.52 24.9 -20.4 -22.6 3
5 -3.033 16546 0.35 35.1 -31.5 53.8 1
6 -3.026 60029 0.32 47.7 -15.5 53.4 1
7 -3.003 133433 0.51 46.6 -15.5 35.9 1
___
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Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels
External Email - Use Caution Hi Kersten, Thanks you so much for your reply and sorry I missed your earlier message. I'll implement the suggestions you've suggested. Thanks again. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ] From: "Kersten Diers, DZNE" To: "Freesurfer support list" Sent: Tuesday, October 29, 2019 9:21:59 PM Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels External Email - Use Caution Hm, I think I replied last Wednesday; anyway, below is the message again. Best regards, Kersten Forwarded Message From : "Diers, Kersten /DZNE" < [ mailto:%22Diers,%20Kersten%20/dzne%22%20%3ckersten.di...@dzne.de%3e | kersten.di...@dzne.de ] > Reply-to: Freesurfer support list To : freesurfer@nmr.mgh.harvard.edu < [ mailto:%22freesur...@nmr.mgh.harvard.edu%22%20%3cfreesur...@nmr.mgh.harvard.edu%3e | freesurfer@nmr.mgh.harvard.edu ] > Subject : Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels Date : Wed, 23 Oct 2019 07:39:54 + External Email - Use Caution Hi Bronwyn, thanks for sending the files. I've taken a look, and suggest that you leave out the '--thmax 5' argument from your mri_surfcluster command. Then, it may still be necessary to set the label threshold value in Freeview to a value below zero. When I run the modified mri_surfcluster command with the example data you provided, the created label resembled the mgh file, i.e. no cut-outs in regions of high significance were present. Best regards, Kersten On Di, 2019-10-29 at 16:46 +1100, Bronwyn Overs wrote: External Email - Use Caution Hi Kersten, Did you recieve the files I dropped to [ mailto:mreu...@nmr.mgh.harvard.edu | mreu...@nmr.mgh.harvard.edu ] on the 16th of October (titled 'BAR_Sydney_FSIssues_SurfThreshLabels.zip')? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ] From: "Kersten Diers, DZNE" To: "Freesurfer support list" Sent: Wednesday, October 16, 2019 2:15:53 AM Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels External Email - Use Caution Hi, please use [ mailto:mreu...@nmr.mgh.harvard.edu | mreu...@nmr.mgh.harvard.edu ] , he'll forward it to me. Thanks, Kersten On Di, 2019-10-15 at 11:03 +1100, Bronwyn Overs wrote: BQ_BEGIN External Email - Use Caution Hi Kersten, That would be very helpful thank you. What email address should I designate as the recipient when using Freesurfer FileDrop? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ] From: "Kersten Diers, DZNE" To: "Freesurfer support list" Sent: Wednesday, October 2, 2019 4:21:32 PM Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels External Email - Use Caution Hi Bronwyn, thanks for the update and additional info. I have to say that I have no very good clue at the moment. Could you maybe upload an examplary file to the Freesurfer FileDrop at [ https://gate.nmr.mgh.harvard.edu/filedrop2/ | https://gate.nmr.mgh.harvard.edu/filedrop2/ ] so that we can take a closer look? Best regards, Kersten On Di, 2019-10-01 at 14:01 +1000, Bronwyn Overs wrote: BQ_BEGIN External Email - Use Caution Hi Kersten, Thank you for your detailed reply and sorry for this delayed response. Yes the top row in my figure (attached again) was produced by using the '--olab' argument with the 'mri_surfcluster' command and then loading each cluster from a different label file. I attempted to follow your suggestion and adjust the label 'threshold' in Freeview to minimum value in my significance map (-5), but this did not display th
Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels
External Email - Use Caution Hi Kersten, Did you recieve the files I dropped to [ mailto:mreu...@nmr.mgh.harvard.edu | mreu...@nmr.mgh.harvard.edu ] on the 16th of October (titled 'BAR_Sydney_FSIssues_SurfThreshLabels.zip')? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ] From: "Kersten Diers, DZNE" To: "Freesurfer support list" Sent: Wednesday, October 16, 2019 2:15:53 AM Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels External Email - Use Caution Hi, please use [ mailto:mreu...@nmr.mgh.harvard.edu | mreu...@nmr.mgh.harvard.edu ] , he'll forward it to me. Thanks, Kersten On Di, 2019-10-15 at 11:03 +1100, Bronwyn Overs wrote: External Email - Use Caution Hi Kersten, That would be very helpful thank you. What email address should I designate as the recipient when using Freesurfer FileDrop? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ] From: "Kersten Diers, DZNE" To: "Freesurfer support list" Sent: Wednesday, October 2, 2019 4:21:32 PM Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels External Email - Use Caution Hi Bronwyn, thanks for the update and additional info. I have to say that I have no very good clue at the moment. Could you maybe upload an examplary file to the Freesurfer FileDrop at [ https://gate.nmr.mgh.harvard.edu/filedrop2/ | https://gate.nmr.mgh.harvard.edu/filedrop2/ ] so that we can take a closer look? Best regards, Kersten On Di, 2019-10-01 at 14:01 +1000, Bronwyn Overs wrote: BQ_BEGIN External Email - Use Caution Hi Kersten, Thank you for your detailed reply and sorry for this delayed response. Yes the top row in my figure (attached again) was produced by using the '--olab' argument with the 'mri_surfcluster' command and then loading each cluster from a different label file. I attempted to follow your suggestion and adjust the label 'threshold' in Freeview to minimum value in my significance map (-5), but this did not display the missing regions - the surface remained the same as row 1 of the attached figure. To provide you with a little more detail about my method - am using 'mri_surfcluster' with the '--olab' argument to derive all of my significant clusters of 100mm^2 or more. I am then using 'mri_label2label' to map each label files (from the 'mri_surfcluster' command) back onto the images for each of my individual subjects, and then generate subject level stats for each cluster using 'mris_anatomical_stats'. At the moment I am concerned that the subject level stats I have derived from my label files do not accurately represent each significant cluster in totality as regions appear to be missing even when i adjust the minimum threshold. As an alternative, when using 'mri_surfcluster', can I substitute the '--o', '--ocn', or '--oannot' arguments for '--olab', and still perform my 'mri_label2label' and 'mris_anatomical_stats' steps? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ] From: "Kersten Diers, DZNE" To: "Freesurfer support list" Sent: Thursday, September 5, 2019 2:13:50 AM Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels External Email - Use Caution Hi, I suppose what we are seeing in the top row of your figure are Freesurfer labels, right? I.e. you probably used the '--olab' argument with the 'mri_surfcluster' command, and are loading each cluster from a different label file? If my speculation is correct, then what you observe could be due to the 'threshold' setting in freeview, i.e. this little box just below the label box in the left part of the GUI. This threshold is by default set t
Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels
External Email - Use Caution Hi Kersten, That would be very helpful thank you. What email address should I designate as the recipient when using Freesurfer FileDrop? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ] From: "Kersten Diers, DZNE" To: "Freesurfer support list" Sent: Wednesday, October 2, 2019 4:21:32 PM Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels External Email - Use Caution Hi Bronwyn, thanks for the update and additional info. I have to say that I have no very good clue at the moment. Could you maybe upload an examplary file to the Freesurfer FileDrop at [ https://gate.nmr.mgh.harvard.edu/filedrop2/ | https://gate.nmr.mgh.harvard.edu/filedrop2/ ] so that we can take a closer look? Best regards, Kersten On Di, 2019-10-01 at 14:01 +1000, Bronwyn Overs wrote: External Email - Use Caution Hi Kersten, Thank you for your detailed reply and sorry for this delayed response. Yes the top row in my figure (attached again) was produced by using the '--olab' argument with the 'mri_surfcluster' command and then loading each cluster from a different label file. I attempted to follow your suggestion and adjust the label 'threshold' in Freeview to minimum value in my significance map (-5), but this did not display the missing regions - the surface remained the same as row 1 of the attached figure. To provide you with a little more detail about my method - am using 'mri_surfcluster' with the '--olab' argument to derive all of my significant clusters of 100mm^2 or more. I am then using 'mri_label2label' to map each label files (from the 'mri_surfcluster' command) back onto the images for each of my individual subjects, and then generate subject level stats for each cluster using 'mris_anatomical_stats'. At the moment I am concerned that the subject level stats I have derived from my label files do not accurately represent each significant cluster in totality as regions appear to be missing even when i adjust the minimum threshold. As an alternative, when using 'mri_surfcluster', can I substitute the '--o', '--ocn', or '--oannot' arguments for '--olab', and still perform my 'mri_label2label' and 'mris_anatomical_stats' steps? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ] From: "Kersten Diers, DZNE" To: "Freesurfer support list" Sent: Thursday, September 5, 2019 2:13:50 AM Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster labels External Email - Use Caution Hi, I suppose what we are seeing in the top row of your figure are Freesurfer labels, right? I.e. you probably used the '--olab' argument with the 'mri_surfcluster' command, and are loading each cluster from a different label file? If my speculation is correct, then what you observe could be due to the 'threshold' setting in freeview, i.e. this little box just below the label box in the left part of the GUI. This threshold is by default set to zero, but lowering it to some sufficiently negative value (i.e. the minimum value in the 'sig' map) should also display those regions that seem to be missing at the moment. At least this is what I observed when I tried to reproduce your observation, i.e. I could create (and reverse by setting another threshold) similar 'cut-outs' in the cluster maps. In addition, you could also load the ouput files that are produced by the '--o', '--ocn', or '--oannot' arguments of the 'mri_surfcluster' command. I would guess that they don't show this pattern of missing areas. Hope this helps, Kersten On Di, 2019-09-03 at 14:00 +1000, Bronwyn Overs wrote: BQ_BEGIN External Email - Use Caution Dear Freesurfer mailing list, I am trying to get to the bottom of a discrepancy between two surface based images generated from the output of an LME analysis. The surfaces in row 1 of the attached image were generated by loading the four FDR significant clusters that were >100mm^2 in the cluster summary file. The surfaces in row 2 of the attached image were generated by loading the significance map generated for
[Freesurfer] DF for Longitudinal LME
External Email - Use Caution Dear Freesurfer Mailing List, I am trying to calculate the effect size of the main and interaction effect clusters that were significant in my vertex-wise LME analysis. For this I need the degrees of freedom for each contrast, but I am confused about how to derive this. My input sample has 218 subjects (153 with 2 time-points, 65 with 1 time-point). The effects for which I need the degrees of freedom are: 1) Main effect of years in the control group (n=112) 2) Main effect of years in the case group (n=106) 3) Main effect of group at baseline (group has two levels, 0 or 1) 4) Interaction between years and group Any assistance you can provide would be great. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Recon-all error
Hi Emma, Thanks for your reply. I just tried running the recon-all process from the beginning using the -all flag and it seems to have fixed whatever the error was and the processing completed successfully. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe> > On 25 Aug 2017, at 11:11 pm, Boyd, Emma <ebo...@mgh.harvard.edu> wrote: > > Hi Bronwyn, > > Doug is out of the office today. What is the command you ran after deleting > everything in the surf folder? Can you send us the recon-all.log? > > Best, > Emma > > > - > Emma Boyd > Research Technician II > Laboratory for Computational Neuroimaging > Martinos Center for Biomedical Imaging > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bronwyn Overs > <b.ov...@neura.edu.au> > Sent: Thursday, August 24, 2017 9:14 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Recon-all error > > Hi Douglas, > > Do you have any thoughts about the new missing directory error I am getting > detailed below? > Kind regards, > Bronwyn Overs > Research Assistant > > Neuroscience Research Australia > Margarete Ainsworth Building > Barker Street Randwick Sydney NSW 2031 Australia > M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 > neura.edu.au <http://neura.edu.au/> > <https://twitter.com/neuraustralia> > <https://www.facebook.com/NeuroscienceResearchAustralia> > <http://www.neura.edu.au/help-research/subscribe> >> On 17 Aug 2017, at 1:16 pm, Bronwyn Overs <b.ov...@neura.edu.au >> <mailto:b.ov...@neura.edu.au>> wrote: >> >> Hi Douglas, >> >> Thanks for your reply. I followed your suggestion and deleted everything in >> the surf folder for each subject. I am not getting the following error: >> >> Reading source surface reg /workingdata/ID_001/surf/lh.sphere.reg >> No such file or directory >> mri_surf2surf: could not read surface /workingdata/ID_001/surf/lh.sphere.reg >> No such file or directory >> Linux katana.neura.edu.au <http://katana.neura.edu.au/> >> 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 >> x86_64 GNU/Linux >> >> recon-all -s ID_001 exited with ERRORS at Thu Aug 17 11:14:08 AEST 2017 >> >> To report a problem, see >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting%5C%5C> >> >> Should I try running the recon-all -all for each subject? >> Kind regards, >> Bronwyn Overs >> Research Assistant >> >> Neuroscience Research Australia >> Margarete Ainsworth Building >> Barker Street Randwick Sydney NSW 2031 Australia >> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 >> neura.edu.au <http://neura.edu.au/> >> <https://twitter.com/neuraustralia> >> <https://www.facebook.com/NeuroscienceResearchAustralia> >> <http://www.neura.edu.au/help-research/subscribe> >>> On 17 Aug 2017, at 8:27 am, Douglas N Greve <gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>> >>> That means that the surfaces are out of sync. the -make-all only works >>> in certain circumstances. You can delete everything in the surf folder >>> (it should all be recreated anyway with -autorecon2-cp) >>> >>> >>> On 08/15/2017 10:04 PM, Bronwyn Overs wrote: >>>> Dear mailing list, >>>> >>>> I am trying to batch a series of 30 MRI images using the following >>>> command: >>>> recon-all -autorecon2-cp -subjid ID001 -qcache >>>> >>>> But for each image the process exits with the following errors: >>>> --- >>>> #@# 1/1 ID_001 Wed Aug 16 11:39:12 AEST 2017 -- >>>> --- >>>> mri_surf2surf --srcsubject ID_001 --srchemi lh --srcsurfreg sphere.reg >>>> --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval >>>> ./tmp.mris_preproc.18138/ID_001.1.mgh --sval >>>> /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume >>>
Re: [Freesurfer] Error with recon-all long
Hi Martin, Thanks for your suggestion, I will try rerunning the base from scratch to see if this makes a difference. With regards to the base and time-point IDs, those included in the files I sent you were actually not the IDs we use. I did a find and replace to remove our actual IDs in case they could be used to identify the participant. We use our subject ID for the base ID (a ten digit number made up of the 3 digit site ID, 4 digit family ID, and 3 digit person ID), and the unique scan ID for the time-point ID (BAR_***, a 3 digit number assigned at the time of scanning). We have 1 or two timepoints per subject. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe> > On 25 Aug 2017, at 7:28 pm, Martin Reuter <mreu...@nmr.mgh.harvard.edu> wrote: > > Hi Bronwyn, > I would guess that there has been a problem with the way you run the base. > Take one case, copy the cross sectionals into a new directory and re-run the > base from scratch. > If your two time points are named like: TPID_001 and TPID_002 then the base > command should be: > > recon-all -base BASEID -tp TPID_001 -tp TPID_002 -all > > this will create a directory called BASEID. > > Then the longitudinal commands will be: > recon-all -long TPID_001 BASEID -all > and > recon-all -long TPID_002 BASEID -all > > > I am a little irritated by the way you call your base (as it looks like you > called it BASEID_001. If 001 is the subject ID, then this makes sense, but > then the time point ID , TPID_001 does not. It is missing an index for the > time point like TPID_001_01 for the first and TPID_001_02 for the next etc. > Please let me know how you call your input data and base IDS. Also how many > time points do you have per subject. > > Best, Martin > > > Am 18.08.2017 um 03:01 schrieb Bruce Fischl: >> Hi Bronwyn >> >> I defer to Martin :) >> Bruce >> On Fri, 18 Aug 2017, Bronwyn Overs wrote: >> >>> Hi Bruce, >>> >>> Please find attached both the command line output and the recon-all log. >>> The command line I ran was: >>> recon-all -long BASEID_001 TPID_001 -all >>> >>> I have already run and reviewed the cross-sectional and base images for >>> this subject and am now at the point of running the longitudinal image for >>> the first time. This is one of 25 longitudinal images that exited with the >>> same error. >>> >>> >>> >>> Kind regards, >>> Bronwyn Overs >>> Research Assistant >>> >>> Neuroscience Research Australia >>> Margarete Ainsworth Building >>> Barker Street Randwick Sydney NSW 2031 Australia >>> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 >>> >>> neura.edu.au <http://neura.edu.au/> <http://neura.edu.au/> >>> <https://twitter.com/neuraustralia> <https://twitter.com/neuraustralia> >>> <https://www.facebook.com/NeuroscienceResearchAustralia> >>> <https://www.facebook.com/NeuroscienceResearchAustralia> >>> <http://www.neura.edu.au/help-research/subscribe> >>> <http://www.neura.edu.au/help-research/subscribe> >>>> On 18 Aug 2017, at 12:57 am, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >>>> <mailto:fis...@nmr.mgh.harvard.edu> wrote: >>>> >>>> Hi Bronwyn >>>> >>>> can you send us the full command line you ran, screen output and >>>> recon-all.log? And maybe a description of where you are in the process? >>>> You already ran all the tps through the cross? And created the base? >>>> >>>> cheers >>>> Bruce >>>> On Thu, 17 Aug 2017, Bronwyn Overs wrote: >>>> >>>>> Hi again list, >>>>> Sorry I made a mistake. The lh.sphere.reg and lh.smoothwm are both in the >>>>> base image directory, but I’m still receiving the mismatch error. Partial >>>>> ls >>>>> -l displayed below: >>>>> [b.overs@katana surf]$ ls -l $SUBJECTS_DIR/BASEID_001/surf >>>>> total 120260 >>>>> ... >>>>> -rw-rw-r-- 1 b.overs GroupID 4554988 Aug 9 13:11 lh.qsphere.nofix >>>>> -rw-rw-r-- 1 b.overs Gr
Re: [Freesurfer] Recon-all error
Hi Douglas, Do you have any thoughts about the new missing directory error I am getting detailed below? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe> > On 17 Aug 2017, at 1:16 pm, Bronwyn Overs <b.ov...@neura.edu.au> wrote: > > Hi Douglas, > > Thanks for your reply. I followed your suggestion and deleted everything in > the surf folder for each subject. I am not getting the following error: > > Reading source surface reg /workingdata/ID_001/surf/lh.sphere.reg > No such file or directory > mri_surf2surf: could not read surface /workingdata/ID_001/surf/lh.sphere.reg > No such file or directory > Linux katana.neura.edu.au <http://katana.neura.edu.au/> > 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 > x86_64 GNU/Linux > > recon-all -s ID_001 exited with ERRORS at Thu Aug 17 11:14:08 AEST 2017 > > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting%5C%5C> > > Should I try running the recon-all -all for each subject? > Kind regards, > Bronwyn Overs > Research Assistant > > Neuroscience Research Australia > Margarete Ainsworth Building > Barker Street Randwick Sydney NSW 2031 Australia > M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 > > neura.edu.au <http://neura.edu.au/> > <https://twitter.com/neuraustralia> > <https://www.facebook.com/NeuroscienceResearchAustralia> > <http://www.neura.edu.au/help-research/subscribe> >> On 17 Aug 2017, at 8:27 am, Douglas N Greve <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> That means that the surfaces are out of sync. the -make-all only works >> in certain circumstances. You can delete everything in the surf folder >> (it should all be recreated anyway with -autorecon2-cp) >> >> >> On 08/15/2017 10:04 PM, Bronwyn Overs wrote: >>> Dear mailing list, >>> >>> I am trying to batch a series of 30 MRI images using the following >>> command: >>> recon-all -autorecon2-cp -subjid ID001 -qcache >>> >>> But for each image the process exits with the following errors: >>> --- >>> #@# 1/1 ID_001 Wed Aug 16 11:39:12 AEST 2017 -- >>> --- >>> mri_surf2surf --srcsubject ID_001 --srchemi lh --srcsurfreg sphere.reg >>> --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval >>> ./tmp.mris_preproc.18138/ID_001.1.mgh --sval >>> /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume >>> >>> --jac --sfmt curv --noreshape --no-cortex >>> Source registration surface changed to sphere.reg >>> Target registration surface changed to sphere.reg >>> srcsubject = ID_001 >>> srcval = >>> /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume >>> srctype= curv >>> trgsubject = fsaverage >>> trgval = ./tmp.mris_preproc.18138/ID_001.1.mgh >>> trgtype= >>> srcsurfreg = sphere.reg >>> trgsurfreg = sphere.reg >>> srchemi= lh >>> trghemi= lh >>> frame = 0 >>> fwhm-in= 0 >>> fwhm-out = 0 >>> label-src = (null) >>> label-trg = (null) >>> OKToRevFaceOrder = 1 >>> Reading source surface reg >>> /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.sphere.reg >>> Loading source data >>> Reading curvature file >>> /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume >>> ERROR: number of vertices in >>> /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume >>> >>> does not match surface (109952,110385) >>> ERROR: reading curvature file >>> Linux katana.neura.edu.au <http://katana.neura.edu.au/> >>> <http://katana.neura.edu.au <http://katana.neura.edu.au/>> >>> 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 >>> x86_64 x86_64 GNU/Linux >>> >>> recon-all -s ID_001 exited with ERRORS at Wed Aug 16 11:39:13 AEST 2017 >
