Re: [Freesurfer] Annotation file's LUT

[Bruce Fischl]

yes, that is all of them
On Thu, 25 Feb 2016, Faeze Vedaei wrote:

> Hi Freesurfer experts,
> I want to have all the label files extracted from the annotation file base
> on Destrieux atlas. I used the command mri_annotaion2label to do this. The
> result is just 75 labels. Are these all the regions included in annotation
> file? Can you let me know how I can access to all the regions (structure
> name) contained in annotation file?
> 
> Thanks,
> Faezeh Vedaei
> 
>
___
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] Fwd: View several Annot files in Tksurfer

[Bruce Fischl]

Hi Faezeh

the annotations label every vertex. How would you view more than one at 
the same time?


cheers
Bruce
On Wed, 24 Feb 2016, Faeze Vedaei wrote:


Hi Freesurfer Experts,
In order to view specific annot files by tksurfer in Freesurfer, I used
mris_label2annot command to create annot files based on Destrieux atlas.
Now, I can import annot file in tksurfer, but just one file at the time. My
aim is to view several annot files by their specific colors in tksurfer
simultaneously. May you help me how can I do this? In advance, I'd
appreciate your consideration.

Regards,
Faezeh Vedaei 


___
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] Annotation file's LUT

[Faeze Vedaei]

Hi Freesurfer experts,

I want to have all the label files extracted from the annotation file base
on Destrieux atlas. I used the command mri_annotaion2label to do this. The
result is just 75 labels. Are these all the regions included in annotation
file? Can you let me know how I can access to all the regions (structure
name) contained in annotation file?

Thanks,
Faezeh Vedaei
___
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] Minor adjustment to RB_all_2008-03-26.gca

[Kok, JG (neuro)]

Hi Bruce,

I'll have a look at mri_ca_train. Thanks again!

Cheers,

Jelmer

Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Verzonden: donderdag 25 februari 2016 20:58
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer] Minor adjustment to RB_all_2008-03-26.gca

Hi Jelmer

no, that won't work as the gca contains more information than that. YOu
will need to use mri_ca_train to create a new gca, which should be
relatively straightforward

cheers
Bruce
  On Thu, 25 Feb 2016, Kok, JG (neuro) wrote:

> Hi Bruce,
>
> Thanks for your quick reply. I do not have manually split asegs, I wish to 
> create them all automatically. I'm hoping it is possible to read 
> RB_all_2008-03-26.gca (preferably in MATLAB, using fread), and adjust all 
> putamen values posterior from the coronal plane through the anterior 
> commissure from (FreeSurferColorLUT)values 12 and 51 to for example values 
> 10012 and 10051 (and subsequently save the new file with fwrite). Do you 
> think this is possible?
>
> Cheers,
>
> Jelmer
>
> 
> Van: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Verzonden: donderdag 25 februari 2016 20:32
> Aan: Freesurfer support list
> Onderwerp: Re: [Freesurfer] Minor adjustment to RB_all_2008-03-26.gca
>
> Hi Jelmer
>
> if you have manually split asegs you can use them as input to mri_ca_train
> to create a new gca that has the separated putamen. You'll need to add a
> couple of entries to FreeSurferColorLUT.txt to specify how to display and
> name the new entries as well
>
> cheers
> Bruce
>
> On Thu, 25 Feb 2016, Kok, JG (neuro) wrote:
>
>> Hi,
>>
>> I wish to split the putamen in an anterior part and a posterior part in >60
>> subjects which have been analyzed by the recon-all stream (FS version
>> 5.3.0). Ideally, I would split the putamen in the atlas (e.g., at the
>> coronal plane through the anterior commissure) and apply this "new" atlas to
>> all subjects, one of the advantages being the bias that would be introduced
>> by splitting the putamena manually in all subjects would be avoided. After
>> some time trying to make this happen, I now think this could be achieved by
>> adjusting RB_all_2008-03-26.gca and applying something like
>>
>> "mri_ca_label -align subject_norm.mgz subject_talairach.m3z
>> RB_all_2008-03-26.gca subject_aseg.auto_noCCseg.PUTAMENA_SEPARATED.mgz".
>>
>> The problem is that till now I wasn't able to figure out how to correctly
>> read the binary file RB_all_2008-03-26.gca. I tried to use the MATLAB
>> function load_gca.m, but that seems to only work up to version 4 of the .gca
>> file format (as GCA_VERSION is set to 4 in the function), and
>> RB_all_2008-03-26.gca seems to be version 5. Also, when trying to read the
>> file anyway in MATLAB using the code written for version 4 and below (by
>> setting GCA_VERSION to 5.0), the code fails (the first gibbs_nlabels is
>> already way too large, although I suspect the error occurs earlier).
>>
>> My questions:
>> 1. Do you think I am following the right track to achieve a sensible
>> splitting of the putamena this way? Or should I try something else?
>> 2. Is there a newer load_gca.m file around which is able to read a version 5
>> .gca file? Or could you point me to the difference in the design of the
>> version 5 .gca file compared to that of the version 4 file so that I can
>> rewrite load_gca.m?
>>
>> Cheers,
>>
>> Jelmer
>>
>> 
>> De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de
>> geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken
>> van dit bericht, het niet openbaar maken of op enige wijze verspreiden of
>> vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een
>> incomplete aankomst of vertraging van dit verzonden bericht.
>>
>> The contents of this message are confidential and only intended for the eyes
>> of the addressee(s). Others than the addressee(s) are not allowed to use
>> this message, to make it public or to distribute or multiply this message in
>> any way. The UMCG cannot be held responsible for incomplete reception or
>> delay of this transferred message.
>>
> ___
> 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 

