[Freesurfer] Paired analysis - mismatch between matrix and contrast

[Nick Corriveau Lecavalier]

Hi Freesurfer team,


I'm trying to run a longitudinal group analysis (2 groups, 2 time points) using 
the paired analysis procedure: 
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis.


I have followed all the instructions but when it comes to the mri_glmfit, it 
says that my contrast files has 2 columns, while the matrix has 44. What did I 
go wrong?


I join with this message the log, fsgd and contrasts files. Thank you!


Nick Corriveau-Lecavalier, B.Sc. (Hons.)
Étudiant au Ph.D. recherche/intervention, option neuropsychologie clinique
Coordonateur à la recherche, Association étudiante des cycles supérieurs en 
psychologie de l'Université de Montréal (AÉCSPUM)
Université de Montréal
Centre de recherche de l'Institut universitaire de gériatrie de Montréal, 
bureau M7819


mri_glmfit.log
Description: mri_glmfit.log


group
Description: group


paired.diff.fsgd
Description: paired.diff.fsgd


paired.fsgd
Description: paired.fsgd
___
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] Gaussian curvature or Mean curvature

[Bruce Fischl]

Hi Han

the ?h.curv files are the mean curvature of the white matter surface with a 
Gaussian smoothing kernel applied to it over space. The ?h.curv.pial is the 
same thing for the pial surface. The ?h.inflated.H is the (unsmoothed) 
curvature of the inflated surface, and the ?h.inflated.K is the same but 
Gaussian curvature.


cheers
Bruce


On Fri, 
16 Sep 2016, Hanbyul Cho wrote:



Dear Bruce Fischl,

Thank you for your explanation.

I think I could not yet fully understand the 'curv' files.
After processed this command,
recon-all -s  -i  -all

the output files were follow as,
surf/?h.curv
surf/?h.curv.pial
surf/?h.inflated.H
surf/?h.inflated.K

I wonder all these output files contained 'spatially smoothed mean
curvature'.

Could I know that the meaning of 'spatially smoothed' ?
Are these output files difference from the output of 'mris_curvature'
command?


I saw the values that 
stats/?h.aparc.stats   and
stats/?h.aparc.a2009s.stats
contained the 'integrated rectified Mean curvature' and 'integrated
rectified Gaussian curvature'.

I wonder these values were if the average curvature of vertices in each
region, or other computed values using different atlas parcellation level.

I appreciate your help.

Best Wishes,

Han.

On Fri, Sep 16, 2016 at 4:37 PM, Bruce Fischl 
wrote:
  Hi Han

  the files ?h.curv contain the spatially smoothed mean curvature.
  You can compute the mean or Gaussian (or principal) curvatures
  of any surface using the mris_curvature command.

  cheers
  Bruce




  On Fri, 16 Sep 2016, Hanbyul Cho wrote:

Dear FreeSurfer Team,


I heard that FreeSurfer could calculate the Gaussian
curvature and Mean
curvature by vertex level.

Do the computed curvature values be saved as the
subject/surf/lh.curv  or
rh.curv  files?


When I prepared the generated mass-univariate data,
I used the mris_preproc
with [--meas curv] option, not [--meas thickness].

mris_preproc --qdec-long qdec.table.dat --target
study_average --hemi lh
--meas curv--out lh.curv.mgh

I wonder this option is right usage to analyze the
cortical curvature. And I
wonder the 'curv' is what specific value is meaning.


If I want to designate the specific curvature
values(Gaussian or Mean
curvature ) to analyze by vertex level, how can I
use the [--meas] option?


Thank you,

Best wishes,

Han.



___
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] Gaussian curvature or Mean curvature

[Hanbyul Cho]

Dear Bruce Fischl,

Thank you for your explanation.

I think I could not yet fully understand the 'curv' files.

After processed this command,
recon-all -s  -i  -all

the output files were follow as,
surf/?h.curv
surf/?h.curv.pial
surf/?h.inflated.H
surf/?h.inflated.K

I wonder all these output files contained 'spatially smoothed mean
curvature'.