Re: [Freesurfer] Error with recon-all long
Hi again list, Sorry I made a mistake. The lh.sphere.reg and lh.smoothwm are both in the base image directory, but I’m still receiving the mismatch error. Partial ls -l displayed below: [b.overs@katana surf]$ ls -l $SUBJECTS_DIR/BASEID_001/surf total 120260 ... -rw-rw-r-- 1 b.overs GroupID 4554988 Aug 9 13:11 lh.qsphere.nofix -rw-rw-r-- 1 b.overs GroupID 4518556 Aug 9 13:35 lh.smoothwm -rw-rw-r-- 1 b.overs GroupID 501887 Aug 9 13:36 lh.smoothwm.BE.crv ... -rw-rw-r-- 1 b.overs GroupID 4507326 Jul 19 19:15 lh.sphere -rw-rw-r-- 1 b.overs GroupID 4507810 Jul 19 19:36 lh.sphere.reg -rw-rw-r-- 1 b.overs GroupID 501887 Aug 9 13:35 lh.sulc … Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe> > On 17 Aug 2017, at 2:39 pm, Bronwyn Overs <b.ov...@neura.edu.au> wrote: > > Dear freesurfer mailing list, > > I have been running the recon-all -long command and received the following > errors: > # > #@# Surf Reg lh Wed Aug 16 18:07:26 AEST 2017 > /mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/TPID_001.long.BASEID_001/scripts > > mris_register -curv -nosulc -norot > /mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh.sphere.reg > > /usr/local/FREESURFER/freesurfer5.3.0/average/lh.average.curvature.filled.buckner40.tif > ../surf/lh.sphere.reg > > using smoothwm curvature for final alignment > disabling initial sulc alignment... > disabling initial rigid alignment... > $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ > $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ > reading surface from > /mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh.sphere.reg... > reading template parameterization from > /usr/local/FREESURFER/freesurfer5.3.0/average/lh.average.curvature.filled.buckner40.tif... > mrisReadTriangleFile(/mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh.smoothwm): > surface doesn't match > /mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh.sphere.reg > > No such file or directory > mrisReadTriangleFile failed. > > No such file or directory > MRISreadOriginalProperties: could not read surface file smoothwm > No such file or directory > ERROR -5 from MRISreadOriginalProperties(). > Linux katana.neura.edu.au <http://katana.neura.edu.au/> > 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 > x86_64 GNU/Linux > > recon-all -s TPID_001.long.BASEID_001 exited with ERRORS at Wed Aug 16 > 18:07:29 AEST 2017 > > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > I checked the surf folder and the lh.sphere.reg file does not appear to be > there. Do you know how this could have happened and how I can fix the problem? > Kind regards, > Bronwyn Overs > Research Assistant > > Neuroscience Research Australia > Margarete Ainsworth Building > Barker Street Randwick Sydney NSW 2031 Australia > M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 > > neura.edu.au <http://neura.edu.au/> > <https://twitter.com/neuraustralia> > <https://www.facebook.com/NeuroscienceResearchAustralia> > <http://www.neura.edu.au/help-research/subscribe> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Error with recon-all long
Dear freesurfer mailing list, I have been running the recon-all -long command and received the following errors: # #@# Surf Reg lh Wed Aug 16 18:07:26 AEST 2017 /mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/TPID_001.long.BASEID_001/scripts mris_register -curv -nosulc -norot /mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh.sphere.reg /usr/local/FREESURFER/freesurfer5.3.0/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment disabling initial sulc alignment... disabling initial rigid alignment... $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from /mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh.sphere.reg... reading template parameterization from /usr/local/FREESURFER/freesurfer5.3.0/average/lh.average.curvature.filled.buckner40.tif... mrisReadTriangleFile(/mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh.smoothwm): surface doesn't match /mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh.sphere.reg No such file or directory mrisReadTriangleFile failed. No such file or directory MRISreadOriginalProperties: could not read surface file smoothwm No such file or directory ERROR -5 from MRISreadOriginalProperties(). Linux katana.neura.edu.au 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s TPID_001.long.BASEID_001 exited with ERRORS at Wed Aug 16 18:07:29 AEST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> I checked the surf folder and the lh.sphere.reg file does not appear to be there. Do you know how this could have happened and how I can fix the problem? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Recon-all error
Hi Douglas, Thanks for your reply. I followed your suggestion and deleted everything in the surf folder for each subject. I am not getting the following error: Reading source surface reg /workingdata/ID_001/surf/lh.sphere.reg No such file or directory mri_surf2surf: could not read surface /workingdata/ID_001/surf/lh.sphere.reg No such file or directory Linux katana.neura.edu.au 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ID_001 exited with ERRORS at Thu Aug 17 11:14:08 AEST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting%5C%5C> Should I try running the recon-all -all for each subject? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe> > On 17 Aug 2017, at 8:27 am, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > That means that the surfaces are out of sync. the -make-all only works > in certain circumstances. You can delete everything in the surf folder > (it should all be recreated anyway with -autorecon2-cp) > > > On 08/15/2017 10:04 PM, Bronwyn Overs wrote: >> Dear mailing list, >> >> I am trying to batch a series of 30 MRI images using the following >> command: >> recon-all -autorecon2-cp -subjid ID001 -qcache >> >> But for each image the process exits with the following errors: >> --- >> #@# 1/1 ID_001 Wed Aug 16 11:39:12 AEST 2017 -- >> --- >> mri_surf2surf --srcsubject ID_001 --srchemi lh --srcsurfreg sphere.reg >> --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval >> ./tmp.mris_preproc.18138/ID_001.1.mgh --sval >> /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume >> >> --jac --sfmt curv --noreshape --no-cortex >> Source registration surface changed to sphere.reg >> Target registration surface changed to sphere.reg >> srcsubject = ID_001 >> srcval = >> /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume >> srctype= curv >> trgsubject = fsaverage >> trgval = ./tmp.mris_preproc.18138/ID_001.1.mgh >> trgtype= >> srcsurfreg = sphere.reg >> trgsurfreg = sphere.reg >> srchemi= lh >> trghemi= lh >> frame = 0 >> fwhm-in= 0 >> fwhm-out = 0 >> label-src = (null) >> label-trg = (null) >> OKToRevFaceOrder = 1 >> Reading source surface reg >> /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.sphere.reg >> Loading source data >> Reading curvature file >> /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume >> ERROR: number of vertices in >> /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume >> >> does not match surface (109952,110385) >> ERROR: reading curvature file >> Linux katana.neura.edu.au <http://katana.neura.edu.au/> >> <http://katana.neura.edu.au <http://katana.neura.edu.au/>> >> 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 >> x86_64 x86_64 GNU/Linux >> >> recon-all -s ID_001 exited with ERRORS at Wed Aug 16 11:39:13 AEST 2017 >> >> To report a problem, see >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> I came across an earlier post in relation to a similar error >> (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009807.html >> >> <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009807.html>) >> where >> it was recommended that you run “recon-all -s subjid -make all” to >> rebuild all files where the dependency chain is wrong. I ran this for >> each of the subjects and then tried to rerun my original recon-all >> command again but got the same error. Do you have any alternate >> suggestions for fixing this problem? >> >> Kind regards, >> >> Bronwyn Overs >> Research Assistant >> >> Neuroscience Research Australia >> >> Neuroscience Research Australia >> Margarete Ainsworth Building >> Barker Street Randwick Sydney NSW 2031 Au
[Freesurfer] Recon-all error
Dear mailing list, I am trying to batch a series of 30 MRI images using the following command: recon-all -autorecon2-cp -subjid ID001 -qcache But for each image the process exits with the following errors: --- #@# 1/1 ID_001 Wed Aug 16 11:39:12 AEST 2017 -- --- mri_surf2surf --srcsubject ID_001 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.18138/ID_001.1.mgh --sval /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume --jac --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = ID_001 srcval = /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume srctype= curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.18138/ID_001.1.mgh trgtype= srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi= lh trghemi= lh frame = 0 fwhm-in= 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.sphere.reg Loading source data Reading curvature file /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume ERROR: number of vertices in /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume does not match surface (109952,110385) ERROR: reading curvature file Linux katana.neura.edu.au 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ID_001 exited with ERRORS at Wed Aug 16 11:39:13 AEST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> I came across an earlier post in relation to a similar error (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009807.html <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009807.html>) where it was recommended that you run “recon-all -s subjid -make all” to rebuild all files where the dependency chain is wrong. I ran this for each of the subjects and then tried to rerun my original recon-all command again but got the same error. Do you have any alternate suggestions for fixing this problem? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Medial Surface Problem
Hi Bruce, I have now re-uploaded all the requested files and info via the ftp site (see below). The zipped file name is fsMedialSurfaceProblem.zip Name (surfer.nmr.mgh.harvard.edu:Bronwyn): anonymous 331 Please specify the password. Password: 230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. ftp> cd transfer/incoming 250 Directory successfully changed. ftp> put fsMedialSurfaceProblem.zip local: fsMedialSurfaceProblem.zip remote: fsMedialSurfaceProblem.zip 229 Entering Extended Passive Mode (|||37889|). 150 Ok to send data. 100% |***| 2017 MiB 51.01 KiB/s00:00 ETA 226 Transfer complete. 2116019235 bytes sent in 11:15:08 (51.01 KiB/s) Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe> > On 5 Jul 2017, at 3:40 am, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > > sure. Can you upload the data again to our ftp site? Don't use the filedrop - > use ftp and make sure you include the cross and the long of all the > timepoints for this subject, and also the coordinates of the location you are > seeing the problem > > > cheers > Bruce > > > On Tue, 4 Jul 2017, Bronwyn Overs wrote: > >> Thanks Bruce. >> Kind regards, >> Bronwyn Overs >> Research Assistant >> Neuroscience Research Australia >> Neuroscience Research Australia >> Margarete Ainsworth Building >> Barker Street Randwick Sydney NSW 2031 Australia >> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 >> neura.edu.au >> Follow @neuraustralia on twitter Follow NeuRA on facebook Subscribe to the >> NeuRA Magazine >> >> On 3 Jul 2017, at 11:55 pm, Bruce Fischl >> <fis...@nmr.mgh.harvard.edu> wrote: >> Hi Bronwyn >> not yet, but we'll get to it soon >> cheers >> Bruce >> On Mon, 3 Jul 2017, Bronwyn Overs wrote: >> >> Hi Bruce, >> Just wanted to check in on the status of reviewing our >> medial surface >> problem. Any luck so far? >> Kind regards, >> Bronwyn Overs >> Research Assistant >> Neuroscience Research Australia >> Neuroscience Research Australia >> Margarete Ainsworth Building >> Barker Street Randwick Sydney NSW 2031 Australia >> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 >> neura.edu.au >> Follow @neuraustralia on twitter Follow NeuRA on facebook >> Subscribe to the >> NeuRA Magazine >> >> On 14 Jun 2017, at 9:52 am, Bronwyn Overs >> <b.ov...@neura.edu.au> >> wrote: >> Hi Bruce, >> That's fine, thanks very much. >> Bronwyn Overs >> Research Assistant >> >> Neuroscience Research Australia >> Margarete Ainsworth Building >> Barker Street Randwick Sydney NSW 2031 Australia >> M 0411 308 769 T +61 2 9399 1883 >> neura.edu.au >> Twitter | Facebook | Subscribe >> ___ >> _ >> From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> >> To: "Freesurfer support list" >> <freesurfer@nmr.mgh.harvard.edu> >> Sent: Wednesday, 14 June, 2017 00:02:04 >> Subject: Re: [Freesurfer] Medial Surface Problem >> thanks Bronwyn >> I got them. It will take a bit for us to get to as this is >> in the long >> stream and we have a new postdoc who will be taking it >> over. >> cheers >> Bruce >> On Tue, 13 Jun >> 2017, Bronwyn Overs wrote: >> > Hi Bruce, >> > Sure, files have been dropped again. >> > >> > Kind regards, >> > >> > Bronwyn Overs >> > Research Assistant >> > >> > Neuroscience Research Australia >> > >> > Neuroscience Research Australia >> > Margarete Ainsworth Building >> > Barker Street Randwick Sydney NSW 2031 Australia >> > M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 >> > >> > neura.edu.au >> > >> > Follow @neuraustralia on twitter Follow NeuRA on
Re: [Freesurfer] Medial Surface Problem
Thanks Bruce. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe> > On 3 Jul 2017, at 11:55 pm, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > > Hi Bronwyn > > not yet, but we'll get to it soon > > cheers > Bruce > On Mon, 3 Jul 2017, Bronwyn Overs wrote: > >> Hi Bruce, >> Just wanted to check in on the status of reviewing our medial surface >> problem. Any luck so far? >> Kind regards, >> Bronwyn Overs >> Research Assistant >> Neuroscience Research Australia >> Neuroscience Research Australia >> Margarete Ainsworth Building >> Barker Street Randwick Sydney NSW 2031 Australia >> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 >> neura.edu.au <http://neura.edu.au/> >> Follow @neuraustralia on twitter Follow NeuRA on facebook Subscribe to the >> NeuRA Magazine >> >> On 14 Jun 2017, at 9:52 am, Bronwyn Overs <b.ov...@neura.edu.au> >> wrote: >> Hi Bruce, >> That's fine, thanks very much. >> Bronwyn Overs >> Research Assistant >> >> Neuroscience Research Australia >> Margarete Ainsworth Building >> Barker Street Randwick Sydney NSW 2031 Australia >> M 0411 308 769 T +61 2 9399 1883 >> neura.edu.au >> Twitter | Facebook | Subscribe >> >> From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> >> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> >> Sent: Wednesday, 14 June, 2017 00:02:04 >> Subject: Re: [Freesurfer] Medial Surface Problem >> thanks Bronwyn >> I got them. It will take a bit for us to get to as this is in the long >> stream and we have a new postdoc who will be taking it over. >> cheers >> Bruce >> On Tue, 13 Jun >> 2017, Bronwyn Overs wrote: >> > Hi Bruce, >> > Sure, files have been dropped again. >> > >> > Kind regards, >> > >> > Bronwyn Overs >> > Research Assistant >> > >> > Neuroscience Research Australia >> > >> > Neuroscience Research Australia >> > Margarete Ainsworth Building >> > Barker Street Randwick Sydney NSW 2031 Australia >> > M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 >> > >> > neura.edu.au >> > >> > Follow @neuraustralia on twitter Follow NeuRA on facebook Subscribe >> to the >> > NeuRA Magazine >> > >> > >> > On 13 Jun 2017, at 11:44 am, Bruce Fischl >> > <fis...@nmr.mgh.harvard.edu> wrote: >> > >> > Hi Bronwyn >> > Can you filedrop it again? I don't think I have it >> > Thanks >> > Bruce >> > >> > On May 15, 2017, at 8:27 PM, Bronwyn Overs <b.ov...@neura.edu.au> >> > wrote: >> > >> > Hi Bruce, >> > Thank you for offering to take a look at this medial surface >> > problem. >> > >> > I have uploaded all of the relevant files to through the >> > Martinos Centre FileDrop v2.0 to your email address >> > (fis...@nmr.mgh.harvard.edu). Please let me know if you require >> > any additional information. >> > >> > Kind regards, >> > >> > Bronwyn Overs >> > Research Assistant >> > >> > Neuroscience Research Australia >> > >> > Neuroscience Research Australia >> > Margarete Ainsworth Building >> > Barker Street Randwick Sydney NSW 2031 Australia >> > M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 >> > >> > neura.edu.au >> > >> > Follow @neuraustralia on twitter Follow NeuRA on facebook >> > Subscribe to the NeuRA Magazine >> > >> > >> > On 5 May 2017, at 8:25 am, Bruce Fischl >> > <fis...@nmr.mgh.harvard.edu> wrote: >> > >> > if someone can upload a dataset as well as the exact >> > coordinates of the problem I'll take a look >> > >> > cheers >> > Bruce >> > >> > On Fri, 5 May 2017, Yann Quidé wrote: >> > >> > Hi all, >> > We also have the same issue, any >> > i
Re: [Freesurfer] Medial Surface Problem
Hi Bruce, Just wanted to check in on the status of reviewing our medial surface problem. Any luck so far? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe> > On 14 Jun 2017, at 9:52 am, Bronwyn Overs <b.ov...@neura.edu.au> wrote: > > Hi Bruce, > > That's fine, thanks very much. > > Bronwyn Overs > Research Assistant > > > Neuroscience Research Australia > Margarete Ainsworth Building > Barker Street Randwick Sydney NSW 2031 Australia > M 0411 308 769 T +61 2 9399 1883 > > neura.edu.au <http://neura.edu.au/> > > Twitter <https://twitter.com/neuraustralia> | Facebook > <https://www.facebook.com/NeuroscienceResearchAustralia> | Subscribe > <http://www.neura.edu.au/help-research/subscribe> > > > > From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> > To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > Sent: Wednesday, 14 June, 2017 00:02:04 > Subject: Re: [Freesurfer] Medial Surface Problem > > thanks Bronwyn > > I got them. It will take a bit for us to get to as this is in the long > stream and we have a new postdoc who will be taking it over. > > cheers > Bruce > On Tue, 13 Jun > 2017, Bronwyn Overs wrote: > > > Hi Bruce, > > Sure, files have been dropped again. > > > > Kind regards, > > > > Bronwyn Overs > > Research Assistant > > > > Neuroscience Research Australia > > > > Neuroscience Research Australia > > Margarete Ainsworth Building > > Barker Street Randwick Sydney NSW 2031 Australia > > M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 > > > > neura.edu.au > > > > Follow @neuraustralia on twitter Follow NeuRA on facebook Subscribe to the > > NeuRA Magazine > > > > > > On 13 Jun 2017, at 11:44 am, Bruce Fischl > > <fis...@nmr.mgh.harvard.edu> wrote: > > > > Hi Bronwyn > > Can you filedrop it again? I don't think I have it > > Thanks > > Bruce > > > > On May 15, 2017, at 8:27 PM, Bronwyn Overs <b.ov...@neura.edu.au> > > wrote: > > > > Hi Bruce, > > Thank you for offering to take a look at this medial surface > > problem. > > > > I have uploaded all of the relevant files to through the > > Martinos Centre FileDrop v2.0 to your email address > > (fis...@nmr.mgh.harvard.edu). Please let me know if you require > > any additional information. > > > > Kind regards, > > > > Bronwyn Overs > > Research Assistant > > > > Neuroscience Research Australia > > > > Neuroscience Research Australia > > Margarete Ainsworth Building > > Barker Street Randwick Sydney NSW 2031 Australia > > M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 > > > > neura.edu.au > > > > Follow @neuraustralia on twitter Follow NeuRA on facebook > > Subscribe to the NeuRA Magazine > > > > > > On 5 May 2017, at 8:25 am, Bruce Fischl > > <fis...@nmr.mgh.harvard.edu> wrote: > > > > if someone can upload a dataset as well as the exact > > coordinates of the problem I'll take a look > > > > cheers > > Bruce > > > > On Fri, 5 May 2017, Yann Quidé wrote: > > > > Hi all, > > We also have the same issue, any > > idea/suggestion? > > Thanks. > > Yann > > > >On 27 Apr 2017, at 9:43 am, Bronwyn Overs > > <b.ov...@neura.edu.au> > >wrote: > > Hi Mailing List, > > Still trying to solve the below medial surface > > problem. Does anyone > > have any ideas? > > Kind regards, > > Bronwyn Overs > > Research Assistant > > Neuroscience Research Australia > > Neuroscience Research Australia > > Margarete Ainsworth Building > > Barker Street Randwick Sydney NSW 2031 > > Australia > > M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 > > 1265 > > neura.edu.au > > Follow @neuraustralia on twitter Follow NeuRA > > on facebook Subscribe to > > the NeuRA Magazine > > > >On