[Freesurfer] Map label from lh to rh

[Makaretz, Sara Johanna]

Hi, I want to map a label from one hemi to the other (all on fsaverage). I 
tried mri_label2label:

mri_label2label --s fsaverage --srchemi lh --trghemi rh --srclabel lh.a.label 
--trglabel rh.flipped_lh.a.label --regmethod surface

but I think I need to specify a reg file to go between hemispheres, does this 
exist somewhere? an error message kindly pointed out that this one does not 
exist: 
/usr/local/freesurfer/stable5_3_0/subjects/fsaverage/surf/rh.lh.sphere.reg
___
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] Minor adjustment to RB_all_2008-03-26.gca

[Bruce Fischl]

Hi Jelmer

no, that won't work as the gca contains more information than that. YOu 
will need to use mri_ca_train to create a new gca, which should be 
relatively straightforward

cheers
Bruce
  On Thu, 25 Feb 2016, Kok, JG (neuro) wrote:

> Hi Bruce,
>
> Thanks for your quick reply. I do not have manually split asegs, I wish to 
> create them all automatically. I'm hoping it is possible to read 
> RB_all_2008-03-26.gca (preferably in MATLAB, using fread), and adjust all 
> putamen values posterior from the coronal plane through the anterior 
> commissure from (FreeSurferColorLUT)values 12 and 51 to for example values 
> 10012 and 10051 (and subsequently save the new file with fwrite). Do you 
> think this is possible?
>
> Cheers,
>
> Jelmer
>
> 
> Van: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Verzonden: donderdag 25 februari 2016 20:32
> Aan: Freesurfer support list
> Onderwerp: Re: [Freesurfer] Minor adjustment to RB_all_2008-03-26.gca
>
> Hi Jelmer
>
> if you have manually split asegs you can use them as input to mri_ca_train
> to create a new gca that has the separated putamen. You'll need to add a
> couple of entries to FreeSurferColorLUT.txt to specify how to display and
> name the new entries as well
>
> cheers
> Bruce
>
> On Thu, 25 Feb 2016, Kok, JG (neuro) wrote:
>
>> Hi,
>>
>> I wish to split the putamen in an anterior part and a posterior part in >60
>> subjects which have been analyzed by the recon-all stream (FS version
>> 5.3.0). Ideally, I would split the putamen in the atlas (e.g., at the
>> coronal plane through the anterior commissure) and apply this "new" atlas to
>> all subjects, one of the advantages being the bias that would be introduced
>> by splitting the putamena manually in all subjects would be avoided. After
>> some time trying to make this happen, I now think this could be achieved by
>> adjusting RB_all_2008-03-26.gca and applying something like
>>
>> "mri_ca_label -align subject_norm.mgz subject_talairach.m3z
>> RB_all_2008-03-26.gca subject_aseg.auto_noCCseg.PUTAMENA_SEPARATED.mgz".
>>
>> The problem is that till now I wasn't able to figure out how to correctly
>> read the binary file RB_all_2008-03-26.gca. I tried to use the MATLAB
>> function load_gca.m, but that seems to only work up to version 4 of the .gca
>> file format (as GCA_VERSION is set to 4 in the function), and
>> RB_all_2008-03-26.gca seems to be version 5. Also, when trying to read the
>> file anyway in MATLAB using the code written for version 4 and below (by
>> setting GCA_VERSION to 5.0), the code fails (the first gibbs_nlabels is
>> already way too large, although I suspect the error occurs earlier).
>>
>> My questions:
>> 1. Do you think I am following the right track to achieve a sensible
>> splitting of the putamena this way? Or should I try something else?
>> 2. Is there a newer load_gca.m file around which is able to read a version 5
>> .gca file? Or could you point me to the difference in the design of the
>> version 5 .gca file compared to that of the version 4 file so that I can
>> rewrite load_gca.m?
>>
>> Cheers,
>>
>> Jelmer
>>
>> 
>> De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de
>> geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken
>> van dit bericht, het niet openbaar maken of op enige wijze verspreiden of
>> vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een
>> incomplete aankomst of vertraging van dit verzonden bericht.
>>
>> The contents of this message are confidential and only intended for the eyes
>> of the addressee(s). Others than the addressee(s) are not allowed to use
>> this message, to make it public or to distribute or multiply this message in
>> any way. The UMCG cannot be held responsible for incomplete reception or
>> delay of this transferred message.
>>
> ___
> 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.
>
> 
> De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de 
> geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken 
> van dit bericht, het niet openbaar maken of op enige wijze verspreiden of 
> vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een 
> 