Could I know that the meaning of 'spatially smoothed' ?
Are these output files difference from the output of 'mris_curvature'
command?


I saw the values that
stats/?h.aparc.stats   and
stats/?h.aparc.a2009s.stats
contained the 'integrated rectified Mean curvature' and 'integrated
rectified Gaussian curvature'.

I wonder these values were if the average curvature of vertices in each
region, or other computed values using different atlas parcellation level.

I appreciate your help.

Best Wishes,

Han.

On Fri, Sep 16, 2016 at 4:37 PM, Bruce Fischl 
wrote:

> Hi Han
>
> the files ?h.curv contain the spatially smoothed mean curvature. You can
> compute the mean or Gaussian (or principal) curvatures of any surface using
> the mris_curvature command.
>
> cheers
> Bruce
>
>
>
>
>
> On Fri, 16 Sep 2016, Hanbyul Cho wrote:
>
> Dear FreeSurfer Team,
>>
>>
>> I heard that FreeSurfer could calculate the Gaussian curvature and Mean
>> curvature by vertex level.
>>
>> Do the computed curvature values be saved as the subject/surf/lh.curv  or
>> rh.curv  files?
>>
>>
>> When I prepared the generated mass-univariate data, I used the
>> mris_preproc
>> with [--meas curv] option, not [--meas thickness].
>>
>> mris_preproc --qdec-long qdec.table.dat --target study_average --hemi lh
>> --meas curv--out lh.curv.mgh
>>
>> I wonder this option is right usage to analyze the cortical curvature.
>> And I
>> wonder the 'curv' is what specific value is meaning.
>>
>>
>> If I want to designate the specific curvature values(Gaussian or Mean
>> curvature ) to analyze by vertex level, how can I use the [--meas] option?
>>
>>
>> Thank you,
>>
>> Best wishes,
>>
>> Han.
>>
>>
>>
> ___
> 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 spc over an ROI

[Martin Reuter]

Hi Rachel,

yes, there is a difference if you compute SPC of the average thickness in an 
ROI or if you average the SPC computed on a vertex level. 

For the second, you can use long_mris_surf to map your third group to fsaverage 
and compute SPC, there is an option to write out the stack, then using the 
label and that stack you can average the values inside the label. I would do 
that in Matlab (read the stack, read the label, select the vertices with that 
label and average). Maybe there are other tools for that. 

Best, Martin


> On Sep 16, 2016, at 5:05 PM, Rachel Romeo  wrote:
> 
> Hi,
> 
> I have 3 participant groups in my data set, all with 2 longitudinal time 
> points approximately evenly spaced. I've run everyone through the 
> longitudinal pipeline, and used the Monte Carlo simulation to find a cluster 
> that differs in SPC between groups 1 and 2. Now I want to calculate the 
> average SPC in that cluster for group 3, simply for qualitative reference. 
> 
> I've extracted the cluster to a label using mri_surfcluster, mapped that 
> label to each of the participants' surfaces using mri_label2label, and used 
> mris_anatomical_stats to extract the average thickness in the ROI, and then I 
> manually calculated SPC per subject. But, no matter whether I use 
> participants' CROSS or LONG surfaces, I can't replicate the average SPC 
> values in the "y.ocn.dat" file generated by the simulation.
> 
> My guess is that the difference arises because of the averaging -- I'm 
> averaging over thickness, and then calculating SPC, whereas I'm guessing that 
> the GLM calculates SPC per voxel, and then averages over the cluster. 
> 
> Is there a way I can extract the average SPC for group 3 over this ROI? 
> 
> Thanks,
> Rachel
> 
> ___
> 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] Gaussian curvature or Mean curvature

[Bruce Fischl]

Hi Han

the files ?h.curv contain the spatially smoothed mean curvature. You can 
compute the mean or Gaussian (or principal) curvatures of any surface 
using the mris_curvature command.


cheers
Bruce




On Fri, 16 Sep 2016, Hanbyul Cho wrote:


Dear FreeSurfer Team,


I heard that FreeSurfer could calculate the Gaussian curvature and Mean
curvature by vertex level.

