[Freesurfer] Inquiries about QDEC inflated surface

[Mahtab Farahbakhsh]

Dear FreeSurfer,

I am comparing two groups of my subjects together in qdec and when I want
to visualize each subject, I can see two different regions for inferior
parietal lobe and supramarginal gyrus. But in the normal pial surface, it
seems like that the labels of both overlap with each other. I'm not sure
how these two are different. Any guidance would be extremely appreciated.

Best Regards,
Mahtab.
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[Freesurfer] Error with qdec

[Mahtab Farahbakhsh]

Dear FreeSurfer,

I am trying to compare my subjects to the healthy group, but when I put the
matrix into qdec, I get the following error:

Normalized matrix condition is 1e+08
Design matrix --
 1.000   0.000   0.000   0.000   68.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   66.000   0.000;
 1.000   0.000   0.000   0.000   40.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   35.000   0.000;
 1.000   0.000   0.000   0.000   72.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   71.000   0.000;
 1.000   0.000   0.000   0.000   22.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   22.000   0.000;
 0.000   1.000   0.000   0.000   0.000   20.000   0.000   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   20.000;

ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08


  1. Your command line:
mri_glmfit --y
/Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/y.mgh
--fsgd
/Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/qdec.fsgd
dods --glmdir
/Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled
--surf fsaverage lh --label
/Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/fsaverage/label/lh.aparc.label
--C
/Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
--C
/Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-Avg-thickness-age-Cor.mat
--C
/Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-Diff-Male-Female-Intercept-thickness.mat
--C
/Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-Diff-Male-Female-Cor-thickness-age.mat
--C
/Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-Diff-spelling-healthy-Intercept-thickness.mat
--C
/Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-Diff-spelling-healthy-Cor-thickness-age.mat
--C
/Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-X-gender2-diagnosis_spelling-Intercept-thickness.mat
--C
/Applications/freesurfer/experimental_data/FAM_TG/DICOM_DATA/qdec/Untitled/contrasts/lh-X-gender2-diagnosis_spelling-Cor-thickness-age.mat



the table file is also attached to the mail.

Would you please kindly guide me with this?

Best Regards,
Mahtab.


qdec.table.spelling.healthy.dat
Description: Binary data


diagnosis_spelling.level
Description: Binary data


gender2.level
Description: Binary data
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[Freesurfer] Integrate SPM activation maps to FreeSurfer structural volumes

[Mahtab Farahbakhsh]

Dear FreeSurfer,

I am trying to register my SPM activation maps to the structural data of
each subjects. Except for the commands I could find for the registration, I
could not find a guide on the registration of activation maps from SPM to
FreeSurfer. Would you please guide me how I should do that?

Best Regards,
Mahtab.
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[Freesurfer] Inquiries about thickness and lgi group analysis

[Mahtab Farahbakhsh]

Dear FreeSurfer,

I am doing group analysis for thickness and LGI values. I have just got the
output and the output of both analyses (sig.mgh file view in Freeview) are
exactly the same. Would you please guide me with this?

Best Regards,
Mahtab.
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[Freesurfer] Error with MatlabR2016a and LGI

[Mahtab Farahbakhsh]

Dear FreeSurfer,

I am trying to calculate LGI for my images, but it seems like that it
doesn't work. I have tried everything, but it's still giving me the same
error.

I'm using FreeSurfer on a mac and my Matlab version is R2016a.

When I try to run "recon-all -s  -localGI", I get this error: ERROR:
Matlab is required to run mris_compute_lgi!.

I have done these so far:
PATH=/Applications/MATLAB_R2016a.app/bin/matlab:$PATH
export PATH

And my $PATH is:
/Applications/MATLAB_R2016a.app/bin/matlab:/usr/local/fsl/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/opt/X11/bin:
No such file or directory

And when I write getmatlab, I get this:
ERROR: Cannot find matlab.
Does not exist or is not in path.

My original Matlab is in the /Applications folder and I also have a folder
named "matlab" in my FreeSurfer folder.