Re: [Freesurfer] Minor adjustment to RB_all_2008-03-26.gca

[Kok, JG (neuro)]

Hi Bruce,

Thanks for your quick reply. I do not have manually split asegs, I wish to 
create them all automatically. I'm hoping it is possible to read 
RB_all_2008-03-26.gca (preferably in MATLAB, using fread), and adjust all 
putamen values posterior from the coronal plane through the anterior commissure 
from (FreeSurferColorLUT)values 12 and 51 to for example values 10012 and 10051 
(and subsequently save the new file with fwrite). Do you think this is possible?

Cheers,

Jelmer


Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Verzonden: donderdag 25 februari 2016 20:32
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer] Minor adjustment to RB_all_2008-03-26.gca

Hi Jelmer

if you have manually split asegs you can use them as input to mri_ca_train
to create a new gca that has the separated putamen. You'll need to add a
couple of entries to FreeSurferColorLUT.txt to specify how to display and
name the new entries as well

cheers
Bruce

On Thu, 25 Feb 2016, Kok, JG (neuro) wrote:

> Hi,
>
> I wish to split the putamen in an anterior part and a posterior part in >60
> subjects which have been analyzed by the recon-all stream (FS version
> 5.3.0). Ideally, I would split the putamen in the atlas (e.g., at the
> coronal plane through the anterior commissure) and apply this "new" atlas to
> all subjects, one of the advantages being the bias that would be introduced
> by splitting the putamena manually in all subjects would be avoided. After
> some time trying to make this happen, I now think this could be achieved by
> adjusting RB_all_2008-03-26.gca and applying something like
>
> "mri_ca_label -align subject_norm.mgz subject_talairach.m3z
> RB_all_2008-03-26.gca subject_aseg.auto_noCCseg.PUTAMENA_SEPARATED.mgz".
>
> The problem is that till now I wasn't able to figure out how to correctly
> read the binary file RB_all_2008-03-26.gca. I tried to use the MATLAB
> function load_gca.m, but that seems to only work up to version 4 of the .gca
> file format (as GCA_VERSION is set to 4 in the function), and
> RB_all_2008-03-26.gca seems to be version 5. Also, when trying to read the
> file anyway in MATLAB using the code written for version 4 and below (by
> setting GCA_VERSION to 5.0), the code fails (the first gibbs_nlabels is
> already way too large, although I suspect the error occurs earlier).
>
> My questions:
> 1. Do you think I am following the right track to achieve a sensible
> splitting of the putamena this way? Or should I try something else?
> 2. Is there a newer load_gca.m file around which is able to read a version 5
> .gca file? Or could you point me to the difference in the design of the
> version 5 .gca file compared to that of the version 4 file so that I can
> rewrite load_gca.m?
>
> Cheers,
>
> Jelmer
>
> 
> De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de
> geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken
> van dit bericht, het niet openbaar maken of op enige wijze verspreiden of
> vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een
> incomplete aankomst of vertraging van dit verzonden bericht.
>
> The contents of this message are confidential and only intended for the eyes
> of the addressee(s). Others than the addressee(s) are not allowed to use
> this message, to make it public or to distribute or multiply this message in
> any way. The UMCG cannot be held responsible for incomplete reception or
> delay of this transferred message.
>
___
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.