Do the computed curvature values be saved as the subject/surf/lh.curv  or
rh.curv  files?


When I prepared the generated mass-univariate data, I used the mris_preproc
with [--meas curv] option, not [--meas thickness].

mris_preproc --qdec-long qdec.table.dat --target study_average --hemi lh
--meas curv--out lh.curv.mgh

I wonder this option is right usage to analyze the cortical curvature. And I
wonder the 'curv' is what specific value is meaning.


If I want to designate the specific curvature values(Gaussian or Mean
curvature ) to analyze by vertex level, how can I use the [--meas] option?


Thank you,

Best wishes,

Han.


___
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] mris_divide_parcellation

[Bruce Fischl]

how would you like them divided? You can also use 
mris_make_face_parcellation to make units of approximately equal area 
(either in the individual or in the group)
On Fri, 16 Sep 2016, Mamashli, 
Fahimeh wrote:



Dear Freesurfer group,
I am going to divide a brain parcellation into divisions using
mris_divide_parcellation. As far as I know from the help comment, this
function "divides one or more parcellations into divisions perpendicular to
the long axis of the label". Is there any other program that does not make
the divisions perpendicular to the long axis? 

Thank you,
Fahimeh

___
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] Gaussian curvature or Mean curvature

[Hanbyul Cho]

Dear FreeSurfer Team,


I heard that FreeSurfer could calculate the Gaussian curvature and Mean
curvature by vertex level.

Do the computed curvature values be saved as the subject/surf/lh.curv  or
rh.curv  files?


When I prepared the generated mass-univariate data, I used the mris_preproc
with [--meas curv] option, not [--meas thickness].

*mris_preproc --qdec-long qdec.table.dat --target study_average --hemi lh
--meas curv--out lh.curv.mgh*

I wonder this option is right usage to analyze the cortical curvature. And
I wonder the 'curv' is what specific value is meaning.


If I want to designate the specific curvature values(Gaussian or Mean
curvature ) to analyze by vertex level, how can I use the [--meas] option?


Thank you,

Best wishes,

Han.
___
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] Dev builds not found

[Bruce Fischl]

Hi Leila

we are experiencing disk problems at Martinos, which are probably causing 
this issue

sorry, not sure when it will be fixed
Bruce


On Fri, 16 Sep 2016, Leila 
Reddy wrote:

> Hi,
> I get an error with mri_nu_correct.mni. I've seen on the FS wiki that this
> is because I have a new version of perl and that I should download the
> development version. However, I cannot access this page
> 
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
> 
> (nothing happens on a linux machine, and I get a 550 Failed to change
> directory error on a Mac). Is there another place I can download the fixed
> version from?
> 
> Thanks,
> Leila
> 
>
___
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 spc over an ROI

[Rachel Romeo]

Hi,

I have 3 participant groups in my data set, all with 2 longitudinal time
points approximately evenly spaced. I've run everyone through the
longitudinal pipeline, and used the Monte Carlo simulation to find a
cluster that differs in SPC between groups 1 and 2. Now I want to calculate
the average SPC in that cluster for group 3, simply for qualitative
reference.

I've extracted the cluster to a label using mri_surfcluster, mapped that
label to each of the participants' surfaces using mri_label2label, and used
mris_anatomical_stats to extract the average thickness in the ROI, and then
I manually calculated SPC per subject. But, no matter whether I use
participants' CROSS or LONG surfaces, I can't replicate the average SPC
values in the "y.ocn.dat" file generated by the simulation.

My guess is that the difference arises because of the averaging -- I'm
averaging over thickness, and then calculating SPC, whereas I'm guessing
that the GLM calculates SPC per voxel, and then averages over the cluster.

Is there a way I can extract the average SPC for group 3 over this ROI?