Re: [Freesurfer] Medial Surface Problem
Hi Bruce, That's fine, thanks very much. Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ] From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Wednesday, 14 June, 2017 00:02:04 Subject: Re: [Freesurfer] Medial Surface Problem thanks Bronwyn I got them. It will take a bit for us to get to as this is in the long stream and we have a new postdoc who will be taking it over. cheers Bruce On Tue, 13 Jun 2017, Bronwyn Overs wrote: > Hi Bruce, > Sure, files have been dropped again. > > Kind regards, > > Bronwyn Overs > Research Assistant > > Neuroscience Research Australia > > Neuroscience Research Australia > Margarete Ainsworth Building > Barker Street Randwick Sydney NSW 2031 Australia > M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 > > neura.edu.au > > Follow @neuraustralia on twitter Follow NeuRA on facebook Subscribe to the > NeuRA Magazine > > > On 13 Jun 2017, at 11:44 am, Bruce Fischl > <fis...@nmr.mgh.harvard.edu> wrote: > > Hi Bronwyn > Can you filedrop it again? I don't think I have it > Thanks > Bruce > > On May 15, 2017, at 8:27 PM, Bronwyn Overs <b.ov...@neura.edu.au> > wrote: > > Hi Bruce, > Thank you for offering to take a look at this medial surface > problem. > > I have uploaded all of the relevant files to through the > Martinos Centre FileDrop v2.0 to your email address > (fis...@nmr.mgh.harvard.edu). Please let me know if you require > any additional information. > > Kind regards, > > Bronwyn Overs > Research Assistant > > Neuroscience Research Australia > > Neuroscience Research Australia > Margarete Ainsworth Building > Barker Street Randwick Sydney NSW 2031 Australia > M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 > > neura.edu.au > > Follow @neuraustralia on twitter Follow NeuRA on facebook > Subscribe to the NeuRA Magazine > > > On 5 May 2017, at 8:25 am, Bruce Fischl > <fis...@nmr.mgh.harvard.edu> wrote: > > if someone can upload a dataset as well as the exact > coordinates of the problem I'll take a look > > cheers > Bruce > > On Fri, 5 May 2017, Yann Quidé wrote: > > Hi all, > We also have the same issue, any > idea/suggestion? > Thanks. > Yann > > On 27 Apr 2017, at 9:43 am, Bronwyn Overs > <b.ov...@neura.edu.au> > wrote: > Hi Mailing List, > Still trying to solve the below medial surface > problem. Does anyone > have any ideas? > Kind regards, > Bronwyn Overs > Research Assistant > Neuroscience Research Australia > Neuroscience Research Australia > Margarete Ainsworth Building > Barker Street Randwick Sydney NSW 2031 > Australia > M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 > 1265 > neura.edu.au > Follow @neuraustralia on twitter Follow NeuRA > on facebook Subscribe to > the NeuRA Magazine > > On 28 Mar 2017, at 10:51 pm, Yann Quidé > <yannqu...@gmail.com> wrote: > Dear all, > I have an equivalent issue with my data. Any > idea on how to fix > this? > Thanks. > Yann > > Begin forwarded message: > From: Bronwyn Overs <b.ov...@neura.edu.au> > Subject: Re: [Freesurfer] Medial Surface > Problem > Date: 20 March 2017 10:28:37 am AEDT > To: Freesurfer support list > <freesurfer@nmr.mgh.harvard.edu> > Reply-To: Freesurfer support list > <freesurfer@nmr.mgh.harvard.edu> > Hello again mailing list, > Can anyone address the possible cause of the > medial > surface problem shown below (overestimating of > rh medial > surface, shows up in the long image and not > the tp or base > images). Forgot to mention that I am using > freesurfer v5.3 > with an updated mris_make_surfaces binary > (sourced from > the developmentversionat > ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binarie > s/cento > s6_x86_64/ ). > Here is the image again: > > Kind regards, > Bronwyn Overs > Research Assistant > Neuroscience Research Australia > Neuroscience Research Australia > Margarete Ainsworth Building > Barker Street Randwick Sydney NSW 2031 > Australia > M 0411 308 769 T +61 2 9399 1883 F
Re: [Freesurfer] Medial Surface Problem
Hi Bruce, Sure, files have been dropped again. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe> > On 13 Jun 2017, at 11:44 am, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > > Hi Bronwyn > Can you filedrop it again? I don't think I have it > Thanks > Bruce > > On May 15, 2017, at 8:27 PM, Bronwyn Overs <b.ov...@neura.edu.au > <mailto:b.ov...@neura.edu.au>> wrote: > >> Hi Bruce, >> >> Thank you for offering to take a look at this medial surface problem. >> >> I have uploaded all of the relevant files to through the Martinos Centre >> FileDrop v2.0 to your email address (fis...@nmr.mgh.harvard.edu >> <mailto:fis...@nmr.mgh.harvard.edu>). Please let me know if you require any >> additional information. >> Kind regards, >> Bronwyn Overs >> Research Assistant >> >> Neuroscience Research Australia >> Margarete Ainsworth Building >> Barker Street Randwick Sydney NSW 2031 Australia >> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 >> >> neura.edu.au <http://neura.edu.au/> >> <https://twitter.com/neuraustralia> >> <https://www.facebook.com/NeuroscienceResearchAustralia> >> <http://www.neura.edu.au/help-research/subscribe> >>> On 5 May 2017, at 8:25 am, Bruce Fischl <fis...@nmr.mgh.harvard.edu >>> <mailto:fis...@nmr.mgh.harvard.edu>> wrote: >>> >>> if someone can upload a dataset as well as the exact coordinates of the >>> problem I'll take a look >>> >>> cheers >>> Bruce >>> >>> On Fri, 5 May 2017, Yann Quidé wrote: >>> >>>> Hi all, >>>> We also have the same issue, any idea/suggestion? >>>> Thanks. >>>> Yann >>>> >>>> On 27 Apr 2017, at 9:43 am, Bronwyn Overs <b.ov...@neura.edu.au >>>> <mailto:b.ov...@neura.edu.au>> >>>> wrote: >>>> Hi Mailing List, >>>> Still trying to solve the below medial surface problem. Does anyone >>>> have any ideas? >>>> Kind regards, >>>> Bronwyn Overs >>>> Research Assistant >>>> Neuroscience Research Australia >>>> Neuroscience Research Australia >>>> Margarete Ainsworth Building >>>> Barker Street Randwick Sydney NSW 2031 Australia >>>> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 >>>> neura.edu.au <http://neura.edu.au/> >>>> Follow @neuraustralia on twitter Follow NeuRA on facebook Subscribe to >>>> the NeuRA Magazine >>>> >>>> On 28 Mar 2017, at 10:51 pm, Yann Quidé >>>> <yannqu...@gmail.com <mailto:yannqu...@gmail.com>> wrote: >>>> Dear all, >>>> I have an equivalent issue with my data. Any idea on how to fix >>>> this? >>>> Thanks. >>>> Yann >>>> >>>> Begin forwarded message: >>>> From: Bronwyn Overs <b.ov...@neura.edu.au <mailto:b.ov...@neura.edu.au>> >>>> Subject: Re: [Freesurfer] Medial Surface Problem >>>> Date: 20 March 2017 10:28:37 am AEDT >>>> To: Freesurfer support list >>>> <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> >>>> Reply-To: Freesurfer support list >>>> <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> >>>> Hello again mailing list, >>>> Can anyone address the possible cause of the medial >>>> surface problem shown below (overestimating of rh medial >>>> surface, shows up in the long image and not the tp or base >>>> images). Forgot to mention that I am using freesurfer v5.3 >>>> with an updated mris_make_surfaces binary (sourced from >>>> the development versionat >>>> ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/cento >>>> <ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/cento> >>>> s6_x86_64/ ). >>>> Here is the image again: >>>> >>>> Kind regards, >>>> Bronwyn Overs >>>> Research Assistant >>>> Neuroscience R
Re: [Freesurfer] Medial Surface Problem
Hi Bruce, Just wanted to check in and see if you had examined the files I uploaded yet? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe> > On 16 May 2017, at 10:27 am, Bronwyn Overs <b.ov...@neura.edu.au> wrote: > > Hi Bruce, > > Thank you for offering to take a look at this medial surface problem. > > I have uploaded all of the relevant files to through the Martinos Centre > FileDrop v2.0 to your email address (fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>). Please let me know if you require any > additional information. > Kind regards, > Bronwyn Overs > Research Assistant > > Neuroscience Research Australia > Margarete Ainsworth Building > Barker Street Randwick Sydney NSW 2031 Australia > M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 > > neura.edu.au <http://neura.edu.au/> > <https://twitter.com/neuraustralia> > <https://www.facebook.com/NeuroscienceResearchAustralia> > <http://www.neura.edu.au/help-research/subscribe> >> On 5 May 2017, at 8:25 am, Bruce Fischl <fis...@nmr.mgh.harvard.edu >> <mailto:fis...@nmr.mgh.harvard.edu>> wrote: >> >> if someone can upload a dataset as well as the exact coordinates of the >> problem I'll take a look >> >> cheers >> Bruce >> >> On Fri, 5 May 2017, Yann Quidé wrote: >> >>> Hi all, >>> We also have the same issue, any idea/suggestion? >>> Thanks. >>> Yann >>> >>> On 27 Apr 2017, at 9:43 am, Bronwyn Overs <b.ov...@neura.edu.au >>> <mailto:b.ov...@neura.edu.au>> >>> wrote: >>> Hi Mailing List, >>> Still trying to solve the below medial surface problem. Does anyone >>> have any ideas? >>> Kind regards, >>> Bronwyn Overs >>> Research Assistant >>> Neuroscience Research Australia >>> Neuroscience Research Australia >>> Margarete Ainsworth Building >>> Barker Street Randwick Sydney NSW 2031 Australia >>> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 >>> neura.edu.au <http://neura.edu.au/> >>> Follow @neuraustralia on twitter Follow NeuRA on facebook Subscribe to >>> the NeuRA Magazine >>> >>> On 28 Mar 2017, at 10:51 pm, Yann Quidé >>> <yannqu...@gmail.com <mailto:yannqu...@gmail.com>> wrote: >>> Dear all, >>> I have an equivalent issue with my data. Any idea on how to fix >>> this? >>> Thanks. >>> Yann >>> >>> Begin forwarded message: >>> From: Bronwyn Overs <b.ov...@neura.edu.au <mailto:b.ov...@neura.edu.au>> >>> Subject: Re: [Freesurfer] Medial Surface Problem >>> Date: 20 March 2017 10:28:37 am AEDT >>> To: Freesurfer support list >>> <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> >>> Reply-To: Freesurfer support list >>> <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> >>> Hello again mailing list, >>> Can anyone address the possible cause of the medial >>> surface problem shown below (overestimating of rh medial >>> surface, shows up in the long image and not the tp or base >>> images). Forgot to mention that I am using freesurfer v5.3 >>> with an updated mris_make_surfaces binary (sourced from >>> the development versionat >>> ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/cento >>> <ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/cento> >>> s6_x86_64/ ). >>> Here is the image again: >>> >>> Kind regards, >>> Bronwyn Overs >>> Research Assistant >>> Neuroscience Research Australia >>> Neuroscience Research Australia >>> Margarete Ainsworth Building >>> Barker Street Randwick Sydney NSW 2031 Australia >>> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 >>> neura.edu.au <http://neura.edu.au/> >>> Follow @neuraustralia on twitter Follow NeuRA on facebook >>> Subscribe to the NeuRA Magazine >>> >>> On 6 Mar 2017, at 1:17 pm, Bronwyn Overs >>> <b.ov...@neura.edu.au <mailto:b.ov...@ne
Re: [Freesurfer] Medial Surface Problem
Hi Bruce, Thank you for offering to take a look at this medial surface problem. I have uploaded all of the relevant files to through the Martinos Centre FileDrop v2.0 to your email address (fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>). Please let me know if you require any additional information. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe> > On 5 May 2017, at 8:25 am, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > > if someone can upload a dataset as well as the exact coordinates of the > problem I'll take a look > > cheers > Bruce > > On Fri, 5 May 2017, Yann Quidé wrote: > >> Hi all, >> We also have the same issue, any idea/suggestion? >> Thanks. >> Yann >> >> On 27 Apr 2017, at 9:43 am, Bronwyn Overs <b.ov...@neura.edu.au> >> wrote: >> Hi Mailing List, >> Still trying to solve the below medial surface problem. Does anyone >> have any ideas? >> Kind regards, >> Bronwyn Overs >> Research Assistant >> Neuroscience Research Australia >> Neuroscience Research Australia >> Margarete Ainsworth Building >> Barker Street Randwick Sydney NSW 2031 Australia >> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 >> neura.edu.au <http://neura.edu.au/> >> Follow @neuraustralia on twitter Follow NeuRA on facebook Subscribe to >> the NeuRA Magazine >> >> On 28 Mar 2017, at 10:51 pm, Yann Quidé >> <yannqu...@gmail.com> wrote: >> Dear all, >> I have an equivalent issue with my data. Any idea on how to fix >> this? >> Thanks. >> Yann >> >> Begin forwarded message: >> From: Bronwyn Overs <b.ov...@neura.edu.au> >> Subject: Re: [Freesurfer] Medial Surface Problem >> Date: 20 March 2017 10:28:37 am AEDT >> To: Freesurfer support list >> <freesurfer@nmr.mgh.harvard.edu> >> Reply-To: Freesurfer support list >> <freesurfer@nmr.mgh.harvard.edu> >> Hello again mailing list, >> Can anyone address the possible cause of the medial >> surface problem shown below (overestimating of rh medial >> surface, shows up in the long image and not the tp or base >> images). Forgot to mention that I am using freesurfer v5.3 >> with an updated mris_make_surfaces binary (sourced from >> the development versionat >> ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/cento >> s6_x86_64/ ). >> Here is the image again: >> >> Kind regards, >> Bronwyn Overs >> Research Assistant >> Neuroscience Research Australia >> Neuroscience Research Australia >> Margarete Ainsworth Building >> Barker Street Randwick Sydney NSW 2031 Australia >> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 >> neura.edu.au <http://neura.edu.au/> >> Follow @neuraustralia on twitter Follow NeuRA on facebook >> Subscribe to the NeuRA Magazine >> >> On 6 Mar 2017, at 1:17 pm, Bronwyn Overs >> <b.ov...@neura.edu.au> wrote: >> Hi mailing list, >> I am currently processing a longitudinal image and >> have come across a problem at the medial surface in >> the long image (step 3). As you can see in the >> attached image, the rh medial surface has been >> significantly overestimated and extends into the lh >> surface. This error showed up only in only 1 of the >> 2 long images for this subject, and both the >> time-point images and the base are perfectly fine. >> Do you know why this is happening? >> >> Kind regards, >> Bronwyn Overs >> Research Assistant >> Neuroscience Research Australia >> Neuroscience Research Australia >> Margarete Ainsworth Building >> Barker Street Randwick Sydney NSW 2031 Australia >> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 >> neura.edu.au <http://neura.edu.au/> >> Follow @neuraustralia on twitter Follow NeuRA on >> facebook Subscribe to the NeuRA Magazine >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> The information in this e-mail is intended only for >> the person to whom it is >> addressed. If you believe this e-mail was sent to
Re: [Freesurfer] Medial Surface Problem
Hi Mailing List, Still trying to solve the below medial surface problem. Does anyone have any ideas? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe> > On 28 Mar 2017, at 10:51 pm, Yann Quidé <yannqu...@gmail.com> wrote: > > Dear all, > > I have an equivalent issue with my data. Any idea on how to fix this? > > Thanks. > > Yann > > >> Begin forwarded message: >> >> From: Bronwyn Overs <b.ov...@neura.edu.au <mailto:b.ov...@neura.edu.au>> >> Subject: Re: [Freesurfer] Medial Surface Problem >> Date: 20 March 2017 10:28:37 am AEDT >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu>> >> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu>> >> >> Hello again mailing list, >> >> Can anyone address the possible cause of the medial surface problem shown >> below (overestimating of rh medial surface, shows up in the long image and >> not the tp or base images). Forgot to mention that I am using freesurfer >> v5.3 with an updated mris_make_surfaces binary (sourced from the development >> version at >> ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/ >> >> <ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/> >> ). >> >> Here is the image again: >> >> >> Kind regards, >> Bronwyn Overs >> Research Assistant >> >> Neuroscience Research Australia >> Margarete Ainsworth Building >> Barker Street Randwick Sydney NSW 2031 Australia >> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 >> >> neura.edu.au <http://neura.edu.au/> >> <https://twitter.com/neuraustralia> >> <https://www.facebook.com/NeuroscienceResearchAustralia> >> <http://www.neura.edu.au/help-research/subscribe> >>> On 6 Mar 2017, at 1:17 pm, Bronwyn Overs <b.ov...@neura.edu.au >>> <mailto:b.ov...@neura.edu.au>> wrote: >>> >>> Hi mailing list, >>> >>> I am currently processing a longitudinal image and have come across a >>> problem at the medial surface in the long image (step 3). As you can see in >>> the attached image, the rh medial surface has been significantly >>> overestimated and extends into the lh surface. This error showed up only in >>> only 1 of the 2 long images for this subject, and both the time-point >>> images and the base are perfectly fine. Do you know why this is happening? >>> >>> >>> >>> >>> Kind regards, >>> Bronwyn Overs >>> Research Assistant >>> >>> Neuroscience Research Australia >>> Margarete Ainsworth Building >>> Barker Street Randwick Sydney NSW 2031 Australia >>> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 >>> >>> neura.edu.au <http://neura.edu.au/> >>> <https://twitter.com/neuraustralia> >>> <https://www.facebook.com/NeuroscienceResearchAustralia> >>> <http://www.neura.edu.au/help-research/subscribe> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.ha
Re: [Freesurfer] Comparing LME models
Great thanks Martin. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe> > On 4 Apr 2017, at 11:47 pm, Martin Reuter <mreu...@nmr.mgh.harvard.edu> wrote: > > Hi Bronwyn, > ok, now I understand. I am not sure which one to take, I guess it won't > matter much. Why don't you try either way and see if you get the same result. > Best, Martin > > On 03/30/2017 12:59 AM, Bronwyn Overs wrote: >> Hi Martin, >> >> Yes this is for a mass univariate approach. Re segmentation I was referring >> to the lhRgs output from the lme_mass_fit_Rgw command: >> lhstats_1RF = lme_mass_fit_Rgw(X,[1],Y,ni,lhTh0_1RF,lhRgs,lhsphere); >> So if both models have the same number of random effect, does it matter >> which lhRgs do I use? >> Kind regards, >> Bronwyn Overs >> Research Assistant >> >> Neuroscience Research Australia >> Margarete Ainsworth Building >> Barker Street Randwick Sydney NSW 2031 Australia >> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 >> >> neura.edu.au <http://neura.edu.au/> >> <https://twitter.com/neuraustralia> >> <https://www.facebook.com/NeuroscienceResearchAustralia> >> <http://www.neura.edu.au/help-research/subscribe> >>> On 30 Mar 2017, at 12:18 am, Martin Reuter <mreu...@nmr.mgh.harvard.edu >>> <mailto:mreu...@nmr.mgh.harvard.edu>> wrote: >>> >>> Hi Bronwyn, >>> is this for a mass univariate approach? What do you mean with segmentation? >>> ROI or vertex-wise vs region-wise? >>> >>> Best, Martin >>> On 03/29/2017 01:23 AM, Bronwyn Overs wrote: >>>> Hi Mailing List, >>>> >>>> If you are comparing two matlab based linear mixed effects models >>>> (vertex-wise) with the same number of random effects (e.g. model with >>>> random effect for time vs. model with random effect for age at baseline), >>>> which segmentation should you use to estimate the parameters for both >>>> models? >>>> Kind regards, >>>> Bronwyn Overs >>>> Research Assistant >>>> >>>> Neuroscience Research Australia >>>> Margarete Ainsworth Building >>>> Barker Street Randwick Sydney NSW 2031 Australia >>>> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 >>>> >>>> neura.edu.au <http://neura.edu.au/> >>>> <https://twitter.com/neuraustralia> >>>> <https://www.facebook.com/NeuroscienceResearchAustralia> >>>> <http://www.neura.edu.au/help-research/subscribe> >>>> >>>> >>>> ___ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline >>> <http://www.partners.org/complianceline> . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > ___ >
Re: [Freesurfer] Comparing LME models
Hi Martin, Yes this is for a mass univariate approach. Re segmentation I was referring to the lhRgs output from the lme_mass_fit_Rgw command: lhstats_1RF = lme_mass_fit_Rgw(X,[1],Y,ni,lhTh0_1RF,lhRgs,lhsphere); So if both models have the same number of random effect, does it matter which lhRgs do I use? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe> > On 30 Mar 2017, at 12:18 am, Martin Reuter <mreu...@nmr.mgh.harvard.edu> > wrote: > > Hi Bronwyn, > is this for a mass univariate approach? What do you mean with segmentation? > ROI or vertex-wise vs region-wise? > > Best, Martin > On 03/29/2017 01:23 AM, Bronwyn Overs wrote: >> Hi Mailing List, >> >> If you are comparing two matlab based linear mixed effects models >> (vertex-wise) with the same number of random effects (e.g. model with random >> effect for time vs. model with random effect for age at baseline), which >> segmentation should you use to estimate the parameters for both models? >> Kind regards, >> Bronwyn Overs >> Research Assistant >> >> Neuroscience Research Australia >> Margarete Ainsworth Building >> Barker Street Randwick Sydney NSW 2031 Australia >> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 >> >> neura.edu.au <http://neura.edu.au/> >> <https://twitter.com/neuraustralia> >> <https://www.facebook.com/NeuroscienceResearchAustralia> >> <http://www.neura.edu.au/help-research/subscribe> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Comparing LME models