 De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de 
geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van 
dit bericht, het niet openbaar maken of op enige wijze verspreiden of 
vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een 
incomplete aankomst of vertraging van dit verzonden bericht.

The contents of this message are confidential and only intended for the eyes of 
the addressee(s). Others than the addressee(s) are not allowed to use this 
message, to make it public or to distribute or multiply this message in any 
way. The UMCG cannot be held responsible for incomplete reception or delay of 
this transferred 

Re: [Freesurfer] Minor adjustment to RB_all_2008-03-26.gca

[Bruce Fischl]

Hi Jelmer

if you have manually split asegs you can use them as input to mri_ca_train 
to create a new gca that has the separated putamen. You'll need to add a 
couple of entries to FreeSurferColorLUT.txt to specify how to display and 
name the new entries as well

cheers
Bruce

On Thu, 25 Feb 2016, Kok, JG (neuro) wrote:

> Hi,
> 
> I wish to split the putamen in an anterior part and a posterior part in >60
> subjects which have been analyzed by the recon-all stream (FS version
> 5.3.0). Ideally, I would split the putamen in the atlas (e.g., at the
> coronal plane through the anterior commissure) and apply this "new" atlas to
> all subjects, one of the advantages being the bias that would be introduced
> by splitting the putamena manually in all subjects would be avoided. After
> some time trying to make this happen, I now think this could be achieved by
> adjusting RB_all_2008-03-26.gca and applying something like
> 
> "mri_ca_label -align subject_norm.mgz subject_talairach.m3z
> RB_all_2008-03-26.gca subject_aseg.auto_noCCseg.PUTAMENA_SEPARATED.mgz".
> 
> The problem is that till now I wasn't able to figure out how to correctly
> read the binary file RB_all_2008-03-26.gca. I tried to use the MATLAB
> function load_gca.m, but that seems to only work up to version 4 of the .gca
> file format (as GCA_VERSION is set to 4 in the function), and
> RB_all_2008-03-26.gca seems to be version 5. Also, when trying to read the
> file anyway in MATLAB using the code written for version 4 and below (by
> setting GCA_VERSION to 5.0), the code fails (the first gibbs_nlabels is
> already way too large, although I suspect the error occurs earlier).
> 
> My questions:
> 1. Do you think I am following the right track to achieve a sensible
> splitting of the putamena this way? Or should I try something else?
> 2. Is there a newer load_gca.m file around which is able to read a version 5
> .gca file? Or could you point me to the difference in the design of the
> version 5 .gca file compared to that of the version 4 file so that I can
> rewrite load_gca.m?
> 
> Cheers,
> 
> Jelmer
> 
> 
> De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de
> geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken
> van dit bericht, het niet openbaar maken of op enige wijze verspreiden of
> vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een
> incomplete aankomst of vertraging van dit verzonden bericht.
> 
> The contents of this message are confidential and only intended for the eyes
> of the addressee(s). Others than the addressee(s) are not allowed to use
> this message, to make it public or to distribute or multiply this message in
> any way. The UMCG cannot be held responsible for incomplete reception or
> delay of this transferred message.
>
___
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] How to invoke skullstrip adjustments and wm control points

[Bruce Fischl]

Hi Ed

if you run the skull stripping the autorecon2 and autorecon3 it should 
detect and preserve your manual interventions

cheers
Bruce


On Thu, 25 Feb 2016, Gronenschild Ed (NP) wrote:

> Hi,
>
> I have made some manual skullstrip adjustments and added a
> number of control points in the white matter.
> How should I proceed with recon-all to incorporate both adjustments?
>
> Cheers,
> Ed
>
> ___
> 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] Permission denied error with mri_surfcluster command

[Jennifer Legault]

Hi Douglas,

Thank you for all your help.  When I say "volume" I do mean the FS
thickness*area measure.  I ran the mri_glmfit with --osgm and for the FWHM
received the value of .925737.  Assuming that this rounds up to 1, I then
went to $FREESURFER_HOME/average/mult-comp-cor/fsaverage to find the CSD
file and I selected the fwhm01 csd file.