Thanks,
Rachel
___
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] mris_divide_parcellation

[Mamashli, Fahimeh]

Dear Freesurfer group,
I am going to divide a brain parcellation into divisions using 
mris_divide_parcellation. As far as I know from the help comment, this function 
"divides one or more parcellations into divisions perpendicular to the long 
axis of the label". Is there any other program that does not make the divisions 
perpendicular to the long axis?

Thank you,
Fahimeh
___
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] Dev builds not found

[Leila Reddy]

Hi,I get an error with mri_nu_correct.mni. I've seen on the FS wiki that this 
is because I have a new version of perl and that I should download the 
development version. However, I cannot access this page 

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
(nothing happens on a linux machine, and I get a 550 Failed to change directory 
error on a Mac). Is there another place I can download the fixed version from?
Thanks,Leila
___
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] Z-stat - z.mgh

[Robby De Pauw]

Hi Doug

Thanks for the information. Could you however upload it again as the files are 
unavailable atm? Due to congresses and holiday, I was not able to download it 
in time.

Thank you in advance and sorry for the incovenience,

Greetings

Robby


On 05/07/16 19:17, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas 
N Greve"  wrote:

You can use the version 6 mri_glmfit which you can get from here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit

On 06/16/2016 07:51 AM, Robby De Pauw wrote:
>
> Dear FreeSurfer users
>
> I am not able to extract the Z-values as they are not present in my 
> output:
>
> z.mgh -- z-stat that corresponds to the significance
>
> Are these Z-values always produced (or only in case of two group 
> comparison)? Is there a way to produce this map myself?
>
> This is my output after fitting the model (mri_glmfit) and after 
> clusterwise correction for MC:
>
> C.dat cache.th13.abs.sig.voxel.mgh
>
> F.asc cache.th13.abs.y.ocn.dat
>
> F.csv cnr.mgh
>
> F.mgh gamma.mgh
>
> cache.th13.abs.pdf.dat gammavar.mgh
>
> cache.th13.abs.sig.cluster.mgh maxvox.dat
>
> cache.th13.abs.sig.cluster.summary sig.asc
>
> cache.th13.abs.sig.masked.mgh sig.csv
>
> cache.th13.abs.sig.ocn.annot sig.mgh
>
> cache.th13.abs.sig.ocn.mgh
>
> I am currently working on the latest version of FreeSurfer:
>
> freesurfer-Darwin-lion-stable-pub-v5.3.0
>
> Thank you for your response,
>
> Greetings
>
> Robby
>
> Robby De Pauw, PT, MT, drs.
>
> *T *+32 09 332 12 19* | Email *robby.dep...@ugent.be 
> 
>
> Ghent University *| *Rehabilitation Sciences and Physiotherapy
>
> Campus Heymans 3B3 (022)
>
> De Pintelaan 185 BE-9000 Ghent
>
> Route to my office 
>
>
>
> ___
> 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


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

Re: [Freesurfer] LGI and MATLAB

[Bruce Fischl]

Hi Alan

make sure matlab is in your path. You can check by typing:


which matlab


cheers
Bruce
On Fri, 16 Sep 
2016, Alan Francis wrote:



Hi Marie -

I have MATLAB and the Image processing toolbox on my MAC. Unfortunately, I
am unable to get FreeSurfer to recognize this (see below) , so I am getting
an error. Is there any way to overcome this?