Would you please guide me what I should do?

Best Regards,
Mahtab.
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Re: [Freesurfer] LGI

[Mahtab Farahbakhsh]

I have the very same problem! Hope to be able to solve it with the guidance 
from Freesurfer.

Best Regards,
Mahtab.



Friday, July 8, 2016, 01:43 +0100 from walidyassi...@gmail.com  
:
>Hello,
>
>Sorry for raising this questions again. I posted this questions a while ago 
>(Twice), but i haven't gotten an answer yet.
>Can i at least know if i can tweak something for this to work? or just give 
>up? 
>I tried downgrading Xquatrz, to 2.7.8, but it still doesn't work! My matlab is 
>2016a, could this be the problem?
>
>
>Thank you for letting me know
>
>WY
>
>On Sat, Jun 25, 2016 at 10:39 AM, Walid Yassin  < walidyassi...@gmail.com > 
>wrote:
>>Hello again,
>>
>>Sorry for posting twice, but does someone know what might be the problem?
>>Thank you in advance.
>>I’m trying to run recon-all -lgi - s Subjectname  on my data but i am
getting this error!
>>***

Error in dsearchn (line 79)
[d(i),t(i)] = min(sum((x-yi).^2,2));

Error in mesh_vertex_nearest (line 29)
nearestIndex = dsearchn(vertices,points);


Error in reorganize_verticeslist (line 28)

[nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:));


Error in make_roi_paths (line 93)
reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim,
verticeslist, step);


>>
ERROR:  make_roi_paths did not complete successfully!


***


*I checked the archives and saw a reply by Marie to someone who had the
same problem.*
*She recommended changing the info inside “SearchProjectionByPial.m" in the
~/Application/freesurfer/matlab directory to:*



***

function [verticeslist]=SearchProjectionOnPial(mesh_total,mesh_outer,perim,
step)

% step is typically set between 5 and 10. Default is 7, increasing it will
% limit redundancies in the resulting path file.

verticeslist=[];
si=max(size(perim));
for t=1:step:si

[nearestIndexMT,nearestValuesMT]=mesh_vertex_nearest(mesh_total.vertices,mesh_outer.vertices(perim(t),:));
verticeslist= [verticeslist nearestIndexMT];
end
verticeslist=unique(vertices list);

***


Which i did, but i am still getting this error!*
Any recommendations on what to do next? I am running MATLAB_R2016.

Thank you in advance,

WY
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[Freesurfer] Error with local Gyrification Index (lGI)

[Mahtab Farahbakhsh]

Dear FreeSurfer,

I am trying to calculate LGI for my images, but it seems like that it
doesn't work. I have tried everything, but it's still giving me the same
error.

I'm using FreeSurfer on a mac and my Matlab version is R2016a.

When I try to run "recon-all -s  -localGI", I get this error: ERROR:
Matlab is required to run mris_compute_lgi!.

I have done these so far:
PATH=/Applications/MATLAB_R2016a.app/bin/matlab:$PATH
export PATH

And my $PATH is:
/Applications/MATLAB_R2016a.app/bin/matlab:/usr/local/fsl/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/opt/X11/bin:
No such file or directory

And when I write getmatlab, I get this:
ERROR: Cannot find matlab.
Does not exist or is not in path.

My original Matlab is in the /Applications folder and I also have a folder
named "matlab" in my FreeSurfer folder.

Would you please guide me what I should do?

Best Regards,
Mahtab.
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[Freesurfer] Inquiries about the curvature

[Mahtab Farahbakhsh]

Dear FreeSurfer,

I am using the mris_anatomical_stats output to calculate the curvature and
thickness indices for different brain areas. However, I am not sure what
the mean and gaussian curvatures mean. I could not find a complete
description on these two. Would you please guide me what principle
curvature and mean and gaussian curvatures means exactly?

I appreciate your concern in advance.