Hi Mailing List, If you are comparing two matlab based linear mixed effects models (vertex-wise) with the same number of random effects (e.g. model with random effect for time vs. model with random effect for age at baseline), which segmentation should you use to estimate the parameters for both models? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] LME mass univariate model
Hi Mailing List, I am fitting an LME model with random effects for B0 and B2, so I am using the following to fit a spatiotemporal model: lhstats = lme_mass_fit_Rgw(X,[1 3],Y,ni,lhTh0,lhRgs,lhsphere); However, prior to this when i am computing the initial temporal covariance estimates, do the square bracketed numbers refer to the random effects as well? So would this be run for random effects at B0 and B2: [lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 3],Y,ni,lhcortex,3); Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe> > On 7 Mar 2017, at 11:57 pm, Martin Reuter <mreu...@nmr.mgh.harvard.edu> wrote: > > Hi Bronwyn, > > to shorten equations, lets set t = years_form_baseline > a = age > g = group > s = sex > > so your model is > Y_ij = b0 + b1 t_ij + b2 a_i + b3 g_i + b4 s_i + b5 t_ij a_i + b6 t_ij g_i + > b7 a_i g_i + b8 t_ij a_i g_i > (as a fist step, I would consider simplifying it, by dropping the age > interactions). > > Anyway > > for male (s_i =0) and controls (g_i = 0) this reduces to > Y_ij = b0 + b1 t_ij + b2 a_i + b5 t_ij a_i > so b1 is the slope for male controls, controlling for age and the slope age > interaction. (0 1 0….) > > Now for female (s=1) patients (g=1) we get this: > > Y_ij = b0 + b1 t_ij + b2 a_i + b3 + b4 + b5 t_ij a_i + b6 t_ij + b7 a_i + b8 > t_ij >= (b0+b3+b4) + (b1 + b6 + b8 ) t_ij + (b2+b7) a_i + b5 t_ij a_i > So the slope for female patients (controlling for age and age time > interaction) would be > (b1 + b6 + b8) > 0 1 0 0 0 0 1 0 1 > > The difference in slope between female patients and male controls would be > 0 0 0 0 0 0 1 0 1 (or the negative of that depending which way you subtract). > Similarly you can look at group differences (controlling for age gender and > interactions). > > Always write out the full model to make sure you understand what you are > doing. > > To complete the picture, here is the contrast for the slope of male patients > 0 1 0 0 0 0 1 0 1 (it is the same as for female patients, because you don’t > have a timeXgender interaction. So that is your patient slope ) > Therefore the > 0 0 0 0 0 0 1 0 1 is the slope difference between the groups. > > I would recommend you talk to a local biostatistician, to make sure you are > actually modelling what you want to model. And that you are interpreting the > results correctly. > > Grüße, Martin > >> On 06 Mar 2017, at 18:56, Bronwyn Overs <b.ov...@neura.edu.au >> <mailto:b.ov...@neura.edu.au>> wrote: >> >> Hi Martin, >> >> Thank you for your response, that is much clearer. >> >> I am also a little confused about how to specify the exact contrasts we wish >> to test and was hoping to get some advice. My design matrix X includes the >> following columns: >> 1. Intercept >> 2. Years from baseline >> 3. Age at baseline >> 4. Group (patients labelled 1, controls 0) >> 5. Gender (females labelled 1, males 0) >> 6. Col 2 (years) * Col 3 (age) >> 7. Col 2 (years) * Col 4 (group) >> 8. Col 3 (age) * Col 4 (group) >> 9. Col 2 (years) * Col 3 (age) * Col 4 (group) >> >> If I test the following contrast, is it giving me the effect of years across >> all groups and genders, or just years for male controls: >> CM.C = [0 1 0 0 0 0 0 0 0] >> >> Also, what contrast should I use to examine the effect of years in my >> patient group irrespective of gender? >> >> Kind regards, >> Bronwyn Overs >> Research Assistant >> >> Neuroscience Research Australia >> Margarete Ainsworth Building >> Barker Street Randwick Sydney NSW 2031 Australia >> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 >> >> neura.edu.au <http://neura.edu.au/> >> <https://twitter.com/neuraustralia> >> <https://www.facebook.com/NeuroscienceResearchAustralia> >> <http://www.neura.edu.au/help-research/subscribe> >>> On 4 Mar 2017, at 12:43 am, Martin Reuter <mreu...@nmr.mgh.harvard.edu >>> <mailto:mreu...@nmr.mgh.harvard.edu>> wrote: >>> >>> Hi Bronwyn, >>> >>> I think years-between-scans should be years-from-baseline-scans . You may >>> need to compute that if what you have is really years between neighbour
Re: [Freesurfer] LME mass univariate model
Hi Martin, Thank you for your response, that is much clearer. I am also a little confused about how to specify the exact contrasts we wish to test and was hoping to get some advice. My design matrix X includes the following columns: 1. Intercept 2. Years from baseline 3. Age at baseline 4. Group (patients labelled 1, controls 0) 5. Gender (females labelled 1, males 0) 6. Col 2 (years) * Col 3 (age) 7. Col 2 (years) * Col 4 (group) 8. Col 3 (age) * Col 4 (group) 9. Col 2 (years) * Col 3 (age) * Col 4 (group) If I test the following contrast, is it giving me the effect of years across all groups and genders, or just years for male controls: CM.C = [0 1 0 0 0 0 0 0 0] Also, what contrast should I use to examine the effect of years in my patient group irrespective of gender? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe> > On 4 Mar 2017, at 12:43 am, Martin Reuter <mreu...@nmr.mgh.harvard.edu> wrote: > > Hi Bronwyn, > > I think years-between-scans should be years-from-baseline-scans . You may > need to compute that if what you have is really years between neighbouring > scans. > > 1. Usually people use intercept and maybe years-from-baseline as random > effects. I would not include too many random effects, as it each adds a lot > of free parameters and you need a lot of data to fit all that in a meaningful > way. Which of your columns are random effects can be passed lme_fit_FS(X,[1 > 2],Y(:,1)+Y(:,2),ni); > for example has column 1 and 2 as random effects. > > 2. You can do a model comparison as described on our wiki > https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels > <https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels> > > You run the more complex model first (do the EM init and maybe RgGrow and RgW > fit) and then the simple one (only the EMinit and RgW fit) and do a > likelihodd ratio test. An example is on the above wiki. > > Best ,Martin > > > > > >> On 27 Feb 2017, at 04:16, Bronwyn Overs <b.ov...@neura.edu.au >> <mailto:b.ov...@neura.edu.au>> wrote: >> >> Dear mailing list, >> >> I am trying to run a LME model using the matlab tools, but I’m unsure how to >> specify the model we wish to run. We have a qdec file that contains the >> following columns: >> fsid, fsid-abse, years between scans, age at baseline, gender, group >> >> We want to specify a model where we can examine four interaction terms >> (years*age, years*group, age*group, years*age*group), as well as random >> effects for the intercept, years and age. My questions are: >> 1. How do we specify a model that will include the random effects we want? >> 2. How do we compare our full model (3 random effects) with a model >> excluding the random effect for age? >> >> Kind regards, >> Bronwyn Overs >> Research Assistant >> >> Neuroscience Research Australia >> Margarete Ainsworth Building >> Barker Street Randwick Sydney NSW 2031 Australia >> M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 >> >> neura.edu.au <http://neura.edu.au/> >> <https://twitter.com/neuraustralia> >> <https://www.facebook.com/NeuroscienceResearchAustralia> >> <http://www.neura.edu.au/help-research/subscribe> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. ___ Freesurfer mailing list Freesu
[Freesurfer] LME mass univariate model
Dear mailing list, I am trying to run a LME model using the matlab tools, but I’m unsure how to specify the model we wish to run. We have a qdec file that contains the following columns: fsid, fsid-abse, years between scans, age at baseline, gender, group We want to specify a model where we can examine four interaction terms (years*age, years*group, age*group, years*age*group), as well as random effects for the intercept, years and age. My questions are: 1. How do we specify a model that will include the random effects we want? 2. How do we compare our full model (3 random effects) with a model excluding the random effect for age? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Percentage of cortex showing significant differences
Dear mailing list, I have completed a matlab based lme analysis using cortical thickness, and now have a list of significant clusters for each coefficient. I now want to know what proportion of the cortex differs significantly for each coefficient. I can add up the total size of the significant clusters for each coefficient, but I don’t know what value to use in the denominator (the total size of the cortex). Would it be the total area of the fsaverage inflated surface that I used in my analysis? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_label2label problem
Hi Doug, Yes i was visualising it on fsaverage. I switched to sub003 and the ROI looks perfect. What a simple mistake, thanks for your help. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe> > On 27 Jan 2017, at 10:26 am, Douglas N Greve <gr...@nmr.mgh.harvard.edu> > wrote: > > Are you visualizing the output on subject sub003? It looks like fsaverage > > > On 01/26/2017 06:23 PM, Bronwyn Overs wrote: >> Hi Mailing list, >> >> I have been running the mri_label2label command and have encountered a >> problem with the newly generated label. The command I am running is as >> follows: >> >> mri_label2label --srclabel >> "$SUBJECTS_DIR/fsaverage/label/lh.sm20.lme.test.B2-0001.label" >> --srcsubject fsaverage_mod --trglabel "Test.label" --trgsubject >> “sub003" --regmethod surface --hemi lh >> >> When I visualise the original label there is a distinct temporal ROI >> outlined. However, when I load the label for my individual >> subject there is no temporal ROI outlined, instead I see numerous >> widely dispersed vertices highlighted across the whole surface of the >> cortex. Can you identify what the issue is? I have attached images >> that show the input and output labels overlayed on an inflated surface. >> >> >> >> >> >> Kind regards, >> >> Bronwyn Overs >> Research Assistant >> >> Neuroscience Research Australia >> >> Neuroscience Research Australia >> Margarete Ainsworth Building >> Barker Street Randwick Sydney NSW 2031 Australia >> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 >> >> neura.edu.au <http://neura.edu.au/> <http://neura.edu.au >> <http://neura.edu.au/>> >> >> Follow @neuraustralia on twitter >> <https://twitter.com/neuraustralia >> <https://twitter.com/neuraustralia>>Follow NeuRA on facebook >> <https://www.facebook.com/NeuroscienceResearchAustralia >> <https://www.facebook.com/NeuroscienceResearchAustralia>>Subscribe to >> the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe >> <http://www.neura.edu.au/help-research/subscribe>> >> >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Yeo 2011 Functional Cortical Parcellations
Thanks very much Thomas. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> On 23/06/2016 4:20 pm, Thomas Yeo wrote: You should be able to use the 5.3 version. Regards, Thomas On Thu, Jun 23, 2016 at 2:16 PM, Bronwyn Overs <b.ov...@neura.edu.au <mailto:b.ov...@neura.edu.au>> wrote: Hi Thomas, Thanks for your reply. The fsaverage directory I have for fs v 5.1 does not include the lh and rh Yeo2011_7Networks_N1000.annot files. I only have this in the 5.3 version of fsaverage. Can I still use the 5.3 version annot files or would I need a seperate set processed with version 5.1? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 <tel:%2B61%202%209399%201883> neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> On 23/06/2016 3:17 pm, Thomas Yeo wrote: Hi Bronwyn, You raise a good point. You can consider creating a cortical mask using aparc+aseg.mgz and use that to mask the networks. However, another approach (which might be more accurate) is to take cortical networks in fsaverage space and transform to your subject's surface and then transform into your subject's volume: # Transform from fsaverage to subject's surface >> mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject --hemi lh --sval-annot /lh.Yeo2011_17Networks_N1000.annot/ --tval $SUBJECTS_DIR/yoursubject/label//lh.Yeo_17Network_native.annot/ # Transform from subject's surface into your subject's volume (I am not super sure about this. You probably want to double check the output is correct) >> /mri_label2vol --annot lh.Yeo2011_17Networks_N1000.HS_001.annot //--o outfile.nii.gz --hemi lh --subject HS_001 //--regheader/ --Thomas On Wed, Jun 22, 2016 at 8:25 AM, Bronwyn Overs <b.ov...@neura.edu.au <mailto:b.ov...@neura.edu.au>> wrote: Hi Mailing List, I am attempting to apply the Yeo 2011 7-network fucntional parcellations to a set of fs MRIs processed with v5.1.0. Below are listed the first three steps I plan to take and I am seeking advice as to: A) Whether this approach is valid. B) Steps to take next. * Steps 1-3: * *1. Run MNI152 1mm template through recon-all* recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid Yeo2011_MNI152_FS recon-all -all -subjid Yeo2011_MNI152_FS *2. Warp the Yeo_atlas1mm.nii.gz to freesurfer nonlinear volumetric space* mri_vol2vol --mov Yeo2011_7Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii --s Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o Yeo2011_atlas_FSI.nii.gz --nearest *3. warp the Yeo_atlas_freesurfer_internal_space.nii.gz to each subject:* mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ Yeo2011_atlas_FSI.nii.gz --m3z talairach.m3z --o Yeo2011_atlas_subjID.nii.gz --nearest --inv-morph When previously mapping the Choi 2012 straital parcellations, steps 4 and 5 were: 4. *Creating a striatal mask in the native subject's space from freesurfer segmented Caudate (11 & 50), Putamen (12 & 51), and Accumbens (26 & 58)*: mri_binarize --i subjID/mri/aparc+aseg.mgz --match 11 --match 12 --match 26 --match 50 --match 51 --match 58 --o striatum_mask.nii.gz *5. **Using this mask to mask the choi striatal parcellations* fslmaths Choi2012_atlas_subjID.nii.gz -mas striatum_mask_subjID.nii.gz Yeo_atlas_subjID_mask.nii.gz Do I need to do a similar thing for the Yeo cortical parcellations and if so what regions should I include in the cortical mask? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research A
Re: [Freesurfer] Yeo 2011 Functional Cortical Parcellations
Hi Thomas, Thanks for your reply. The fsaverage directory I have for fs v 5.1 does not include the lh and rh Yeo2011_7Networks_N1000.annot files. I only have this in the 5.3 version of fsaverage. Can I still use the 5.3 version annot files or would I need a seperate set processed with version 5.1? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> On 23/06/2016 3:17 pm, Thomas Yeo wrote: Hi Bronwyn, You raise a good point. You can consider creating a cortical mask using aparc+aseg.mgz and use that to mask the networks. However, another approach (which might be more accurate) is to take cortical networks in fsaverage space and transform to your subject's surface and then transform into your subject's volume: # Transform from fsaverage to subject's surface >> mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject --hemi lh --sval-annot /lh.Yeo2011_17Networks_N1000.annot/ --tval $SUBJECTS_DIR/yoursubject/label//lh.Yeo_17Network_native.annot/ # Transform from subject's surface into your subject's volume (I am not super sure about this. You probably want to double check the output is correct) >> /mri_label2vol --annot lh.Yeo2011_17Networks_N1000.HS_001.annot //--o outfile.nii.gz --hemi lh --subject HS_001 //--regheader/ --Thomas On Wed, Jun 22, 2016 at 8:25 AM, Bronwyn Overs <b.ov...@neura.edu.au <mailto:b.ov...@neura.edu.au>> wrote: Hi Mailing List, I am attempting to apply the Yeo 2011 7-network fucntional parcellations to a set of fs MRIs processed with v5.1.0. Below are listed the first three steps I plan to take and I am seeking advice as to: A) Whether this approach is valid. B) Steps to take next. * Steps 1-3: * *1. Run MNI152 1mm template through recon-all* recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid Yeo2011_MNI152_FS recon-all -all -subjid Yeo2011_MNI152_FS *2. Warp the Yeo_atlas1mm.nii.gz to freesurfer nonlinear volumetric space* mri_vol2vol --mov Yeo2011_7Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii --s Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o Yeo2011_atlas_FSI.nii.gz --nearest *3. warp the Yeo_atlas_freesurfer_internal_space.nii.gz to each subject:* mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ Yeo2011_atlas_FSI.nii.gz --m3z talairach.m3z --o Yeo2011_atlas_subjID.nii.gz --nearest --inv-morph When previously mapping the Choi 2012 straital parcellations, steps 4 and 5 were: 4. *Creating a striatal mask in the native subject's space from freesurfer segmented Caudate (11 & 50), Putamen (12 & 51), and Accumbens (26 & 58)*: mri_binarize --i subjID/mri/aparc+aseg.mgz --match 11 --match 12 --match 26 --match 50 --match 51 --match 58 --o striatum_mask.nii.gz *5. **Using this mask to mask the choi striatal parcellations* fslmaths Choi2012_atlas_subjID.nii.gz -mas striatum_mask_subjID.nii.gz Yeo_atlas_subjID_mask.nii.gz Do I need to do a similar thing for the Yeo cortical parcellations and if so what regions should I include in the cortical mask? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 <tel:%2B61%202%209399%201883> neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly
[Freesurfer] Yeo 2011 Functional Cortical Parcellations
Hi Mailing List, I am attempting to apply the Yeo 2011 7-network fucntional parcellations to a set of fs MRIs processed with v5.1.0. Below are listed the first three steps I plan to take and I am seeking advice as to: A) Whether this approach is valid. B) Steps to take next. * Steps 1-3: * *1. Run MNI152 1mm template through recon-all* recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid Yeo2011_MNI152_FS recon-all -all -subjid Yeo2011_MNI152_FS *2. Warp the Yeo_atlas1mm.nii.gz to freesurfer nonlinear volumetric space* mri_vol2vol --mov Yeo2011_7Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii --s Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o Yeo2011_atlas_FSI.nii.gz --nearest *3. warp the Yeo_atlas_freesurfer_internal_space.nii.gz to each subject:* mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ Yeo2011_atlas_FSI.nii.gz --m3z talairach.m3z --o Yeo2011_atlas_subjID.nii.gz --nearest --inv-morph When previously mapping the Choi 2012 straital parcellations, steps 4 and 5 were: 4. *Creating a striatal mask in the native subject's space from freesurfer segmented Caudate (11 & 50), Putamen (12 & 51), and Accumbens (26 & 58)*: mri_binarize --i subjID/mri/aparc+aseg.mgz --match 11 --match 12 --match 26 --match 50 --match 51 --match 58 --o striatum_mask.nii.gz *5. **Using this mask to mask the choi striatal parcellations* fslmaths Choi2012_atlas_subjID.nii.gz -mas striatum_mask_subjID.nii.gz Yeo_atlas_subjID_mask.nii.gz Do I need to do a similar thing for the Yeo cortical parcellations and if so what regions should I include in the cortical mask? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Stats for Yeo and Choi Parcellations
Hi Thomas,
Thanks, I have taken your advise and used the LooseMask for the 7
network parcellation in steps 3a and b. How do I now mask it again with
FreeSurfer's segmentation of striatal regions as you have suggested?
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883
neura.edu.au <http://neura.edu.au>
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<https://twitter.com/neuraustralia>Follow NeuRA on facebook
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On 9/05/2016 12:29 pm, Thomas Yeo wrote:
Hi Bronwyn,
I was using that as a placeholder. You can use any of these:
Choi2012_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
Choi2012_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
Depending on whether you want the 7 or 17 networks and/or whether you
want to use the loose or tight mask. My suggestion is to use the
LooseMask and then after the parcellation has been project to the
subject's native space, you can mask it again with FreeSurfer's
segmentation of striatal regions (e.g., caudate, putamen and nucleus
accumbens) in your subject's native MRI.
For Step 2, you can use FSL_MNI152_FreeSurferConformed_1mm.nii or you
can use the MNI152 1mm template distributed by FSL.
Regards,
Thomas
On Mon, May 9, 2016 at 9:37 AM, Bronwyn Overs <b.ov...@neura.edu.au
<mailto:b.ov...@neura.edu.au>> wrote:
Hi Thomas,
I am not sure which file you are referring to when you say
"Choi_atlas1mm.nii.gz". The files I have from the freesurfer wiki are:
Choi_JNeurophysiol12_MNI152_README
Choi2012_7Networks_ColorLUT.txt
Choi2012_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
Choi2012_7NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_7NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
Choi2012_17Networks_ColorLUT.txt
Choi2012_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
Choi2012_17NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_17NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
FSL_MNI152_FreeSurferConformed_1mm.nii.gz
Which if any of these should I designate as the source in step 3a?
Also for step 2 I used "FSL_MNI152_FreeSurferConformed_1mm.nii",
is this correct?
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 <tel:%2B61%202%209399%201883>
neura.edu.au <http://neura.edu.au>
Follow @neuraustralia on twitter
<https://twitter.com/neuraustralia>Follow NeuRA on facebook
<https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe
to the NeuRA Magazine
<http://www.neura.edu.au/help-research/subscribe>
On 6/05/2016 12:50 am, Thomas Yeo wrote:
Hi Doug, the Choi file is a striatal functional connectivity
atlas which we distribute. It's under the average directory.