Thanks,

Alan

afrancis-mac:~ afrancis$ export FREESURFER_HOME=/Applications/freesurfer
afrancis-mac:~ afrancis$ source /Applications/freesurfer/SetUpFreeSurfer.sh
 freesurfer-Darwin-lion-stable-pub-v5.3.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer
FSFAST_HOME   /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/subjects
MNI_DIR   /Applications/freesurfer/mni
FSL_DIR   /usr/local/fsl
afrancis-mac:~ afrancis$ export
MATLABPATH=/Applications/MATLAB_R2015a.app/bin
afrancis-mac:~ afrancis$ export PATH=${MATLABPATH}/bin:${PATH}
afrancis-mac:~ afrancis$ recon-all -s DM55 -localGI
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
Actual FREESURFER_HOME /Applications/freesurfer
-rw-rw-rw-  1 root  wheel  948660 Sep 16 09:50
/Applications/freesurfer/subjects/DM55/scripts/recon-all.log
Darwin afrancis-mac.mclean.harvard.edu 14.5.0 Darwin Kernel Version 14.5.0:
Thu Jun 16 19:58:21 PDT 2016; root:xnu-2782.50.4~1/RELEASE_X86_64 x86_64
INFO: current FREESURFER_HOME does not match that of previous processing.
    Current: /Applications/freesurfer
    Previous: /cm/shared/freesurfer
/Applications/freesurfer/subjects/DM55/surf
#
#@# Local Gyrification Index lh Fri Sep 16 09:55:23 EDT 2016
\n mris_compute_lgi --i lh.pial \n
ERROR: Matlab is required to run mris_compute_lgi!
Darwin afrancis-mac.mclean.harvard.edu 14.5.0 Darwin Kernel Version 14.5.0:
Thu Jun 16 19:58:21 PDT 2016; root:xnu-2782.50.4~1/RELEASE_X86_64 x86_64

recon-all -s DM55 exited with ERRORS at Fri Sep 16 09:55:23 EDT 2016

For more details, see the log file
/Applications/freesurfer/subjects/DM55/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

--
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

Alan N. Francis PhD
Instructor - Imaging Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu
afran...@mclean.harvard.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] LGI and MATLAB

[Alan Francis]

Hi Marie -

I have MATLAB and the Image processing toolbox on my MAC. Unfortunately, I
am unable to get FreeSurfer to recognize this (see below) , so I am getting
an error. Is there any way to overcome this?

Thanks,

Alan

afrancis-mac:~ afrancis$ export FREESURFER_HOME=/Applications/freesurfer
afrancis-mac:~ afrancis$ source /Applications/freesurfer/SetUpFreeSurfer.sh
 freesurfer-Darwin-lion-stable-pub-v5.3.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer
FSFAST_HOME   /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/subjects
MNI_DIR   /Applications/freesurfer/mni
FSL_DIR   /usr/local/fsl
afrancis-mac:~ afrancis$ export
MATLABPATH=/Applications/MATLAB_R2015a.app/bin
afrancis-mac:~ afrancis$ export PATH=${MATLABPATH}/bin:${PATH}
afrancis-mac:~ afrancis$ recon-all -s DM55 -localGI
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
Actual FREESURFER_HOME /Applications/freesurfer
-rw-rw-rw-  1 root  wheel  948660 Sep 16 09:50
/Applications/freesurfer/subjects/DM55/scripts/recon-all.log
Darwin afrancis-mac.mclean.harvard.edu 14.5.0 Darwin Kernel Version 14.5.0:
Thu Jun 16 19:58:21 PDT 2016; root:xnu-2782.50.4~1/RELEASE_X86_64 x86_64
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /Applications/freesurfer
Previous: /cm/shared/freesurfer
/Applications/freesurfer/subjects/DM55/surf
#
#@# Local Gyrification Index lh Fri Sep 16 09:55:23 EDT 2016
\n mris_compute_lgi --i lh.pial \n
ERROR: Matlab is required to run mris_compute_lgi!
Darwin afrancis-mac.mclean.harvard.edu 14.5.0 Darwin Kernel Version 14.5.0:
Thu Jun 16 19:58:21 PDT 2016; root:xnu-2782.50.4~1/RELEASE_X86_64 x86_64

recon-all -s DM55 exited with ERRORS at Fri Sep 16 09:55:23 EDT 2016

For more details, see the log file
/Applications/freesurfer/subjects/DM55/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

-- 
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

*Alan N. Francis PhD*
Instructor - Imaging Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu 
afran...@mclean.harvard.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.