I then ran the mri_surfcluster command, however, I got the following error:

ERROR: you have specified srcsubjid=fsaverage on cmdline, but
CSD file was created with fsaverage

Any suggestions you have would be appreciated.

Best,

Jen

On Thu, Feb 11, 2016 at 1:32 PM, Douglas N Greve 
wrote:

> by "volume" do you mean a VBM-type analysis or do you mean the volume
> that comes out of FS (thickness*area)? If you are going to use a
> clusterwise correction, then you have to have a FWHM measurement. You
> can try analyzing it in mri_glmfit with --osgm just to get the FWHM out
> of it.
>
> You should be able to output a .mgh file instead of a .w file
>
>
> On 02/11/2016 01:07 PM, Jennifer Legault wrote:
> > That's very useful, thank you.  In terms of FWHM, I am examining gray
> > matter volume, not cortical thickness, and was previously instructed
> > by Martin Reuter not to smooth these data.  Do you think it would make
> > sense then to just use the fwhm01?  And in terms of the voxel-wise
> > threshold, is there a commonly used value for GM volume data?  I am
> > still new to freesurfer and I appreciate any feedback.
> >
> > For visualization, after I run the mri_surfcluster the only outputs
> > are a summary file and a .w file, and freeview doesn't accept this
> > format.  Is it possible to have a cluster-wise corrected map (a
> > sig.cluster.mgh file) as they do for the Clusterwise Correction for
> > Multiple Comparisons tutorial here
> > ?
> >
> >
> > Best,
> >
> > Jen
> >
> > On Thu, Feb 11, 2016 at 11:39 AM, Douglas N Greve
> > > wrote:
> >
> >
> >
> > On 02/11/2016 11:19 AM, Jennifer Legault wrote:
> > > Thank you for your response.  Do I need to run the glm_fit-sim
> > command
> > > to make the csd file?  I feel this would be inappropriate for my
> > data
> > > since I already ran the LME model.
> > No, look in $FREESURFER_HOME/average/mult-comp-cor/fsaverage. You
> will
> > need the FWHM though
> > >
> > > Second, is there an argument to make an output file that can be
> > > visualized via freeview?  In other words, how can I view my cluster
> > > thresholded data?
> > You can use freeview, something like
> > freeview -f lh.inflated:overlay=sig.mgh
> > There are other options for loading annotations and curvature. See
> the
> > freeview help
> > >
> > > Your help is greatly appreciated,
> > >
> > > Jen
> > >
> > >
> > >
> > > On Wed, Feb 10, 2016 at 11:04 PM, Douglas Greve
> > > 
> >  > >> wrote:
> > >
> > > There is a (very long) command line on that page. Mainly you
> > need
> > > a csd file. To get that you need the FWHM of your analysis, the
> > > voxel-wise threshold, and the sign of the contrast (or abs).
> > Then
> > > the relevant output will be the --sum. You can run it with
> > --help
> > > to get more info.
> > >
> > >
> > > On 2/10/16 5:11 PM, Jennifer Legault wrote:
> > >> Thank you very much for your help!  I still received a "cannot
> > >> read file type" error when I only added the path to the output
> > >> --o part, however when I also added the path to the input
> file,
> > >> it worked!
> > >>
> > >> I do have one more question: Which argument can I add so
> > that in
> > >> my output file I see the clusterwise P value, like it is shown
> > >> here
> > >>
> >  <
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSummary
> >?
> > >>
> > >> Best,
> > >>
> > >> Jen
> > >>
> > >> On Wed, Feb 10, 2016 at 1:50 PM, Douglas N Greve
> > >> 
> >  > >> wrote:
> > >>
> > >> I meant for the output files, so the --o in particular
> > >>
> > >> On 02/10/2016 01:47 PM, Jennifer Legault wrote:
> > >> > Douglas,
> > >> >
> > >> > Thank you for your quick response. When I add --sd
> > >> [path_location], I
> > >> > get the following error:
> > >> > Loading source values
> > >> > mri_read(): couldn't determine type of 

Re: [Freesurfer] How to invoke skullstrip adjustments and wm control points

[Kok, JG (neuro)]

Hi Ed,

I'm not sure if this'll help you, but I read your question right after I posted 
mine, and thought to let you know the solution I used in cases where I had to 
add control points:

"
Or Make Life Easier

recon-all -make all -s subjid
"

is copied from one of the Freesurfer Powerpoint slides. It worked great for me, 
and I suspect it will also work in your case. As far as I understand, using 
this command Freesurfer will look for the first function in the pipeline where 
some of the input has been modified, and performs all recon-all steps from 
there.