Hi Bronwyn,
To transform the Choi's striatal atlas to your individual
subject, Here's a (non-ideal) suggestion I previously suggested
to another user:
1) Assuming you are quite happy with the freesurfer striatal
parcellation in your individual subjects, then I am assuming
freesurfer nonlinear registration (talairach.m3z) is working
quite well. Talairach.m3z warps your subject to an internal
freesurfer space (kinda like MNI305, but not quite). Let's say
the freesurfer recon-all output is at /SUBJECT_FS/
2) Run the MNI152 1mm template (the one from FSL) through
recon-all. Recon-all will give you a Talairach.m3z that allows
you to map the MNI152 1mm template to the internal freesurfer
space. Let's say the freesurfer recon-all output is at
/MNI152_FS/
3) Then do the following:
a) warp the Choi_atlas1mm.nii.gz to freesurfer nonlinear
volumetric space:
>> setenv SUBJECTS_DIR
>> mri_vol2vol_used --mov Choi_atlas1mm.nii.gz --s MNI152_FS
--targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z
talairach.m3z --o Choi_atlas_freesurfer_internal_space.nii.gz
--interp nearest
b) warp the Choi_atlas_freesurfer_internal_space.nii.gz to your
subject:
>> setenv SUBJ
Re: [Freesurfer] Stats for Yeo and Choi Parcellations
Hi Thomas, I am not sure which file you are referring to when you say "Choi_atlas1mm.nii.gz". The files I have from the freesurfer wiki are: Choi_JNeurophysiol12_MNI152_README Choi2012_7Networks_ColorLUT.txt Choi2012_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz Choi2012_7NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz Choi2012_7NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz Choi2012_17Networks_ColorLUT.txt Choi2012_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz Choi2012_17NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz Choi2012_17NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz FSL_MNI152_FreeSurferConformed_1mm.nii.gz Which if any of these should I designate as the source in step 3a? Also for step 2 I used "FSL_MNI152_FreeSurferConformed_1mm.nii", is this correct? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> On 6/05/2016 12:50 am, Thomas Yeo wrote: Hi Doug, the Choi file is a striatal functional connectivity atlas which we distribute. It's under the average directory. Hi Bronwyn, To transform the Choi's striatal atlas to your individual subject, Here's a (non-ideal) suggestion I previously suggested to another user: 1) Assuming you are quite happy with the freesurfer striatal parcellation in your individual subjects, then I am assuming freesurfer nonlinear registration (talairach.m3z) is working quite well. Talairach.m3z warps your subject to an internal freesurfer space (kinda like MNI305, but not quite). Let's say the freesurfer recon-all output is at /SUBJECT_FS/ 2) Run the MNI152 1mm template (the one from FSL) through recon-all. Recon-all will give you a Talairach.m3z that allows you to map the MNI152 1mm template to the internal freesurfer space. Let's say the freesurfer recon-all output is at /MNI152_FS/ 3) Then do the following: a) warp the Choi_atlas1mm.nii.gz to freesurfer nonlinear volumetric space: >> setenv SUBJECTS_DIR >> mri_vol2vol_used --mov Choi_atlas1mm.nii.gz --s MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o Choi_atlas_freesurfer_internal_space.nii.gz --interp nearest b) warp the Choi_atlas_freesurfer_internal_space.nii.gz to your subject: >> setenv SUBJECTS_DIR >> mri_vol2vol --mov $SUBJECTS_DIR/AD_SUBJECT_FS/mri/norm.mgz --s AD_SUBJECT_FS --targ Choi_atlas_freesurfer_internal_space.nii.gz --m3z talairach.m3z --o Choi_atlas_AD_subject.nii.gz --interp nearest --inv-morph This is not optimal because of the double interpolation. You might want to use the MNI template instead of the Choi_atlas to test the above, so you can check the goodness of the warp. The final warped MNI template should hopefully look identical to your subject. If that works, then use the Choi_atlas. Note that mri_vol2vol does not work properly for talairach.m3z below version 5, so you should use version 5x mri_vol2vol. Regards, Thomas On Thu, May 5, 2016 at 10:24 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: On 5/4/16 11:40 PM, Bronwyn Overs wrote: Hi Freesurfer Mailing List, I wish to extract stats for my sample for the Yeo 2011 cortical parcellations and the Choi 2012 striatal parcellations (7 networks) that are provided for download on the freesurfer wiki. My questions are as follows: 1. I noticed that the Yeo 2011 annot files are already available in fsaverage/label. How do I map these annot file to each of my subjects so that I can extract stats? Use mri_surf2surf with the --save-annot option 2. For the Choi 2012 files I wish to use Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz . How do I map this file to each of my subjects so that I can extract stats for the 7Network parcellation? I don't know about this file. Where is it? Is it something we distribute? doug -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 <tel:%2B61%202%209399%201883> neura.edu.au <http://neura.edu.au> Foll
Re: [Freesurfer] Stats for Yeo and Choi Parcellations
Hi Doug, I tried to run the mri_surf2surf command as follows and got this error: [b.overs~]$ mri_surf2surf --srcsubject fsaverage --srcsurfval lh.Yeo2011_7Networks_N1000.annot --trgsubject testsubj --trgsurfval lh.Yeo2011_7Networks_N1000.annot --hemi lh --save-annot ERROR: Option --save-annot unknown [b.overs~]$ I could not see any --save annot option in the help file. I am running this correctly? Should I be suing the .mgz file as the input or is the annotation file ok as this is what I want to resample? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> On 6/05/2016 12:24 am, Douglas Greve wrote: On 5/4/16 11:40 PM, Bronwyn Overs wrote: Hi Freesurfer Mailing List, I wish to extract stats for my sample for the Yeo 2011 cortical parcellations and the Choi 2012 striatal parcellations (7 networks) that are provided for download on the freesurfer wiki. My questions are as follows: 1. I noticed that the Yeo 2011 annot files are already available in fsaverage/label. How do I map these annot file to each of my subjects so that I can extract stats? Use mri_surf2surf with the --save-annot option 2. For the Choi 2012 files I wish to use Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz . How do I map this file to each of my subjects so that I can extract stats for the 7Network parcellation? I don't know about this file. Where is it? Is it something we distribute? doug -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Stats for Yeo and Choi Parcellations
Hi Freesurfer Mailing List, I wish to extract stats for my sample for the Yeo 2011 cortical parcellations and the Choi 2012 striatal parcellations (7 networks) that are provided for download on the freesurfer wiki. My questions are as follows: 1. I noticed that the Yeo 2011 annot files are already available in fsaverage/label. How do I map these annot file to each of my subjects so that I can extract stats? 2. For the Choi 2012 files I wish to use Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz . How do I map this file to each of my subjects so that I can extract stats for the 7Network parcellation? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] MNI coords in GLM cluster
Hi Freesurfer mailing list, Is there a way to determine if a specific MNI location is included in any of the clusters that are significant in a freesurfer GLM analysis (after monte-carlo)? We have a specific coordinate of interested from a previous analysis (e.g. -21, 11, -17) and wish to know if this is included in any of the significant clusters from an alternate GLM in freesurfer. -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Longitudinal analysis with single timepoint scans
Thanks very much Martin. That's perfect. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> On 20/01/2016 4:54 am, Martin Reuter wrote: Hi Bronwyn, with FS 5.3 you can run the single-tp images through a 'fake' longitudinal stream. After processing crossectionally simply run the base with only the single time point, and then run the long with that base. This will make the results comparable as the images will go through same processing steps. If it makes sense to include them into your model depends on what you are testing and how many there are. In linear mixed effects models, having a extra few single time point values helps for the estimation of cross subject variance. Best, Martin On 01/18/2016 05:09 PM, Bronwyn Overs wrote: Hi Freesurfer Mailing List, We are running a longitudinal analysis (in R) using 2 time points with scans that have been through the Freesurfer longitudinal pipeline. We were also hoping to incorporate individuals with only a single scan into our analysis. Does it make sense to use long images (2 timepoints) with cross images (1 timepoint) in the same analysis, or can they not be used together because the cross sectional images have not undergone the same processing steps? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web :http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Longitudinal analysis with single timepoint scans
Hi Freesurfer Mailing List, We are running a longitudinal analysis (in R) using 2 time points with scans that have been through the Freesurfer longitudinal pipeline. We were also hoping to incorporate individuals with only a single scan into our analysis. Does it make sense to use long images (2 timepoints) with cross images (1 timepoint) in the same analysis, or can they not be used together because the cross sectional images have not undergone the same processing steps? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Get summary stats for ROI
Hi Freesurfer Mailing List, I have just completed a GLM analysis with monte carlo correction and now have my "cache.th13.abs.sig.cluster.mgh" files showing the significant clusters for a specific contrast. I would now like to get mean cortical thickness values for these ROIs in another unrelated MRI sample. What is the simplest means of mapping these clusters to my other sample so that I can extract the stats? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Create surface overlay from p-values
Hi Freesurfer mailing list, Using an external software package we have completed of analysis for the vtx-wise thickness data extracted from freesurfer. We now have a p-value array containing one value for each vtx, and we would like to map this back onto the brain surface. Is there a way to create a .mgh overlay from our array of p-values using fsaverage as the subject? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Extracting individual vertex values for surfaces mapped to fsaverage
Dear mailing list,
For each of the subjects in our study, we would like to extract the
thickness values at each vertex for the surface that has been mapped to
fsaverage (so that the number of vertices is identical for all of our
subjects). After changing to a specific participants "surf" directory
and starting matlab, could I use the following command and file to
extract the data I want?:
[thick, fnum] = read_curv('lh.thickness.fwhm10.fsaverage.mgh')
Also, how do I then determine the annotation associated with each vertex
for each subject?
--
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883
neura.edu.au <http://neura.edu.au>
Follow @neuraustralia on twitter
<https://twitter.com/neuraustralia>Follow NeuRA on facebook
<https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the
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Re: [Freesurfer] Extracting individual vertex values for surfaces mapped to fsaverage
Hi Bruce,
Following up on your comment below, if I am using
'lh.thickness.fwhm10.fsaverage.mgh' for my thickness values, do I read
in the lh.aparc.annot file in the subjects directory? I tried doing this
for one of my participants, and the vector of thickness values has
163842 columns, while my aparc file has 116407. Or should I be reading
in the lh.aparc.annot from fsaverage?
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883
neura.edu.au <http://neura.edu.au>
Follow @neuraustralia on twitter
<https://twitter.com/neuraustralia>Follow NeuRA on facebook
<https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the
NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>
On 14/10/2015 11:47 pm, Bruce Fischl wrote:
Hi Bronwyn
you can use read_annotation.m to read in the parcellation that you want and
go from there.
cheers
Bruce
On Wed, 14 Oct 2015, Bronwyn Overs wrote:
Dear mailing list,
For each of the subjects in our study, we would like to extract the thickness
values at each vertex for the surface that has been mapped to fsaverage (so
that the number of vertices is identical for all of our subjects). After
changing to a specific participants "surf" directory and starting matlab,
could I use the following command and file to extract the data I want?:
[thick, fnum] = read_curv('lh.thickness.fwhm10.fsaverage.mgh')
Also, how do I then determine the annotation associated with each vertex for
each subject?
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[Freesurfer] Problem with fsgd file
Dear mailing list, I am trying to run a longitudinal 2 stage model using mri_glmfit. Here is the command I am using: mri_glmfit --fsgd long-2stage_ConAR.fsgd --glmdir long-2stage_ConAR.area.lh.spc.glmdir --y long-ConAR.lh.area-spc.stack.fwhm10.mgh dods --C me_age-all.mtx --C me_gender.mtx --C me_group.mtx --C int_ageXgroup.mtx --C int_ageXgender.mtx --C int_genderXgroup.mtx --C int_ageXgenderXgroup.mtx --surf fsaverage lh --label long-ConAR.lh.area.fsaverage.cortex.label However, when I try to run the command it has problems reading my fsgd file. I have attached my file for reference and here are the errors it spits out: gdfReadHeader: reading long-2stage_ConAR.fsgd INFO: ignoring tag 7541001001 INFO: ignoring tag 7541002001 INFO: ignoring tag 7541003001 INFO: ignoring tag 7541006001 INFO: ignoring tag 7541009001 INFO: ignoring tag 7541011004 INFO: ignoring tag 7541012004 INFO: ignoring tag 7541017001 INFO: ignoring tag 7541018001 INFO: ignoring tag 7541020001 INFO: ignoring tag 7541022001 INFO: ignoring tag 7541023001 INFO: ignoring tag 7541024001 INFO: ignoring tag 7541026001 INFO: ignoring tag 7541030001 INFO: ignoring tag 7541031001 INFO: ignoring tag 7541036001 INFO: ignoring tag 7541040001 INFO: ignoring tag 7541041001 INFO: ignoring tag 7541042001 INFO: ignoring tag 7541044001 INFO: ignoring tag 7541046001 INFO: ignoring tag 7541047001 INFO: ignoring tag 7541048004 INFO: ignoring tag 7541049001 INFO: ignoring tag 7541052001 INFO: ignoring tag 7541055001 INFO: ignoring tag 7541057001 INFO: ignoring tag 7541058001 INFO: ignoring tag 7541059001 INFO: ignoring tag 7541060001 INFO: ignoring tag 7541062001 INFO: ignoring tag 7541070001 INFO: ignoring tag 7541075001 INFO: ignoring tag 7541078001 INFO: ignoring tag 7541080001 INFO: ignoring tag 7541084001 INFO: ignoring tag 7541085001 INFO: ignoring tag 7541088001 INFO: ignoring tag 7541090001 INFO: ignoring tag 7541093001 INFO: ignoring tag 7541094001 INFO: ignoring tag 7541096001 INFO: ignoring tag 7541097004 INFO: ignoring tag 7541099001 INFO: ignoring tag 754111 INFO: ignoring tag 7541101001 INFO: ignoring tag 7541102001 INFO: ignoring tag 7541103001 INFO: ignoring tag 7541106001 INFO: ignoring tag 7541108001 INFO: ignoring tag 7541110004 INFO: ignoring tag 7541112001 INFO: ignoring tag 7541114001 INFO: ignoring tag 7541116001 INFO: ignoring tag 7541118001 INFO: ignoring tag 7541119001 INFO: ignoring tag 7541120001 INFO: ignoring tag 7541124001 INFO: ignoring tag 7541125001 INFO: ignoring tag 7541132004 INFO: ignoring tag 7541133001 INFO: ignoring tag 7541139001 INFO: ignoring tag 7541142001 INFO: ignoring tag 7541143001 INFO: ignoring tag 7541146001 INFO: ignoring tag 7541149001 INFO: ignoring tag 7541150001 INFO: ignoring tag 7541151001 INFO: ignoring tag 7541156001 INFO: ignoring tag 7541161001 INFO: ignoring tag 7541165001 INFO: ignoring tag 7541168001 INFO: ignoring tag 7541175001 INFO: ignoring tag 7541177001 INFO: ignoring tag 7541178001 INFO: ignoring tag 7541182001 INFO: ignoring tag 7541185001 INFO: ignoring tag 7541188001 INFO: ignoring tag 7541190004 INFO: ignoring tag 7541192004 INFO: ignoring tag 7541196001 INFO: ignoring tag 7541198001 INFO: ignoring tag 7541209001 INFO: ignoring tag 7541223001 INFO: ignoring tag 7541227001 INFO: ignoring tag 7541334001 INFO: ignoring tag 7541337001 INFO: ignoring tag 7541345001 INFO: ignoring tag 7541346001 INFO: ignoring tag 7541353001 INFO: ignoring tag 7541366001 INFO: ignoring tag 7541378001 INFO: ignoring tag 7541383001 INFO: ignoring tag 7541388001 INFO: ignoring tag 7541391001 INFO: ignoring tag 7541396001 INFO: ignoring tag 754141 INFO: ignoring tag 7541401001 INFO: ignoring tag 7541402001 INFO: ignoring tag 7541409001 INFO: ignoring tag 7541411001 INFO: ignoring tag 7541412001 INFO: ignoring tag 7541421001 INFO: ignoring tag 7541442004 INFO: ignoring tag 7541443001 INFO: ignoring tag 7541445001 WARNING: gdfReadV1: class genderM-groupCtl is defined but not used. INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 years -nan -nan 1 age_mc -nan -nan Class Means of each Continuous Variable 1 genderM-groupCtl -nan -nan 2 genderF-groupCtl -nan -nan 3 genderM-groupAR -nan -nan 4 genderF-groupAR -nan -nan INFO: gd2mtx_method is dods ERROR: Option dods unknown Can you tell me what is wrong? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> GroupDescriptorFile 1 Title longGLM_group-gender-years-mcage Class genderM-groupCt
Re: [Freesurfer] Longitudinal Two Stage Model using mri_glmfit
Thanks Martin. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> On 29/09/2015 12:16 am, Martin Reuter wrote: Hi Bronwyn, you can probably drop the --cortex in the glmfit, as the --label should take care of that. I don't remember what is the best way of finding the subject with holes. I think you would - open the surface with intersect label with tksurfer, click into the hole to find a vertex that is inside it. - Then you need for all your subjects the label mapped to fsaverage (not sure if these are stored with long_mris_slopes, but maybe they are in each base and called something with "fsaverage" in the name). - Label files are simple text files that contain a list of vertices in the label, so you need to find the ones where this vertex id is missing. That can be automated, e.g. with a shell script (or in matlab). Best, Martin On 09/27/2015 07:48 PM, Bronwyn Overs wrote: Hi Martin, Is there are holes in the intersected label, is there a recommended method for identifying which subjects caused the holes? I am hoping to run my two-stage model using an fsgd file and contrast vectors in the same way I have completed cross-sectional analyses previously. Will the following commands work? Does it still make sense to use the --cortex flag for mri_glmfit? long_mris_slopes --qdec cross.qdec.table.dat --meas lh --hemi thickness \ --sd "$SUBJECTS_DIR" --do-spc --do-stack --do-label \ --time years --qcache fsaverage \ --stack-spc case-control.thickness.lh-spc.stack.mgh \ --isec-labels case-control.fsaverage.cortex.label mri_glmfit --fsgd case-control.fsgd --glmdir long_case-control --y case-control.thickness.lh-spc.stack.mgh dods --C contrast1.mtx --C contrast2.mtx --surf fsaverage thickness --label case-control.fsaverage.cortex.label --cortex mri_glmfit-sim --glmdir long_case-control--cache 2 abs --cwpvalthresh 0.05 --2spaces Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> On 26/09/2015 1:36 am, Martin Reuter wrote: Hi Bronwyn, yes --stack-spc was needed. About your questions: 1. there is a section in the help text about Cortex Labels (scroll up). If you run qcache (where the subject data is mapped to a common template, e.g. fsaverage), you can specify --isec-labels < output> to do three things: a) it takes the cortex label from each subject and maps it to fsaverage (or whatever target you specified in --qcache) and intersects the labels there. b) it uses this intersected label for smoothing to ensure that no outside-cortex values get smoothed and averaged anywhere, and c) it writes out this intersected label . This is the recommended approach, but you may have difficulties as some subjects can have pretty ugly cortex masks and when intersecting all you may get something with holes. So inspect the intersected label. The if it has many holes in important regions, you should probably check, edit or remove the subjects that are responsible. 2. It should not differ (much), but it is numerically more stable if you use time-from-baseline. 3. --generic-time can be used in cases such as test-retest data, where you want just 1 and 2 for the two time points in all subjects. (the time delta is always 1 between neighboring time points). Best, Martin On 09/24/2015 11:26 PM, Bronwyn Overs wrote: Hi Martin, Sorry i have just realised that I need to add the --stack-spc flag to my long_mris_slopes command to get the stacked file for my glm analysis. I now have three other questions about long_mris_slopes: 1. When you run --isec-lables with the flag --meas thickness, is the output file specific to the thickness, or is it just related to the subject surface in general. 2. For my --time flag, will the output measures (e.g. spc) differ if I use years between scans (e.g. 0, 2) vs age at each scan (e.g. 14, 16)? 2. What is the flag --generic-time used for? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia
Re: [Freesurfer] Longitudinal Two Stage Model using mri_glmfit
Hi Martin, Is there are holes in the intersected label, is there a recommended method for identifying which subjects caused the holes? I am hoping to run my two-stage model using an fsgd file and contrast vectors in the same way I have completed cross-sectional analyses previously. Will the following commands work? Does it still make sense to use the --cortex flag for mri_glmfit? long_mris_slopes --qdec cross.qdec.table.dat --meas lh --hemi thickness \ --sd "$SUBJECTS_DIR" --do-spc --do-stack --do-label \ --time years --qcache fsaverage \ --stack-spc case-control.thickness.lh-spc.stack.mgh \ --isec-labels case-control.fsaverage.cortex.label mri_glmfit --fsgd case-control.fsgd --glmdir long_case-control --y case-control.thickness.lh-spc.stack.mgh dods --C contrast1.mtx --C contrast2.mtx --surf fsaverage thickness --label case-control.fsaverage.cortex.label --cortex mri_glmfit-sim --glmdir long_case-control--cache 2 abs --cwpvalthresh 0.05 --2spaces Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> On 26/09/2015 1:36 am, Martin Reuter wrote: Hi Bronwyn, yes --stack-spc was needed. About your questions: 1. there is a section in the help text about Cortex Labels (scroll up). If you run qcache (where the subject data is mapped to a common template, e.g. fsaverage), you can specify --isec-labels < output> to do three things: a) it takes the cortex label from each subject and maps it to fsaverage (or whatever target you specified in --qcache) and intersects the labels there. b) it uses this intersected label for smoothing to ensure that no outside-cortex values get smoothed and averaged anywhere, and c) it writes out this intersected label . This is the recommended approach, but you may have difficulties as some subjects can have pretty ugly cortex masks and when intersecting all you may get something with holes. So inspect the intersected label. The if it has many holes in important regions, you should probably check, edit or remove the subjects that are responsible. 2. It should not differ (much), but it is numerically more stable if you use time-from-baseline. 3. --generic-time can be used in cases such as test-retest data, where you want just 1 and 2 for the two time points in all subjects. (the time delta is always 1 between neighboring time points). Best, Martin On 09/24/2015 11:26 PM, Bronwyn Overs wrote: Hi Martin, Sorry i have just realised that I need to add the --stack-spc flag to my long_mris_slopes command to get the stacked file for my glm analysis. I now have three other questions about long_mris_slopes: 1. When you run --isec-lables with the flag --meas thickness, is the output file specific to the thickness, or is it just related to the subject surface in general. 2. For my --time flag, will the output measures (e.g. spc) differ if I use years between scans (e.g. 0, 2) vs age at each scan (e.g. 14, 16)? 2. What is the flag --generic-time used for? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> On 25/09/2015 10:55 am, Bronwyn Overs wrote: Hi Martin, I wanted to ask about getting the stacked SPC values for use with mri_glmfit. I ran the following long_mri_slopes command but cannot identify which if any is the stacked spc mgh file: long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR Do I need to run another command to produced a stacked spc file for use with glm_fit? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAu
Re: [Freesurfer] Longitudinal Two Stage Model using mri_glmfit
Hi Martin, Sorry i have just realised that I need to add the --stack-spc flag to my long_mris_slopes command to get the stacked file for my glm analysis. I now have three other questions about long_mris_slopes: 1. When you run --isec-lables with the flag --meas thickness, is the output file specific to the thickness, or is it just related to the subject surface in general. 2. For my --time flag, will the output measures (e.g. spc) differ if I use years between scans (e.g. 0, 2) vs age at each scan (e.g. 14, 16)? 2. What is the flag --generic-time used for? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> On 25/09/2015 10:55 am, Bronwyn Overs wrote: Hi Martin, I wanted to ask about getting the stacked SPC values for use with mri_glmfit. I ran the following long_mri_slopes command but cannot identify which if any is the stacked spc mgh file: long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR Do I need to run another command to produced a stacked spc file for use with glm_fit? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> On 23/09/2015 12:15 am, Martin Reuter wrote: Hi Bronwyn, yes that is possible, you would pass the SPC values stack as y. See https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel for an example (that one uses percent change with respect to baseline, pc1, but you can do the same with symmetrized percent change (spc)). Best, Martin On 09/22/2015 03:13 AM, Bronwyn Overs wrote: Dear freesurfer mailing list, Is it possible to run a longitudinal two stage model from the command line using mri_glmift, instead of using the qdec gui? If so, what --y would you pass to use the preprocessed spc values? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web :http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Longitudinal Two Stage Model using mri_glmfit