Re: [Freesurfer] hide colored slices in 3d view?

[Ruopeng Wang]

Hi Jessica,

There is no such command-line option in version 5.3. Sorry.

Ruopeng

> On Sep 16, 2016, at 10:44 AM, j.oschw...@psychologie.uzh.ch wrote:
> 
> 
> Hi Freesurfer users,
> 
> I wrote a script to automatize taking screenshots in Freeview. Unfortunately, 
> in the 3d view the colored slices are automatically included in the picture.  
> Is there a way to hide them? I am using the current 5.3 version of 
> Freesurfer. 
> I know that the development build includes this option (-hide-3d-slices), but 
> I cannot access the FTP server right now to download it. Is there probably 
> also a command in the version I am currently using? 
> 
> Best
> Jessica
> ___
> 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] hide colored slices in 3d view?

[j . oschwald]

Hi Freesurfer users,

I wrote a script to automatize taking screenshots in Freeview. Unfortunately, 
in the 3d view the colored slices are automatically included in the picture.  
Is there a way to hide them? I am using the current 5.3 version of Freesurfer. 
I know that the development build includes this option (-hide-3d-slices), but I 
cannot access the FTP server right now to download it. Is there probably also a 
command in the version I am currently using? 

Best
Jessica
___
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: Tkregister2 error, moveable not present just white screen

[A Nunes]

>
> Hi Doug and all,
>

I just resend this email in case it did not reach, any help will be
appreciated.

>
> Thanks for your help. I was using the preprocessed thinking that after
> motion correction it would be more accurate and --init-header because they
> where acquired in the same session. I changed to a raw moveable and the
> results did not change for the following:
>
> With -init-fsl the moveable is now showing, but about 40% of the subjects
> the registration has fail, in many cases the moveable is rotated with
> respect to the target. I tried to use -init-spm but then the moveable and
> target don't even overlay.
>
> I also tried to use a successful registration .dat from another subject
> using the command  --init-reg $SUBJECTS_DIR/subj2/mri/register.dat  but
> the registration is not accurate.
>
> In many cases there is the WARNING: initial G-W contrast was negative, but
> expected positive. If the mov data has a T1 contrast, re-run with --T1. if
> I run the same command changing --bold to --T1 the results aren't good, as
> well as if I try -int $SUBJECTS_DIR/subj//T1.mgz.
>
> Is there anything else to try rather than manual registration? I just have
> the T1 and the fmri.  Would you recommend another registration method?
>
> Thanks
> Adonay
>
>
> On Mon, Sep 12, 2016 at 12:37 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> I think the problem is the initialization. I noticed you used
>> --init-header. This should only be used if the two volumes were acquired
>> during the same session and the direction cosines (ie, geometry) info is
>> accurate for both. Is this the case? I noticed that the input has
>> "preproc" in the name, so I'm a bit suspicious. You can try --init-fsl
>> instead
>>
>>
>> On 09/12/2016 01:36 PM, A Nunes wrote:
>> > Hi Doug
>> >
>> > I can't see any errors in the log file, and with other datasets I did
>> > not have this issue. My register.dat is:
>> >
>> > 50664
>> > 3.00
>> > 4.50
>> > 0.15
>> > 9.996076822280884e-01 -2.117119915783405e-02 -1.833262108266354e-02
>> > 3.139470825195312e+02
>> > 1.872027479112148e-02 1.825972087681293e-02 9.996579289436340e-01
>> > 2.150849456787109e+02
>> > -2.082921005785465e-02 -9.996089935302734e-01 1.864889077842236e-02
>> > 4.339286499023438e+02
>> > 0 0 0 1
>> > round
>> >
>> > and my register.dat.log is:
>> >
>> > setenv SUBJECTS_DIR /Users/adonay/Desktop/data/freesurfer/5
>> > cd /Users/adonay/Desktop/data/prepo_cpac
>> > /Applications/freesurfer/bin/bbregister --s 50664 --mov
>> > 50664_preprocessed.nii.gz --init-header --reg
>> > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/register.dat --bold
>> >
>> > $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
>> > Darwin sc-155014 15.6.0 Darwin Kernel Version 15.6.0: Mon Aug 29
>> > 20:21:34 PDT 2016; root:xnu-3248.60.11~1/RELEASE_X86_64 x86_64
>> > FREESURFER_HOME /Applications/freesurfer
>> > mri_convert 50664_preprocessed.nii.gz
>> > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregi
>> ster.14726/template.nii
>> > mri_convert 50664_preprocessed.nii.gz
>> > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregi
>> ster.14726/template.nii
>> >
>> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>> > reading from 50664_preprocessed.nii.gz...
>> > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
>> > i_ras = (-1, -0, 0)
>> > j_ras = (-0, 1, 0)
>> > k_ras = (-0, -0, 1)
>> > writing to
>> > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregi
>> ster.14726/template.nii...
>> > tkregister2_cmdl --s 50664 --mov
>> > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregi
>> ster.14726/template.nii
>> > --regheader --reg
>> > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregi
>> ster.14726/reg.init.dat
>> > --noedit
>> > tkregister_tcl /Applications/freesurfer/tktools/tkregister2.tcl
>> > INFO: no target volume specified, assuming FreeSurfer orig volume.
>> > target  volume orig
>> > movable volume
>> > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregi
>> ster.14726/template.nii
>> > reg file
>> > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregi
>> ster.14726/reg.init.dat
>> > LoadVol0
>> > ZeroCRAS   0
>> > $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
>> > Diagnostic Level -1
>> > INFO: loading target
>> > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/orig.mgz
>> > Ttarg: 
>> > -1.000   0.000   0.000   128.000;
>> >  0.000   0.000   1.000  -128.000;
>> >  0.000  -1.000   0.000   128.000;
>> >  0.000   0.000   0.000   1.000;
>> > INFO: loading movable
>> > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregi
>> ster.14726/template.nii
>> > Tmov: 
>> > -3.000   0.000   0.000   96.000;
>> >  0.000   0.000   4.500  -63.000;
>> >  0.000  -3.000   0.000   96.000;
>> >  0.000   0.000   0.000   1.000;
>> > mkheaderreg = 1, float2int = 0
>> > Computing reg from header (and possibly input matrix)
>> 