Best Regards,
Mahtab.
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Re: [Freesurfer] Problem with FreeSurfer template and control subject

[Mahtab Farahbakhsh]

Dear Bruce,

Thank you for your response.

So would you please guide me how I should register the image into MNI152
coordination?
And is the cvs_avg35_inMNI152, the MNI152 template?

Best Regards,
Mahtab.

On 3 June 2016 at 13:48, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:

> Hi Mahtab
>
> we do all the analysis in native space and don't transform the data to a
> template (although we do compute mappings to various templates).
>
> As for your other question, there are too many variables to control for
> (age, gender, scanner type, sequence) for us to distribute a normative
> database. You will probably need to scan some controls.
>
> cheers
> Bruce
>
>
> On Fri, 3 Jun 2016, Mahtab Farahbakhsh wrote:
>
> Dear Freesurfer,
>> The data that I'm using as a part of my study contains only the patients'
>> T1
>> images and we have not collected any control subjects yet. I want to
>> compare
>> the cortical thickness of these subjects with a template (instead of a
>> control subject), but I'm confused which volume I need to choose. When I
>> run
>> recon-all, does it transform the slices based on the fsaverage? Is
>> fsaverage
>> based on Talairach template or MNI or something else?
>>
>> Would you please guide me with the question and inform me what template
>> volume is the best for me to use instead of my control subjects?
>>
>> Best Regards,
>> Mahtab.
>>
>>
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[Freesurfer] Problem with FreeSurfer template and control subject

[Mahtab Farahbakhsh]

Dear Freesurfer,

The data that I'm using as a part of my study contains only the patients'
T1 images and we have not collected any control subjects yet. I want to
compare the cortical thickness of these subjects with a template (instead
of a control subject), but I'm confused which volume I need to choose. When
I run recon-all, does it transform the slices based on the fsaverage? Is
fsaverage based on Talairach template or MNI or something else?

Would you please guide me with the question and inform me what template
volume is the best for me to use instead of my control subjects?

Best Regards,
Mahtab.
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Re: [Freesurfer] Error with mris_anatomical_stats

[Mahtab Farahbakhsh]

Dear Douglas,

The wm.mgz is in the mri folder so it's in:

Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz.

Best Regards,
Mahtab.

Sent from myMail for iOS


Thursday, May 19, 2016, 16:19 +0100 from gr...@nmr.mgh.harvard.edu  
<gr...@nmr.mgh.harvard.edu>:
>The second one is a valid command (1st is not). What is the full path to 
>the wm.mgz file that is in your anlayzed data?
>
>On 05/19/2016 10:33 AM, Mahtab Farahbakhsh wrote:
>> Dear Bruce,
>>
>> This is the input command and the output that I get:
>>
>> bash-3.2$ mris_anatomical_stats -l anon/label/lh.BA45.label -f anon lh 
>> anon lh
>> limiting computations to label anon/label/lh.BA45.label.
>> reading volume 
>> /Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz...
>> mghRead(/Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz, 
>> -1): could not open file
>> mris_anatomical_stats: could not read input volume 
>> /Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz
>>
>> or:
>>
>> mris_anatomical_stats -l anon/label/lh.BA45.label anon lh
>> limiting computations to label anon/label/lh.BA45.label.
>> reading volume 
>> /Applications/freesurfer/experimental_data/TG/anon/anon/mri/wm.mgz...
>> mghRead(/Applications/freesurfer/experimental_data/TG/anon/anon/mri/wm.mgz, 
>> -1): could not open file
>> mris_anatomical_stats: could not read input volume 
>> /Applications/freesurfer/experimental_data/TG/anon/anon/mri/wm.mgz
>>
>>
>> This is the SUBJECTS_DIR
>>
>> export SUBJECTS_DIR=/Applications/freesurfer/experimental_data/TG/anon
>>
>> cd $SUBJECTS_DIR
>>
>> Best Regards,
>> Mahtab.
>>
>>
>> On 19 May 2016 at 13:41, Bruce Fischl < fis...@nmr.mgh.harvard.edu
>> > wrote:
>>
>> Hi Mahtab
>>
>> can you please send the screen output of the command you ran and
>> what it printed, and also what the environment variable
>> SUBJECTS_DIR is?
>>
>> cheers
>> Bruce
>>
>> On Thu, 19 May 2016, Mahtab Farahbakhsh wrote:
>>
>> Dear FreeSurfer,
>> I have a problem when I use mris_anatomical_stats. It gives me
>> an error
>> saying that it couldn't read the input volume which is the
>> wm.mgz file.
>> would you please help me how I should fix this problem?
>>
>> Best Regards,
>> Mahtab.
>>
>>
>> ___
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>>  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.
>>
>>
>>
>>
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>
>-- 
>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
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>
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Re: [Freesurfer] Error with mris_anatomical_stats