Hi Martin, I wanted to ask about getting the stacked SPC values for use with mri_glmfit. I ran the following long_mri_slopes command but cannot identify which if any is the stacked spc mgh file: long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR Do I need to run another command to produced a stacked spc file for use with glm_fit? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> On 23/09/2015 12:15 am, Martin Reuter wrote: Hi Bronwyn, yes that is possible, you would pass the SPC values stack as y. See https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel for an example (that one uses percent change with respect to baseline, pc1, but you can do the same with symmetrized percent change (spc)). Best, Martin On 09/22/2015 03:13 AM, Bronwyn Overs wrote: Dear freesurfer mailing list, Is it possible to run a longitudinal two stage model from the command line using mri_glmift, instead of using the qdec gui? If so, what --y would you pass to use the preprocessed spc values? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web :http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Longitudinal Two Stage Model using mri_glmfit
Hi Martin, Thanks for clarifying. As a follow-up, is it ok to use age or mean centered at each scan as the timing variable with the two-stage model? Regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 neura.edu.au Twitter | Facebook | Subscribe From: "Martin Reuter" <mreu...@nmr.mgh.harvard.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Thursday, September 24, 2015 2:51:05 AM Subject: Re: [Freesurfer] Longitudinal Two Stage Model using mri_glmfit Hi Bronwyn, what Doug indicates here is that he thinks it is possible to do an ANOVA style analysis from a single FSGD and command (something like this: https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova ) But this would not be good in situations where you have different many time points per subjects or differently spaced time points. In fact the best way to analyze longitudinal data is to use our Linear Mixed Effects Matlab toolbox. If you have the same number of time points for all subjects and they are spaced approx. the same, the 2-stage model is usually good enough. See here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics for an overview. Best, Martin On 09/22/2015 08:53 PM, Bronwyn Overs wrote: Hi Douglas, Sorry I don't know what you mean by the different mri_glmfit levels? Also how do you use two fsgd files simultaneously (I assume one file for time 1 and the other for time 2)? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 neura.edu.au On 23/09/2015 12:16 am, Douglas Greve wrote: BQ_BEGIN If you intend to compute a slope for each subject (first level mri_glmfit), then input the slopes to the 2nd level to test for effects of interest. Is this what you mean? It is probably possible to do this with a single FSGD file and single command line, but it is much easier to set up and understand if you use two. doug On 9/22/15 3:13 AM, Bronwyn Overs wrote: BQ_BEGIN Dear freesurfer mailing list, Is it possible to run a longitudinal two stage model from the command line using mri_glmift, instead of using the qdec gui? If so, what --y would you pass to use the preprocessed spc values? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 neura.edu.au ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. BQ_END ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer BQ_END -- Martin Reuter, PhD Assistant Professor of Radiology, Harvard Medical School Assistant Professor of Neurology, Harvard Medical School A.A.Martinos Center for Biomedical Imaging Massachusetts General Hospital Research Affiliate, CSAIL, MIT Phone: +1-617-724-5652 Web : http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http:/
[Freesurfer] Longitudinal Two Stage Model using mri_glmfit
Dear freesurfer mailing list, Is it possible to run a longitudinal two stage model from the command line using mri_glmift, instead of using the qdec gui? If so, what --y would you pass to use the preprocessed spc values? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Longitudinal Two Stage Model using mri_glmfit
Hi Douglas, Sorry I don't know what you mean by the different mri_glmfit levels? Also how do you use two fsgd files simultaneously (I assume one file for time 1 and the other for time 2)? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> On 23/09/2015 12:16 am, Douglas Greve wrote: If you intend to compute a slope for each subject (first level mri_glmfit), then input the slopes to the 2nd level to test for effects of interest. Is this what you mean? It is probably possible to do this with a single FSGD file and single command line, but it is much easier to set up and understand if you use two. doug On 9/22/15 3:13 AM, Bronwyn Overs wrote: Dear freesurfer mailing list, Is it possible to run a longitudinal two stage model from the command line using mri_glmift, instead of using the qdec gui? If so, what --y would you pass to use the preprocessed spc values? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Extreme mean values for significant clusters (using GLM)
Hi all, I am still a little confused as to how the individual values are calculated for the significant clusters in the GLM model. Is the cluster mapped backed on the individual brain and the mean thickness for that region is printed out for each individual? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 14/04/2015 9:29 am, Bronwyn Overs wrote: Hi Doug, Sorry which file should the mri_segstats command be in? Also, I am still unclear on how the individual values in cache.th13.abs.y.ocn.dat are calculated. Could you possibly explain this? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 13/04/2015 11:34 pm, Douglas Greve wrote: I'm not sure what the problem is, but it occurs to me that computing the mean over the cluster is probably not what should be done. Instead, the total should be computed. In the header of that file, there should be a command line for mri_segstats. Cut and paste that into a shell and add --accumulate and see if the numbers get more reasonable. doug On 4/6/15 9:48 PM, Bronwyn Overs wrote: Dear Freesurfer Mailing List, I have just run a GLM analysis using mri_glmfit with area as the measure of interest. For each of my significant contrasts, I extracted the mean area for each subjects from the corresponding cache.th13.abs.y.ocn.dat file. I then plotted these values to examine the nature of the interaction. In doing so I identified three individuals who had extreme mean area values (up to 11 sd from the average of the mean area) for many of the significant clusters. For each of these individuals I cannot see any problems with the freesurfer .mgz files or the cortical segmentation. So my questions are: 1. Are extreme mean values for significant clusters in GLM a problem? If so, do you have any idea what could be causing these values if the scans appear to be well segmented? 2. If the significant clusters are calculated at a group level, how are the individual mean values (in cache.th13.abs.y.ocn.dat) generated? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustralia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e
Re: [Freesurfer] Excluded high intensity gray matter
Thanks Bruce. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 16/04/2015 12:12 pm, Bruce Fischl wrote: Hi Bronwyn I don't think there's anything to be done. The images don't carry enough information to generate reliable estimates in those regions, so all you can do is ignore them. cheers Bruce On Thu, 16 Apr 2015, Bronwyn Overs wrote: HI Bruce, It isn't messing stuff up elsewhere, but I am just worried about including this participant in GLM analysis if this problem cannot be fixed. What would you recommend? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 16/04/2015 6:45 am, Bruce Fischl wrote: Hi Bronwyn what is your goal? You won't ever get good surfaces there. Is it messing stuff up elsewhere? cheers Bruce On Wed, 15 Apr 2015, Bronwyn Overs wrote: Dear Freesurfer mailing list, I am currently editing a scan (using fs version 5.3) and have come across a section of the inferior temporal gyrus that appears to be blown out (intensity of up to 154). As such, freesurfer has excluded this section from the pial boundary (see below image). I do not want to add control points as I do not know if any of this section is white matter. This regions extends through about 15 slices. Any suggestions as to how I could approach this problem? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Excluded high intensity gray matter
HI Bruce, It isn't messing stuff up elsewhere, but I am just worried about including this participant in GLM analysis if this problem cannot be fixed. What would you recommend? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 16/04/2015 6:45 am, Bruce Fischl wrote: Hi Bronwyn what is your goal? You won't ever get good surfaces there. Is it messing stuff up elsewhere? cheers Bruce On Wed, 15 Apr 2015, Bronwyn Overs wrote: Dear Freesurfer mailing list, I am currently editing a scan (using fs version 5.3) and have come across a section of the inferior temporal gyrus that appears to be blown out (intensity of up to 154). As such, freesurfer has excluded this section from the pial boundary (see below image). I do not want to add control points as I do not know if any of this section is white matter. This regions extends through about 15 slices. Any suggestions as to how I could approach this problem? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Extreme mean values for significant clusters (using GLM)
Hi Doug, Sorry which file should the mri_segstats command be in? Also, I am still unclear on how the individual values in cache.th13.abs.y.ocn.dat are calculated. Could you possibly explain this? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 13/04/2015 11:34 pm, Douglas Greve wrote: I'm not sure what the problem is, but it occurs to me that computing the mean over the cluster is probably not what should be done. Instead, the total should be computed. In the header of that file, there should be a command line for mri_segstats. Cut and paste that into a shell and add --accumulate and see if the numbers get more reasonable. doug On 4/6/15 9:48 PM, Bronwyn Overs wrote: Dear Freesurfer Mailing List, I have just run a GLM analysis using mri_glmfit with area as the measure of interest. For each of my significant contrasts, I extracted the mean area for each subjects from the corresponding cache.th13.abs.y.ocn.dat file. I then plotted these values to examine the nature of the interaction. In doing so I identified three individuals who had extreme mean area values (up to 11 sd from the average of the mean area) for many of the significant clusters. For each of these individuals I cannot see any problems with the freesurfer .mgz files or the cortical segmentation. So my questions are: 1. Are extreme mean values for significant clusters in GLM a problem? If so, do you have any idea what could be causing these values if the scans appear to be well segmented? 2. If the significant clusters are calculated at a group level, how are the individual mean values (in cache.th13.abs.y.ocn.dat) generated? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustralia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Extreme mean values for significant clusters (using GLM)
Dear Freesurfer Mailing List, I sent the below email last week and have not yet recieved a reply. Does anyone have any ideas about the problem I am experiencing? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 7/04/2015 11:48 am, Bronwyn Overs wrote: Dear Freesurfer Mailing List, I have just run a GLM analysis using mri_glmfit with area as the measure of interest. For each of my significant contrasts, I extracted the mean area for each subjects from the corresponding cache.th13.abs.y.ocn.dat file. I then plotted these values to examine the nature of the interaction. In doing so I identified three individuals who had extreme mean area values (up to 11 sd from the average of the mean area) for many of the significant clusters. For each of these individuals I cannot see any problems with the freesurfer .mgz files or the cortical segmentation. So my questions are: 1. Are extreme mean values for significant clusters in GLM a problem? If so, do you have any idea what could be causing these values if the scans appear to be well segmented? 2. If the significant clusters are calculated at a group level, how are the individual mean values (in cache.th13.abs.y.ocn.dat) generated? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustralia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_glmfit skipping .mtx files
Hi Doug, Yes the appear on the 2nd run (including only the missing contrasts). Thanks for that suggestion. Still unsure why they didn't appear with the 1st run though. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 3/04/2015 7:04 am, Douglas N Greve wrote: The limit should be 100. If you run mri_glmfit a 2nd time just with the missing contrasts, do they appear? On 04/02/2015 02:34 AM, Bronwyn Overs wrote: Dear freesurfer mailing list, Is there a limit to the number of .mtx files you can feed to mri_glmfit? I am running an anlysis with 25 different .mtx files, and when the analysis runs it just skips the 22nd and 23rd .mtx file. This means these contrasts are also missing from the glmdir. Do you know how I can fix this? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Extreme mean values for significant clusters (using GLM)
Dear Freesurfer Mailing List, I have just run a GLM analysis using mri_glmfit with area as the measure of interest. For each of my significant contrasts, I extracted the mean area for each subjects from the corresponding cache.th13.abs.y.ocn.dat file. I then plotted these values to examine the nature of the interaction. In doing so I identified three individuals who had extreme mean area values (up to 11 sd from the average of the mean area) for many of the significant clusters. For each of these individuals I cannot see any problems with the freesurfer .mgz files or the cortical segmentation. So my questions are: 1. Are extreme mean values for significant clusters in GLM a problem? If so, do you have any idea what could be causing these values if the scans appear to be well segmented? 2. If the significant clusters are calculated at a group level, how are the individual mean values (in cache.th13.abs.y.ocn.dat) generated? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustralia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_glmfit skipping .mtx files
Dear freesurfer mailing list, Is there a limit to the number of .mtx files you can feed to mri_glmfit? I am running an anlysis with 25 different .mtx files, and when the analysis runs it just skips the 22nd and 23rd .mtx file. This means these contrasts are also missing from the glmdir. Do you know how I can fix this? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses
Hi Doug, I am still trying to resolve the different results for GLMs completed in Freesurfer and SPSS. Interestingly, I get the same p-values for each method when I remove my continuous covariate (age) from the model (leaving gender, group, and genderXgroup effects). This suggests that the two methods are treating covariates in a different manner. Unfortunately, SPSS does allow you to print out the GLM design matrix or use the design matrix from mri_glmfit as an input. However, I am able to print out the contrast matrices for the analysis, which look like this: Contrast Intercept Age [Gender=Female] [Gender=Male] [diagnosis=Case] [diagnosis=Control] [diagnosis=Case] * [Gender=Female] [diagnosis=Case] * [Gender=Male] [diagnosis=Control] * [Gender=Female] [diagnosis=Control] * [Gender=Male] Intercept 1 0 0.5 0.5 0.5 0.5 0.250.25 0.250.25 Age 0 1 0 0 0 0 0 0 0 0 gender 0 0 1 -1 0 0 0.5 -0.50.5 -0.5 diagnosis 0 0 0 0 1 -1 0.5 0.5 -0.5-0.5 gender*diagnosis0 0 0 0 0 0 1 -1 -1 1 While for mri_glmfit, the contrast vectors look like this: Intercept Intercept Intercept Intercept Age Slope Age Slope Age Slope Age Slope contrast Male-Case Female-Case Male-Control Female-Control Male-Case Female-Case Male-Control Female-Control age 0 0 0 0 0.5 0.5 0.5 0.5 gender 0.5 -0.50.5 -0.50 0 0 0 group 0.5 0.5 -0.5-0.50 0 0 0 gender*group0.5 -0.5-0.50.5 0 0 0 0 From this information, do you know if there is a way to work out why the two methods are producing different results when a continuous covariate is included in the model? I am fairly stumped and would great appreciate any further insight you can provide. Compared to Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 9/02/2015 9:47 am, Bronwyn Overs wrote: Thanks. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 7/02/2015 3:16 am, Douglas N Greve wrote: It should be 10^-abs(sig) On 02/06/2015 12:53 AM, Bronwyn Overs wrote: Hi Doug, Thanks for all of your help. I am investigating the differences between the design matrices now. I have one more query about the sig.table.dat file put out by the GLM using the parcellated ROIs. When I transform each of the values in this file to p values using 10^value, some of the resulting p-value are 1. Do you know why this would be happening? Here is an example of one of my sig.table.dat files, where 10^.799 = 6.295: lh.aparc.thicknessme_gender_ageRem me_group_ageRem lh_bankssts_thickness 0.107 -2.752 lh_caudalanteriorcingulate_thickness -2.616 -0.190 lh_caudalmiddlefrontal_thickness -0.701 -4.258 lh_cuneus_thickness 0.799 -1.178 lh_entorhinal_thickness 1.669 -4.129 lh_fusiform_thickness -0.088 -6.808 lh_inferiorparietal_thickness -0.665 -1.477 lh_inferiortemporal_thickness 0.149 -7.985 lh_isthmuscingulate_thickness -0.476 -2.393 lh_lateraloccipital_thickness 0.212 -1.189 lh_lateralorbitofrontal_thickness 0.288 -7.657 lh_lingual_thickness1.148 -1.594 lh_medialorbitofrontal_thickness1.405 -4.461 lh_middletemporal_thickness 0.727 -7.215 lh_parahippocampal_thickness -1.059 -2.854 lh_paracentral_thickness -0.514 -0.282 lh_parsopercularis_thickness0.444 -3.541 lh_parsorbitalis_thickness -0.110 -7.075 lh_parstriangularis_thickness 0.244 -4.769 lh_pericalcarine_thickness 0.376 -0.218 lh_postcentral_thickness -0.485 -0.832 lh_posteriorcingulate_thickness-0.135 -1.241 lh_precentral_thickness 0.196 -2.102 lh_precuneus_thickness
Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses
Thanks. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 7/02/2015 3:16 am, Douglas N Greve wrote: It should be 10^-abs(sig) On 02/06/2015 12:53 AM, Bronwyn Overs wrote: Hi Doug, Thanks for all of your help. I am investigating the differences between the design matrices now. I have one more query about the sig.table.dat file put out by the GLM using the parcellated ROIs. When I transform each of the values in this file to p values using 10^value, some of the resulting p-value are 1. Do you know why this would be happening? Here is an example of one of my sig.table.dat files, where 10^.799 = 6.295: lh.aparc.thicknessme_gender_ageRem me_group_ageRem lh_bankssts_thickness 0.107 -2.752 lh_caudalanteriorcingulate_thickness -2.616 -0.190 lh_caudalmiddlefrontal_thickness -0.701 -4.258 lh_cuneus_thickness 0.799 -1.178 lh_entorhinal_thickness 1.669 -4.129 lh_fusiform_thickness -0.088 -6.808 lh_inferiorparietal_thickness -0.665 -1.477 lh_inferiortemporal_thickness 0.149 -7.985 lh_isthmuscingulate_thickness -0.476 -2.393 lh_lateraloccipital_thickness 0.212 -1.189 lh_lateralorbitofrontal_thickness 0.288 -7.657 lh_lingual_thickness1.148 -1.594 lh_medialorbitofrontal_thickness1.405 -4.461 lh_middletemporal_thickness 0.727 -7.215 lh_parahippocampal_thickness -1.059 -2.854 lh_paracentral_thickness -0.514 -0.282 lh_parsopercularis_thickness0.444 -3.541 lh_parsorbitalis_thickness -0.110 -7.075 lh_parstriangularis_thickness 0.244 -4.769 lh_pericalcarine_thickness 0.376 -0.218 lh_postcentral_thickness -0.485 -0.832 lh_posteriorcingulate_thickness-0.135 -1.241 lh_precentral_thickness 0.196 -2.102 lh_precuneus_thickness 0.018 -1.361 lh_rostralanteriorcingulate_thickness -1.208 -2.073 lh_rostralmiddlefrontal_thickness 0.437 -4.470 lh_superiorfrontal_thickness -0.141 -2.743 lh_superiorparietal_thickness -0.288 -0.365 lh_superiortemporal_thickness 0.227 -4.646 lh_supramarginal_thickness -1.185 -1.354 lh_frontalpole_thickness -0.325 -0.521 lh_temporalpole_thickness -0.067 -4.074 lh_transversetemporal_thickness-0.009 -1.618 lh_insula_thickness 0.553 -6.063 Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 5/02/2015 10:46 am, Douglas N Greve wrote: How sure are you that you are using the exact same model? Can you output the design matrix from SPSS? Can you input the FS design matrix into SPSS? Are you sure you are using the exact same input data? On 02/04/2015 06:32 PM, Bronwyn Overs wrote: Ahh right. I have just understood which part of the output I needed to look at. However, for the ROI GLM there are only 1-2 regions that were significantly different between groups, while the SPSS ANCOVA showed significant group differences for the majority of parcellated regions. I have confirmed that I am using the exact same model for each, so it is only the analysis method that differs. Do you know why these two methods would produce such disparate results? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.auhttp://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazinehttp://www.neura.edu.au/help-research/subscribe On 5/02/2015 3:16 am, Douglas N Greve wrote: I'm not sure that I understand what I'm looking at. If it is an ROI analysis, then there is no surface, it should be about 40 numbers, one for each ROI. On 02/03/2015 06:26 PM, Bronwyn Overs wrote: Hi Doug, Thanks for your correction. I have now completed the FDR for my case-control comparisons
Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses
Hi Doug, Thanks for all of your help. I am investigating the differences between the design matrices now. I have one more query about the sig.table.dat file put out by the GLM using the parcellated ROIs. When I transform each of the values in this file to p values using 10^value, some of the resulting p-value are 1. Do you know why this would be happening? Here is an example of one of my sig.table.dat files, where 10^.799 = 6.295: lh.aparc.thicknessme_gender_ageRem me_group_ageRem lh_bankssts_thickness 0.107 -2.752 lh_caudalanteriorcingulate_thickness -2.616 -0.190 lh_caudalmiddlefrontal_thickness -0.701 -4.258 lh_cuneus_thickness 0.799 -1.178 lh_entorhinal_thickness 1.669 -4.129 lh_fusiform_thickness -0.088 -6.808 lh_inferiorparietal_thickness -0.665 -1.477 lh_inferiortemporal_thickness 0.149 -7.985 lh_isthmuscingulate_thickness -0.476 -2.393 lh_lateraloccipital_thickness 0.212 -1.189 lh_lateralorbitofrontal_thickness 0.288 -7.657 lh_lingual_thickness1.148 -1.594 lh_medialorbitofrontal_thickness1.405 -4.461 lh_middletemporal_thickness 0.727 -7.215 lh_parahippocampal_thickness -1.059 -2.854 lh_paracentral_thickness -0.514 -0.282 lh_parsopercularis_thickness0.444 -3.541 lh_parsorbitalis_thickness -0.110 -7.075 lh_parstriangularis_thickness 0.244 -4.769 lh_pericalcarine_thickness 0.376 -0.218 lh_postcentral_thickness -0.485 -0.832 lh_posteriorcingulate_thickness-0.135 -1.241 lh_precentral_thickness 0.196 -2.102 lh_precuneus_thickness 0.018 -1.361 lh_rostralanteriorcingulate_thickness -1.208 -2.073 lh_rostralmiddlefrontal_thickness 0.437 -4.470 lh_superiorfrontal_thickness -0.141 -2.743 lh_superiorparietal_thickness -0.288 -0.365 lh_superiortemporal_thickness 0.227 -4.646 lh_supramarginal_thickness -1.185 -1.354 lh_frontalpole_thickness -0.325 -0.521 lh_temporalpole_thickness -0.067 -4.074 lh_transversetemporal_thickness-0.009 -1.618 lh_insula_thickness 0.553 -6.063 Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 5/02/2015 10:46 am, Douglas N Greve wrote: How sure are you that you are using the exact same model? Can you output the design matrix from SPSS? Can you input the FS design matrix into SPSS? Are you sure you are using the exact same input data? On 02/04/2015 06:32 PM, Bronwyn Overs wrote: Ahh right. I have just understood which part of the output I needed to look at. However, for the ROI GLM there are only 1-2 regions that were significantly different between groups, while the SPSS ANCOVA showed significant group differences for the majority of parcellated regions. I have confirmed that I am using the exact same model for each, so it is only the analysis method that differs. Do you know why these two methods would produce such disparate results? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 5/02/2015 3:16 am, Douglas N Greve wrote: I'm not sure that I understand what I'm looking at. If it is an ROI analysis, then there is no surface, it should be about 40 numbers, one for each ROI. On 02/03/2015 06:26 PM, Bronwyn Overs wrote: Hi Doug, Thanks for your correction. I have now completed the FDR for my case-control comparisons, and it appears that none of the regions survived. This is again quite confusing given the large number of parcellated regions that survived FDR in the SPSS ANCOVA. Can you confirm that this screenshot of the sig.mgh file from ROI analysis looks as you would expect (it looks very strange to me): Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.auhttp://neura.edu.au Follow @neuraustralia on twitter https://twitter.com
Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses
Ahh right. I have just understood which part of the output I needed to
look at. However, for the ROI GLM there are only 1-2 regions that were
significantly different between groups, while the SPSS ANCOVA showed
significant group differences for the majority of parcellated regions. I
have confirmed that I am using the exact same model for each, so it is
only the analysis method that differs. Do you know why these two methods
would produce such disparate results?