Cheers,

Jelmer




Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Gronenschild Ed (NP) 
[ed.gronensch...@maastrichtuniversity.nl]
Verzonden: donderdag 25 februari 2016 19:19
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: [Freesurfer] How to invoke skullstrip adjustments and wm control 
points

Hi,

I have made some manual skullstrip adjustments and added a
number of control points in the white matter.
How should I proceed with recon-all to incorporate both adjustments?

Cheers,
Ed

___
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.


 De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de 
geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van 
dit bericht, het niet openbaar maken of op enige wijze verspreiden of 
vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een 
incomplete aankomst of vertraging van dit verzonden bericht.

The contents of this message are confidential and only intended for the eyes of 
the addressee(s). Others than the addressee(s) are not allowed to use this 
message, to make it public or to distribute or multiply this message in any 
way. The UMCG cannot be held responsible for incomplete reception or delay of 
this transferred message.

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Minor adjustment to RB_all_2008-03-26.gca

[Kok, JG (neuro)]

Hi,

I wish to split the putamen in an anterior part and a posterior part in >60 
subjects which have been analyzed by the recon-all stream (FS version 5.3.0). 
Ideally, I would split the putamen in the atlas (e.g., at the coronal plane 
through the anterior commissure) and apply this "new" atlas to all subjects, 
one of the advantages being the bias that would be introduced by splitting the 
putamena manually in all subjects would be avoided. After some time trying to 
make this happen, I now think this could be achieved by adjusting 
RB_all_2008-03-26.gca and applying something like

"mri_ca_label -align subject_norm.mgz subject_talairach.m3z 
RB_all_2008-03-26.gca subject_aseg.auto_noCCseg.PUTAMENA_SEPARATED.mgz".

The problem is that till now I wasn't able to figure out how to correctly read 
the binary file RB_all_2008-03-26.gca. I tried to use the MATLAB function 
load_gca.m, but that seems to only work up to version 4 of the .gca file format 
(as GCA_VERSION is set to 4 in the function), and RB_all_2008-03-26.gca seems 
to be version 5. Also, when trying to read the file anyway in MATLAB using the 
code written for version 4 and below (by setting GCA_VERSION to 5.0), the code 
fails (the first gibbs_nlabels is already way too large, although I suspect the 
error occurs earlier).

My questions:
1. Do you think I am following the right track to achieve a sensible splitting 
of the putamena this way? Or should I try something else?
2. Is there a newer load_gca.m file around which is able to read a version 5 
.gca file? Or could you point me to the difference in the design of the version 
5 .gca file compared to that of the version 4 file so that I can rewrite 
load_gca.m?

Cheers,

Jelmer

De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de 
geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van 
dit bericht, het niet openbaar maken of op enige wijze verspreiden of 
vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een 
incomplete aankomst of vertraging van dit verzonden bericht.

The contents of this message are confidential and only intended for the eyes of 
the addressee(s). Others than the addressee(s) are not allowed to use this 
message, to make it public or to distribute or multiply this message in any 
way. The UMCG cannot be held responsible for incomplete reception or delay of 
this transferred message.
___
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] How to invoke skullstrip adjustments and wm control points

[Gronenschild Ed (NP)]

Hi,

I have made some manual skullstrip adjustments and added a
number of control points in the white matter.
How should I proceed with recon-all to incorporate both adjustments?

Cheers,
Ed

___
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] Problem with brainstem substructures segmentation

[Riccardo Gubellini]

Dear Freesurfer users,

We have downloaded the Freesurfer 6.0 version since we are really
interested in the brainstem segmentation.
We are working with a pc equipped with a 3.6 GHz CPU and 16 GB RAM.
We installed freesurfer6.0 on a virtual machine Linux (CentOs 6.7)
enabling  4vcpu 11Gb of RAM.
Disk space was 50 GB and after installation we have 15 GB free for data.

We have launched recon-all –all  for some cases and everything went right.
Then we have tried to launch recon-all –all –s nameofsunbject
–brainstem-structures
and the process, after about 6 hours, stacks, during  the SegmentSubject
process and after having computing hyperparameters for estimation of
Gaussian parameters.
Do you have any ideas of what is happening?

Thank you for your help!

Riccardo Gubellini
___
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.