Re: [Freesurfer] Display FSL PALM(permutation) stats in freeview

[Anderson M. Winkler]

Hi Ajay,

To open the .mgz files produced by PALM you would first load the surface in
FreeView (at the top of the left panel, click on "Surface" then on the
button with a "+" sign), then after the surface has been loaded, in the
menu "Overlay" in the left panel, select "Load generic..." and load the
.mgz file you'd like to see. After loading there will be a button
"Configure overlay" that opens a window where the colourbar can be set,
etc. For 0.05 the threshold would be -log10(0.05) = 1.301.

Hope this helps.

All the best,

Anderson


On 15 September 2016 at 19:46, Ajay Kurani  wrote:

> Hello Freesurfer Experts,
>I was running permutation simulations on cortical thickness data and I
> had an issue with non-orthogonal covariates with mri_glmfit-sim -perm.  I
> then tried FSL's PALM which is an extension of randomize to calculate
> threshold free stats.  I saved the output as logp(which is similar to qdec
> I believe), however I have not been able to load the stats files
> correctly.  The output of palm is lh.thickness_tfce.mgz for my various
> contrasts.
>
> 1) Is .mgz the proper format for the stats files or do I need to convert
> this to another type like .mgh etc?
>
> 2) Can I display this in freeview or is another program needed?  I also
> tried tksurfer but when I loaded the stats file as an overlay nothing
> displayed.  I want to make sure that the stats is loaded as an overlay in
> freeview/tksurfer and if so, do I need to select anything special so that
> it scales the logp values correctly?
>
> Thanks,
> Ajay
>
> ___
> 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.