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.au http://neura.edu.au
Follow @neuraustralia on twitter
https://twitter.com/neuraustraliaFollow NeuRA on facebook
https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the
NeuRA Magazine http://www.neura.edu.au/help-research/subscribe
On 5/02/2015 3:16 am, Douglas N Greve wrote:
I'm not sure that I understand what I'm looking at. If it is an ROI
analysis, then there is no surface, it should be about 40 numbers, one
for each ROI.
On 02/03/2015 06:26 PM, Bronwyn Overs wrote:
Hi Doug,
Thanks for your correction.
I have now completed the FDR for my case-control comparisons, and it
appears that none of the regions survived. This is again quite
confusing given the large number of parcellated regions that survived
FDR in the SPSS ANCOVA. Can you confirm that this screenshot of the
sig.mgh file from ROI analysis looks as you would expect (it looks
very strange to me):
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.auhttp://neura.edu.au
Follow @neuraustralia on twitter
https://twitter.com/neuraustraliaFollow NeuRA on facebook
https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to
the NeuRA Magazinehttp://www.neura.edu.au/help-research/subscribe
On 4/02/2015 9:35 am, Douglas Greve wrote:
Yes, it should be .^
On 2/3/15 5:33 PM, Bronwyn Overs wrote:
Hi Doug,
I am having a problem with the line in Matlab 2014b:
p = 10^-abs(sigmat);
I keep getting the following error:
Error using ^
Inputs must be a scalar and a square matrix.
To compute elementwise POWER, use POWER (.^)
instead.
Do you know why this would be?
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.auhttp://neura.edu.au
Follow @neuraustralia on twitter
https://twitter.com/neuraustraliaFollow NeuRA on facebook
https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to
the NeuRA Magazinehttp://www.neura.edu.au/help-research/subscribe
On 4/02/2015 2:22 am, Douglas Greve wrote:
There is not a way to do it from the command line. You can do it in
matlab, something like
sig = MRIread('sig.mgh');
sigmat = fast_vol2mat(sig);
p = 10^-abs(sigmat);
fdr = .05;
pthresh = fast_fdrthresh(p,fdr);
ind = find(p pthresh); % This will be a list of ROI indices that
survive FDR
doug
On 2/2/15 10:26 PM, Bronwyn Overs wrote:
Hi Doug,
That makes perfect sense. Just one more thing then, how do you
conduct an FDR via the command line for an ROI mri_glmfit analysis?
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.auhttp://neura.edu.au
Follow @neuraustralia on twitter
https://twitter.com/neuraustraliaFollow NeuRA on facebook
https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe
to the NeuRA Magazine
http://www.neura.edu.au/help-research/subscribe
On 3/02/2015 2:00 pm, Douglas Greve wrote:
This is not something you would run the MC sim on because there
is no clustering, it is just a list of ROIs with their p-values.
The p-values are uncorrected. You can do bonferoni correction
across all the ROIs (or just the ones you are interested in). You
could do FDR too.
doug
On 2/2/15 9:39 PM, Bronwyn Overs wrote:
Thanks Doug, that worked well.
However, is it possible to run a monte-carlo simulation with
this GLM ROI analysis? I attempted to run it using the following
command...
mri_glmfit-sim --glmdir
DesikanROIAnal_case-control.thick.lh.glmdir --cache 1.3 abs
--cwpvalthresh 0.05 --2spaces
and received the following error:
ERROR: could not determine file for
DesikanROIAnal_case-control.thick.lh.glmdir/mask
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick
Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses
Hi Doug, I am not sure how to run an ROI analysis using mri_glmfit. Is there a wiki page detailing this method (I was unable to find one)? Is the first step to map lh.aparc.label and rh.aparc.label from fsaverage to each of my individual subjects using mri_label2label? When I do so and then view the mapped label for an individual subject in freeview, it appears to be a continuous label for all of the parcellated regions combined. Is this correct? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 3/02/2015 3:31 am, Douglas Greve wrote: First, I would run the ROI analysis in mri_glmfit to see if you get the same results as in SPSS. In the handfull of these cases, no one has been able to correctly replicate the FS design matrix in SPSS, so I suspect that is part of the discrepancy. The other thing is that ROI and vertex-wise analyses are simply different. As an extreme example, if some of the vertices are pos and some are neg then they would cancel out when you average them in an ROI but individually could be significant at the vertex level. If you analyze the average over the cluster then that should come out as significant. doug On 2/1/15 11:36 PM, Bronwyn Overs wrote: Dear FreeSurfer Mailing List, I have a sample of schizophrenia and control subjects for whom I have run a case-control analysis of cortical thickness using two separate methods (GLM vertex-wise analysis in freesurfer, repeated measures ANCOVA analysis of parcellated data in SPSS). However, for each methods of analysis I am getting extremely different results. For the GLM in Freesurfer I have only 1 small cluster in the frontal lobe that differs between cases and controls (controlling for all other IVs, FWMH = 10mm, cluster-forming threshold= .05, cluster-wise pval=.05), while for the ANCOVA method all but 8 of the parcellated regions differ significantly between groups (p.05). For both methods I have used the same model of predictors (independent variables = gender, group, scanning site; covariate = age) and exactly the same sample of participants. I have also replicated the GLM analysis using the QDEC GUI to ensure that I had no made any mistakes. Can you provide any insight into why I would be seeing such different results for each method using the same data set? My findings using the ANCOVA analysis make much more sense to me, given previous findings of reduced cortical thickness in schizophrenia subjects. I was surprised not to find the same pattern of effects using the GLM analysis. -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses
Hi Doug, That makes perfect sense. Just one more thing then, how do you conduct an FDR via the command line for an ROI mri_glmfit analysis? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 3/02/2015 2:00 pm, Douglas Greve wrote: This is not something you would run the MC sim on because there is no clustering, it is just a list of ROIs with their p-values. The p-values are uncorrected. You can do bonferoni correction across all the ROIs (or just the ones you are interested in). You could do FDR too. doug On 2/2/15 9:39 PM, Bronwyn Overs wrote: Thanks Doug, that worked well. However, is it possible to run a monte-carlo simulation with this GLM ROI analysis? I attempted to run it using the following command... mri_glmfit-sim --glmdir DesikanROIAnal_case-control.thick.lh.glmdir --cache 1.3 abs --cwpvalthresh 0.05 --2spaces and received the following error: ERROR: could not determine file for DesikanROIAnal_case-control.thick.lh.glmdir/mask Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 3/02/2015 11:03 am, Douglas Greve wrote: Even easier. Run aparcstats2table, then run mri_glmfit passing the output of aparcstats2table with --table (instead of --y). There's something on the wiki about it, also look for the ROI tutorial. doug On 2/2/15 6:20 PM, Bronwyn Overs wrote: Hi Doug, I am not sure how to run an ROI analysis using mri_glmfit. Is there a wiki page detailing this method (I was unable to find one)? Is the first step to map lh.aparc.label and rh.aparc.label from fsaverage to each of my individual subjects using mri_label2label? When I do so and then view the mapped label for an individual subject in freeview, it appears to be a continuous label for all of the parcellated regions combined. Is this correct? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 3/02/2015 3:31 am, Douglas Greve wrote: First, I would run the ROI analysis in mri_glmfit to see if you get the same results as in SPSS. In the handfull of these cases, no one has been able to correctly replicate the FS design matrix in SPSS, so I suspect that is part of the discrepancy. The other thing is that ROI and vertex-wise analyses are simply different. As an extreme example, if some of the vertices are pos and some are neg then they would cancel out when you average them in an ROI but individually could be significant at the vertex level. If you analyze the average over the cluster then that should come out as significant. doug On 2/1/15 11:36 PM, Bronwyn Overs wrote: Dear FreeSurfer Mailing List, I have a sample of schizophrenia and control subjects for whom I have run a case-control analysis of cortical thickness using two separate methods (GLM vertex-wise analysis in freesurfer, repeated measures ANCOVA analysis of parcellated data in SPSS). However, for each methods of analysis I am getting extremely different results. For the GLM in Freesurfer I have only 1 small cluster in the frontal lobe that differs between cases and controls (controlling for all other IVs, FWMH = 10mm, cluster-forming threshold= .05, cluster-wise pval=.05), while for the ANCOVA method all but 8 of the parcellated regions differ significantly between groups (p.05). For both methods I have used the same model of predictors (independent variables = gender, group, scanning site; covariate = age) and exactly the same sample of participants. I have also replicated the GLM analysis using the QDEC GUI to ensure that I had no made any mistakes. Can you provide any insight into why I would be seeing such different results for each
Re: [Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses
Thanks Doug, that worked well. However, is it possible to run a monte-carlo simulation with this GLM ROI analysis? I attempted to run it using the following command... mri_glmfit-sim --glmdir DesikanROIAnal_case-control.thick.lh.glmdir --cache 1.3 abs --cwpvalthresh 0.05 --2spaces and received the following error: ERROR: could not determine file for DesikanROIAnal_case-control.thick.lh.glmdir/mask Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 3/02/2015 11:03 am, Douglas Greve wrote: Even easier. Run aparcstats2table, then run mri_glmfit passing the output of aparcstats2table with --table (instead of --y). There's something on the wiki about it, also look for the ROI tutorial. doug On 2/2/15 6:20 PM, Bronwyn Overs wrote: Hi Doug, I am not sure how to run an ROI analysis using mri_glmfit. Is there a wiki page detailing this method (I was unable to find one)? Is the first step to map lh.aparc.label and rh.aparc.label from fsaverage to each of my individual subjects using mri_label2label? When I do so and then view the mapped label for an individual subject in freeview, it appears to be a continuous label for all of the parcellated regions combined. Is this correct? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 3/02/2015 3:31 am, Douglas Greve wrote: First, I would run the ROI analysis in mri_glmfit to see if you get the same results as in SPSS. In the handfull of these cases, no one has been able to correctly replicate the FS design matrix in SPSS, so I suspect that is part of the discrepancy. The other thing is that ROI and vertex-wise analyses are simply different. As an extreme example, if some of the vertices are pos and some are neg then they would cancel out when you average them in an ROI but individually could be significant at the vertex level. If you analyze the average over the cluster then that should come out as significant. doug On 2/1/15 11:36 PM, Bronwyn Overs wrote: Dear FreeSurfer Mailing List, I have a sample of schizophrenia and control subjects for whom I have run a case-control analysis of cortical thickness using two separate methods (GLM vertex-wise analysis in freesurfer, repeated measures ANCOVA analysis of parcellated data in SPSS). However, for each methods of analysis I am getting extremely different results. For the GLM in Freesurfer I have only 1 small cluster in the frontal lobe that differs between cases and controls (controlling for all other IVs, FWMH = 10mm, cluster-forming threshold= .05, cluster-wise pval=.05), while for the ANCOVA method all but 8 of the parcellated regions differ significantly between groups (p.05). For both methods I have used the same model of predictors (independent variables = gender, group, scanning site; covariate = age) and exactly the same sample of participants. I have also replicated the GLM analysis using the QDEC GUI to ensure that I had no made any mistakes. Can you provide any insight into why I would be seeing such different results for each method using the same data set? My findings using the ANCOVA analysis make much more sense to me, given previous findings of reduced cortical thickness in schizophrenia subjects. I was surprised not to find the same pattern of effects using the GLM analysis. -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list
[Freesurfer] Different results for GLM analysis of parcellated regions and vertex-wise analyses
Dear FreeSurfer Mailing List, I have a sample of schizophrenia and control subjects for whom I have run a case-control analysis of cortical thickness using two separate methods (GLM vertex-wise analysis in freesurfer, repeated measures ANCOVA analysis of parcellated data in SPSS). However, for each methods of analysis I am getting extremely different results. For the GLM in Freesurfer I have only 1 small cluster in the frontal lobe that differs between cases and controls (controlling for all other IVs, FWMH = 10mm, cluster-forming threshold= .05, cluster-wise pval=.05), while for the ANCOVA method all but 8 of the parcellated regions differ significantly between groups (p.05). For both methods I have used the same model of predictors (independent variables = gender, group, scanning site; covariate = age) and exactly the same sample of participants. I have also replicated the GLM analysis using the QDEC GUI to ensure that I had no made any mistakes. Can you provide any insight into why I would be seeing such different results for each method using the same data set? My findings using the ANCOVA analysis make much more sense to me, given previous findings of reduced cortical thickness in schizophrenia subjects. I was surprised not to find the same pattern of effects using the GLM analysis. -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Freesurfer Calculation of Vertex-Wise Area
Yes that makes perfect sense. Thanks very much. On 17 Jan 2015, at 7:01, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: I don't have a core paper on the area mapping (which is more complicated than mapping thickness). Anderson Winkler wrote a paper on the subject, but we are not using his method. Our method is relatively simple. Each vertex in fsaverage is mapped back to the individual to find the closest vertex. The thickness or area at this vertex is then assigned to the vertex in fsaverage. There will be some fsaverage vertices that map to the same vertex in the individual. For thickness, this is not a problem. For area or volume, we divide the value by the number of fsaverage vertices that share the individual vertex to preserve the total. This may leave some vertices in the individual that were never a closest vertex. We loop through these vertices and do a reverse map back to fsaverage to find the closest vertex. These fsaverage vertices will then have multiple vertices from the individual. For thickness, we compute the mean of the source vertices. For area or volume we compute the sum (must preserve the total). make sense? doug On 01/16/2015 12:00 AM, Bronwyn Overs wrote: I meant that as well as the mapping of the area to the average space. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 16/01/2015 3:58 pm, Douglas Greve wrote: The computation is pretty simple, it is just the average of the area of the surrounding triangle. Is that what you mean or do you mean the mapping of said area to the average space? doug On 1/15/15 11:37 PM, Bronwyn Overs wrote: Dear Mailing List, I would like to understand how freesurfer calculates the surface area at each voxel to be used in the GLM procedure. Is there a key methods paper that describes this process, and can this method be explained in simple terms? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Freesurfer Calculation of Vertex-Wise Area
Dear Mailing List, I would like to understand how freesurfer calculates the surface area at each voxel to be used in the GLM procedure. Is there a key methods paper that describes this process, and can this method be explained in simple terms? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Different significant regions with different cluster wise thresholds
Hi Doug, Thanks, that makes it very clear. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 19/12/2014 4:52 am, Douglas N Greve wrote: OK, I've figured out what's going on. The cluster @ threshold of 1.3 in superior temporal breaks up into 3 very small clusters when the threshold is changed to 2.0, none of which are significant. There is a cluster in middle temporal at 1.3 but it is not very significant (p=.17), but it stays a single cluster when the threshold is changed to 2.0. The size of the cluster drops by a factor of 2 but it is still large enough to be significant (p=.043). This is just one of the problems with the cluster method. doug On 12/17/2014 05:52 PM, Bronwyn Overs wrote: Hi Doug, The problem is with the int_genderXgroup contrast (between .05 .01 cluster forming thresholds). Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 18/12/2014 4:42 am, Douglas N Greve wrote: There are a bunch of contrasts there. Which one had the discrepancy? doug On 12/15/2014 07:43 PM, Bronwyn Overs wrote: Hi Douglas, I uploaded my glmdir to you on the 3/12/14 (named site-gender-group-prothaplotype.area.lh.glmdir.zip). Can you see what the problem is? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.auhttp://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazinehttp://www.neura.edu.au/help-research/subscribe On 27/11/2014 1:31 pm, Bronwyn Overs wrote: Thanks Douglas, I will upload it then. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.auhttp://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazinehttp://www.neura.edu.au/help-research/subscribe On 27/11/2014 1:30 pm, Douglas Greve wrote: Through the file drop at the end of this email. But you might want to wait until next week as I will be out of the office until Dec 4. doug On 11/26/14 12:50 AM, Bronwyn Overs wrote: Hi Douglas, How exactly should I upload the glmdir? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.auhttp://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 11/11/2014 4:19 am, Douglas N Greve wrote: Can you upload the gtlmdir and I'll take a look? On 11/06/2014 08:19 PM, Bronwyn Overs wrote: I believe it is the cluster-forming threshold. I was running the following: mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache 1.3 abs --cwpvalthresh 0.05 --2spaces mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache 2 abs --cwpvalthresh 0.05 --2spaces Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.auhttp://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazinehttp://www.neura.edu.au/help-research/subscribe On 7/11/2014 4:03 am, Douglas N Greve wrote: Do
Re: [Freesurfer] Different significant regions with different cluster wise thresholds
Hi Doug, The problem is with the int_genderXgroup contrast (between .05 .01 cluster forming thresholds). Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 18/12/2014 4:42 am, Douglas N Greve wrote: There are a bunch of contrasts there. Which one had the discrepancy? doug On 12/15/2014 07:43 PM, Bronwyn Overs wrote: Hi Douglas, I uploaded my glmdir to you on the 3/12/14 (named site-gender-group-prothaplotype.area.lh.glmdir.zip). Can you see what the problem is? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 27/11/2014 1:31 pm, Bronwyn Overs wrote: Thanks Douglas, I will upload it then. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 27/11/2014 1:30 pm, Douglas Greve wrote: Through the file drop at the end of this email. But you might want to wait until next week as I will be out of the office until Dec 4. doug On 11/26/14 12:50 AM, Bronwyn Overs wrote: Hi Douglas, How exactly should I upload the glmdir? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 11/11/2014 4:19 am, Douglas N Greve wrote: Can you upload the gtlmdir and I'll take a look? On 11/06/2014 08:19 PM, Bronwyn Overs wrote: I believe it is the cluster-forming threshold. I was running the following: mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache 1.3 abs --cwpvalthresh 0.05 --2spaces mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache 2 abs --cwpvalthresh 0.05 --2spaces Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.auhttp://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazinehttp://www.neura.edu.au/help-research/subscribe On 7/11/2014 4:03 am, Douglas N Greve wrote: Do you mean cluster-wise threshold or cluster-forming threshold? On 11/06/2014 01:12 AM, Bronwyn Overs wrote: Dear Freesurfer Mailing list, While running a glm anlaysis with monte carlo correction (using cluster wise thresholds of .05 .01), I encountered the following issue: When examining the clusters formed for each of the different cluster wise thresholds, the .05 threshold resulted in a superior temporal cluster, while the .01 threshold resulted in a two lateral occipital clusters that did not overlap with the cluster from the .05 threshold. Do you know why there would be no overlap between significant regions at different cluster wise thresholds? I was aware that a cluster which is significant at .05 may split or be smaller at .01, but I do not know why entirely different regions would be significant. -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.auhttp://neura.edu.au Follow @neuraustralia on twitter https://twitter.com
Re: [Freesurfer] Different significant regions with different cluster wise thresholds
Hi Douglas, I uploaded my glmdir to you on the 3/12/14 (named site-gender-group-prothaplotype.area.lh.glmdir.zip). Can you see what the problem is? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 27/11/2014 1:31 pm, Bronwyn Overs wrote: Thanks Douglas, I will upload it then. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 27/11/2014 1:30 pm, Douglas Greve wrote: Through the file drop at the end of this email. But you might want to wait until next week as I will be out of the office until Dec 4. doug On 11/26/14 12:50 AM, Bronwyn Overs wrote: Hi Douglas, How exactly should I upload the glmdir? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 11/11/2014 4:19 am, Douglas N Greve wrote: Can you upload the gtlmdir and I'll take a look? On 11/06/2014 08:19 PM, Bronwyn Overs wrote: I believe it is the cluster-forming threshold. I was running the following: mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache 1.3 abs --cwpvalthresh 0.05 --2spaces mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache 2 abs --cwpvalthresh 0.05 --2spaces Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.auhttp://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazinehttp://www.neura.edu.au/help-research/subscribe On 7/11/2014 4:03 am, Douglas N Greve wrote: Do you mean cluster-wise threshold or cluster-forming threshold? On 11/06/2014 01:12 AM, Bronwyn Overs wrote: Dear Freesurfer Mailing list, While running a glm anlaysis with monte carlo correction (using cluster wise thresholds of .05 .01), I encountered the following issue: When examining the clusters formed for each of the different cluster wise thresholds, the .05 threshold resulted in a superior temporal cluster, while the .01 threshold resulted in a two lateral occipital clusters that did not overlap with the cluster from the .05 threshold. Do you know why there would be no overlap between significant regions at different cluster wise thresholds? I was aware that a cluster which is significant at .05 may split or be smaller at .01, but I do not know why entirely different regions would be significant. -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.auhttp://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazinehttp://www.neura.edu.au/help-research/subscribe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] mri_glmfit error
Thanks Douglas. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 3/12/2014 3:53 pm, Douglas Greve wrote: You have a --C that is not followed by a contrast file. doug On 11/26/14 10:58 PM, Bronwyn Overs wrote: Dear Freesurfer Mailing list, I have been attempting to run the following command in freesurfer v5.3.0: mri_glmfit --y site-gender-group-prothaplotype.thick.lh.10.mgh --fsgd site-gender-group-prothaplotype.fsgd dods --C me_site-BrisVsMelb.mtx --C me_site-BrisVsPer.mtx --C me_site-MelbVsPer.mtx --C --surf fsaverage lh --cortex --glmdir site-gender-group-prothaplotype.thick.lh.glmdir Unfortunely, I keep getting the following error: ERROR: Option lh unknown Do you know why this would be? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_glmfit error
Dear Freesurfer Mailing list, I have been attempting to run the following command in freesurfer v5.3.0: mri_glmfit --y site-gender-group-prothaplotype.thick.lh.10.mgh --fsgd site-gender-group-prothaplotype.fsgd dods --C me_site-BrisVsMelb.mtx --C me_site-BrisVsPer.mtx --C me_site-MelbVsPer.mtx --C --surf fsaverage lh --cortex --glmdir site-gender-group-prothaplotype.thick.lh.glmdir Unfortunely, I keep getting the following error: ERROR: Option lh unknown Do you know why this would be? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Different significant regions with different cluster wise thresholds
Hi Douglas, How exactly should I upload the glmdir? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 11/11/2014 4:19 am, Douglas N Greve wrote: Can you upload the gtlmdir and I'll take a look? On 11/06/2014 08:19 PM, Bronwyn Overs wrote: I believe it is the cluster-forming threshold. I was running the following: mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache 1.3 abs --cwpvalthresh 0.05 --2spaces mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache 2 abs --cwpvalthresh 0.05 --2spaces Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 7/11/2014 4:03 am, Douglas N Greve wrote: Do you mean cluster-wise threshold or cluster-forming threshold? On 11/06/2014 01:12 AM, Bronwyn Overs wrote: Dear Freesurfer Mailing list, While running a glm anlaysis with monte carlo correction (using cluster wise thresholds of .05 .01), I encountered the following issue: When examining the clusters formed for each of the different cluster wise thresholds, the .05 threshold resulted in a superior temporal cluster, while the .01 threshold resulted in a two lateral occipital clusters that did not overlap with the cluster from the .05 threshold. Do you know why there would be no overlap between significant regions at different cluster wise thresholds? I was aware that a cluster which is significant at .05 may split or be smaller at .01, but I do not know why entirely different regions would be significant. -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.auhttp://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazinehttp://www.neura.edu.au/help-research/subscribe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Different significant regions with different cluster wise thresholds
I believe it is the cluster-forming threshold. I was running the following: mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache 1.3 abs --cwpvalthresh 0.05 --2spaces mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache 2 abs --cwpvalthresh 0.05 --2spaces Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 7/11/2014 4:03 am, Douglas N Greve wrote: Do you mean cluster-wise threshold or cluster-forming threshold? On 11/06/2014 01:12 AM, Bronwyn Overs wrote: Dear Freesurfer Mailing list, While running a glm anlaysis with monte carlo correction (using cluster wise thresholds of .05 .01), I encountered the following issue: When examining the clusters formed for each of the different cluster wise thresholds, the .05 threshold resulted in a superior temporal cluster, while the .01 threshold resulted in a two lateral occipital clusters that did not overlap with the cluster from the .05 threshold. Do you know why there would be no overlap between significant regions at different cluster wise thresholds? I was aware that a cluster which is significant at .05 may split or be smaller at .01, but I do not know why entirely different regions would be significant. -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Different significant regions with different cluster wise thresholds
Dear Freesurfer Mailing list, While running a glm anlaysis with monte carlo correction (using cluster wise thresholds of .05 .01), I encountered the following issue: When examining the clusters formed for each of the different cluster wise thresholds, the .05 threshold resulted in a superior temporal cluster, while the .01 threshold resulted in a two lateral occipital clusters that did not overlap with the cluster from the .05 threshold. Do you know why there would be no overlap between significant regions at different cluster wise thresholds? I was aware that a cluster which is significant at .05 may split or be smaller at .01, but I do not know why entirely different regions would be significant. -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Unknown problem with fsgd file
Dear Freesurfer Mailing list, I have been attempting to run mri_glmfit using a complicated fsgd file (1 categorical varible with 5 levels, 3 categorical variables with 2 levels, age as covariate). When I run the command, I receive the following error: gdfReadHeader: reading site-gender-group-riskhaplotype.fsgd Input line 5, subjid = 100121, class siteMelbourne-anyRiskAnyRisk-genderFemale-groupControl not defined FSGDF Format Error: file = site-gender-group-riskhaplotype.fsgd, tag=Input I have double checked the fsgd file and confirmed that the class for participant 100121 was specific correctly at the beginning of the file (correct spelling and case was used). So I cannot identify the source of the error. Can you advise me as to what may be going wrong? My full fsgd file begins like this (I have 389 subjects but have provided only the first 20 for brevity): GroupDescriptorFile 1 Title GLM_SiteGender Class siteBrisbane-anyProtNoProt-genderMale-groupCase Class siteBrisbane-anyProtNoProt-genderFemale-groupCase Class siteBrisbane-anyProtNoProt-genderMale-groupControl Class siteBrisbane-anyProtNoProt-genderFemale-groupControl Class siteBrisbane-anyProtAnyProt-genderMale-groupCase Class siteBrisbane-anyProtAnyProt-genderFemale-groupCase Class siteBrisbane-anyProtAnyProt-genderMale-groupControl Class siteBrisbane-anyProtAnyProt-genderFemale-groupControl Class siteMelbourne-anyProtNoProt-genderMale-groupCase Class siteMelbourne-anyProtNoProt-genderFemale-groupCase Class siteMelbourne-anyProtNoProt-genderMale-groupControl Class siteMelbourne-anyProtNoProt-genderFemale-groupControl Class siteMelbourne-anyProtAnyProt-genderMale-groupCase Class siteMelbourne-anyProtAnyProt-genderFemale-groupCase Class siteMelbourne-anyProtAnyProt-genderMale-groupControl Class siteMelbourne-anyProtAnyProt-genderFemale-groupControl Class siteNewcastle-anyProtNoProt-genderMale-groupCase Class siteNewcastle-anyProtNoProt-genderFemale-groupCase Class siteNewcastle-anyProtNoProt-genderMale-groupControl Class siteNewcastle-anyProtNoProt-genderFemale-groupControl Class siteNewcastle-anyProtAnyProt-genderMale-groupCase Class siteNewcastle-anyProtAnyProt-genderFemale-groupCase Class siteNewcastle-anyProtAnyProt-genderMale-groupControl Class siteNewcastle-anyProtAnyProt-genderFemale-groupControl Class sitePerth-anyProtNoProt-genderMale-groupCase Class sitePerth-anyProtNoProt-genderFemale-groupCase Class sitePerth-anyProtNoProt-genderMale-groupControl Class sitePerth-anyProtNoProt-genderFemale-groupControl Class sitePerth-anyProtAnyProt-genderMale-groupCase Class sitePerth-anyProtAnyProt-genderFemale-groupCase Class sitePerth-anyProtAnyProt-genderMale-groupControl Class sitePerth-anyProtAnyProt-genderFemale-groupControl Class siteSydney-anyProtNoProt-genderMale-groupCase Class siteSydney-anyProtNoProt-genderFemale-groupCase Class siteSydney-anyProtNoProt-genderMale-groupControl Class siteSydney-anyProtNoProt-genderFemale-groupControl Class siteSydney-anyProtAnyProt-genderMale-groupCase Class siteSydney-anyProtAnyProt-genderFemale-groupCase Class siteSydney-anyProtAnyProt-genderMale-groupControl Class siteSydney-anyProtAnyProt-genderFemale-groupControl Variables age Input 100105SA sitePerth-anyProtNoProt-genderMale-groupCase 23 Input 100112SA siteBrisbane-anyProtAnyProt-genderMale-groupCase 22 Input 100117SA siteBrisbane-anyProtNoProt-genderMale-groupCase 39 Input 100118 siteBrisbane-anyProtNoProt-genderFemale-groupCase 30 Input 100121 siteMelbourne-anyProtAnyProt-genderFemale-groupControl 21 Input 100122 siteMelbourne-anyProtAnyProt-genderMale-groupControl 53 Input 100151 siteMelbourne-anyProtNoProt-genderFemale-groupControl 58 Input 100185SA siteBrisbane-anyProtNoProt-genderFemale-groupControl 24 Input 100187 siteBrisbane-anyProtNoProt-genderMale-groupCase 24 Input 100189 siteBrisbane-anyProtNoProt-genderFemale-groupCase 21 Input 100190 siteSydney-anyProtNoProt-genderMale-groupControl 41 Input 100191 siteMelbourne-anyProtAnyProt-genderFemale-groupControl 19 Input 100193SA siteSydney-anyProtNoProt-genderMale-groupControl 26 Input 100196 siteBrisbane-anyProtNoProt-genderMale-groupControl 55 Input 100197SA siteBrisbane-anyProtNoProt-genderFemale-groupCase 30 Input 100200SA siteBrisbane-anyProtNoProt-genderMale-groupControl 39 Input 100204 siteSydney-anyProtAnyProt-genderFemale-groupControl 50 Input 100208 siteBrisbane-anyProtNoProt-genderMale-groupControl 25 Input 100209SA siteBrisbane-anyProtAnyProt-genderMale-groupCase 35 Input 100214 siteSydney-anyProtAnyProt-genderMale-groupCase 44 The mri_glmfit command I am using is as follows: mri_glmfit --y site-gender-group-prothaplotype.thick.lh.10.mgh --fsgd site-gender-group-prothaplotype.fsgd dods --C gender.mtx --C group.mtx --C haplotype.mtx --C groupXgender.mtx --C haplotypeXgender.mtx --C groupXhaplotype.mtx --C genderXgroupXhaplotype.mtx --surf fsaverage lh --cortex --glmdir site-gender-group-prothaplotype.thick.lh.glmdir -- Kind regards, Bronwyn Overs Research Assistant
[Freesurfer] Trouble specifying contrast vectors
-0.5 -0.5 -0.5 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 0.5 0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Interaction between gender, group, haplotype: 0.5 -0.5 -0.5 0.5 -0.5 0.5 0.5 -0.5 0.5 -0.5 -0.5 0.5 -0.5 0.5 0.5 -0.5 0.5 -0.5 -0.5 0.5 -0.5 0.5 0.5 -0.5 0.5 -0.5 -0.5 0.5 -0.5 0.5 0.5 -0.5 0.5 -0.5 -0.5 0.5 -0.5 0.5 0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] GLM contrast vector for continuous variable interaction
Thanks Douglas. That is exactly what I wanted. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 21/10/2014 2:37 am, Douglas N Greve wrote: I think this is the contrast you need 00000000 0.50.50.50.5 - 0.5 -0.5-0.5-0.5 On 10/19/2014 06:33 PM, Bronwyn Overs wrote: Dear Freesurfer Mailing List, I am running a GLM in freesurfer 2 categorical variables (2 levels), and three continuous variables (age, prs, sles). My fsgd file looks like this: GroupDescriptorFile 1 Title GLM_sles-group-gender-age Class genderMale-groupControl Class genderFemale-groupControl Class genderMale-groupAtRisk Class genderFemale-groupAtRisk Variables age prs sles Input ID_001 genderFemale-groupAtRisk 20 21 96 Input ID_002 genderFemale-groupControl 21 13 79 ... I want to test for an interaction between prs and sles, while controlling for age, gender, and group. Can you tell me if the following contrast vector will correctly test for this interaction: 000000000 0 0 0 0.50.50.50.5 000000000.50.50.5 0.5 0 0 0 0 -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] GLM contrast vector for continuous variable interaction
Dear Freesurfer Mailing List, I am running a GLM in freesurfer 2 categorical variables (2 levels), and three continuous variables (age, prs, sles). My fsgd file looks like this: GroupDescriptorFile 1 Title GLM_sles-group-gender-age Class genderMale-groupControl Class genderFemale-groupControl Class genderMale-groupAtRisk Class genderFemale-groupAtRisk Variables age prs sles Input ID_001 genderFemale-groupAtRisk 20 21 96 Input ID_002 genderFemale-groupControl 21 13 79 ... I want to test for an interaction between prs and sles, while controlling for age, gender, and group. Can you tell me if the following contrast vector will correctly test for this interaction: 000000000 0 0 0 0.5 0.50.50.5 000000000.50.50.50.5 0 0 0 0 -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Extracting Group Means for Cortical Thickness
Hi Doug, Thanks for your response. I was able to follow the steps you detailed and have ended up with a .dat file containing a list of values for each subject. Just a couple of follow up questions: 1. In my analysis I was using rh thickness as a dependent measure. So, do the individual values I have generated (using the below command) represent average thickness of the labelled area for each subject? 2. If I where using area or volume as the dependant measure, how would i generate label specific stats for those measures? 2. Are the generated stats measured in mm2? 3. What is the function of the flag --id 1? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 22/08/2014 3:27 am, Douglas N Greve wrote: Create a label of the cluster, then run mri_segstats --slabel fsaverage lh /path/to/your.label --i y.mgh --id 1 --avgwf cluster.dat where y.mgh is the file created by qdec in the qdec output folder and make sure to use the full path to the label. The output will be cluster.dat and it will have have a value for each subject. Does this work for you? doug On 08/20/2014 07:36 PM, Bronwyn Overs wrote: Dear Mailing List, I have just completed a QDEC (v5.1.0) analysis of the following design: Measure:thickness Smoothing (FWHM):10 Hemisphere:lh 2 Discrete (Fixed Factors):group (2 levels, AtRisk Control) and gene (2 levels, CC TTorTC) 1 Nuisance Factos:age On completion of the analysis, I have selected the following results in the display tab: Does the average thickness, acounting for group, differ between CC and TTorTC?. I have then completed an FDR correction by clicking the Set Using FDR (Rate 0.05) button. The following info is then printed to the terminal window: MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.05, vwth=4.74798 Found 59 of 163842 vertices above FDR threshold (of 4.74798) I have then hit Find Clusters and Goto Max and found there to be a single cluster in the medialorbitofrontal, with a size of 26.09 mm2. I would now like to know what the mean thickness is for that cluster at each level of my gene variable. How can this information be obtained? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Extracting Group Means for Cortical Thickness
Hi Doug, Thanks again for your prompt response. That is all very clear! Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 25/08/2014 12:21 pm, Douglas Greve wrote: On 8/24/14 8:54 PM, Bronwyn Overs wrote: Hi Doug, Thanks for your response. I was able to follow the steps you detailed and have ended up with a .dat file containing a list of values for each subject. Just a couple of follow up questions: 1. In my analysis I was using rh thickness as a dependent measure. So, do the individual values I have generated (using the below command) represent average thickness of the labelled area for each subject? Yes 2. If I where using area or volume as the dependant measure, how would i generate label specific stats for those measures? Do you mean you want to run qdec using area or volume to generate a new label or that you want to get area and volume measures for the thickness-based label? If the latter, then run qdec with area/volume as the dependent measure making sure to spec a different output folder. This will create a new y.mgh file. Then run the mri_segstats command on it. 2. Are the generated stats measured in mm2? For thickness, they will be mm, area mm2, volume mm3. 3. What is the function of the flag --id 1? It just says to generate stats for the label. If you don't include that flag, then it will generate 2 numbers, one for all the vertices in the label, and one for all vertices not in the label doug Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe On 22/08/2014 3:27 am, Douglas N Greve wrote: Create a label of the cluster, then run mri_segstats --slabel fsaverage lh /path/to/your.label --i y.mgh --id 1 --avgwf cluster.dat where y.mgh is the file created by qdec in the qdec output folder and make sure to use the full path to the label. The output will be cluster.dat and it will have have a value for each subject. Does this work for you? doug On 08/20/2014 07:36 PM, Bronwyn Overs wrote: Dear Mailing List, I have just completed a QDEC (v5.1.0) analysis of the following design: Measure:thickness Smoothing (FWHM):10 Hemisphere:lh 2 Discrete (Fixed Factors):group (2 levels, AtRisk Control) and gene (2 levels, CC TTorTC) 1 Nuisance Factos:age On completion of the analysis, I have selected the following results in the display tab: Does the average thickness, acounting for group, differ between CC and TTorTC?. I have then completed an FDR correction by clicking the Set Using FDR (Rate 0.05) button. The following info is then printed to the terminal window: MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.05, vwth=4.74798 Found 59 of 163842 vertices above FDR threshold (of 4.74798) I have then hit Find Clusters and Goto Max and found there to be a single cluster in the medialorbitofrontal, with a size of 26.09 mm2. I would now like to know what the mean thickness is for that cluster at each level of my gene variable. How can this information be obtained? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.auhttp://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazinehttp://www.neura.edu.au/help-research/subscribe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only
[Freesurfer] Extracting Group Means for Cortical Thickness
Dear Mailing List, I have just completed a QDEC (v5.1.0) analysis of the following design: Measure:thickness Smoothing (FWHM):10 Hemisphere:lh 2 Discrete (Fixed Factors):group (2 levels, AtRisk Control) and gene (2 levels, CC TTorTC) 1 Nuisance Factos:age On completion of the analysis, I have selected the following results in the display tab: Does the average thickness, acounting for group, differ between CC and TTorTC?. I have then completed an FDR correction by clicking the Set Using FDR (Rate 0.05) button. The following info is then printed to the terminal window: MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.05, vwth=4.74798 Found 59 of 163842 vertices above FDR threshold (of 4.74798) I have then hit Find Clusters and Goto Max and found there to be a single cluster in the medialorbitofrontal, with a size of 26.09 mm2. I would now like to know what the mean thickness is for that cluster at each level of my gene variable. How can this information be obtained? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