[Mahtab Farahbakhsh]

Dear Bruce,

This is the input command and the output that I get:

bash-3.2$ mris_anatomical_stats -l anon/label/lh.BA45.label -f anon lh anon
lh
limiting computations to label anon/label/lh.BA45.label.
reading volume
/Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz...
mghRead(/Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz,
-1): could not open file
mris_anatomical_stats: could not read input volume
/Applications/freesurfer/experimental_data/TG/anon/lh/mri/wm.mgz

or:

mris_anatomical_stats -l anon/label/lh.BA45.label anon lh
limiting computations to label anon/label/lh.BA45.label.
reading volume
/Applications/freesurfer/experimental_data/TG/anon/anon/mri/wm.mgz...
mghRead(/Applications/freesurfer/experimental_data/TG/anon/anon/mri/wm.mgz,
-1): could not open file
mris_anatomical_stats: could not read input volume
/Applications/freesurfer/experimental_data/TG/anon/anon/mri/wm.mgz


This is the SUBJECTS_DIR

export SUBJECTS_DIR=/Applications/freesurfer/experimental_data/TG/anon

cd $SUBJECTS_DIR
Best Regards,
Mahtab.


On 19 May 2016 at 13:41, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:

> Hi Mahtab
>
> can you please send the screen output of the command you ran and what it
> printed, and also what the environment variable SUBJECTS_DIR is?
>
> cheers
> Bruce
>
> On Thu, 19 May 2016, Mahtab Farahbakhsh wrote:
>
> Dear FreeSurfer,
>> I have a problem when I use mris_anatomical_stats. It gives me an error
>> saying that it couldn't read the input volume which is the wm.mgz file.
>> would you please help me how I should fix this problem?
>>
>> Best Regards,
>> Mahtab.
>>
>>
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[Freesurfer] Error with mris_anatomical_stats

[Mahtab Farahbakhsh]

Dear FreeSurfer,

I have a problem when I use mris_anatomical_stats. It gives me an error
saying that it couldn't read the input volume which is the wm.mgz file.
would you please help me how I should fix this problem?

Best Regards,
Mahtab.
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Re: [Freesurfer] Defining ROI and Finding the Cortical Thickness

[Mahtab Farahbakhsh]

Dear Douglas,

To define my new label, I choose the ROI section and choose "New ROI". Then
I save it, but it doesn't work properly. In addition, I cant save it on
fsaverage.

Best Regards,
Mahtab.


On 12 May 2016 at 22:08, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote:

>
>
> On 05/12/2016 05:46 AM, Mahtab Farahbakhsh wrote:
> > Dear freeSurfer,
> >
> > I have problems with defining new labels for my brain scan or even of
> > fsaverage. I need to define a new label (ROI) to be able to find the
> > grey matter thickness for that specific region.
> >
> > My first problem is that when I define a new label on fsaverage, it
> > does not save it for me and it gives me the following error:
> >
> >
> mghRead(/Applications/freesurfer/experimental_data/TG/fsaverage/mri/wm.mgz,
> > -1): could not open file
> > /Applications/freesurfer/Freeview.app/Contents/MacOS/Freeview: could
> > not open label file
> > /Applications/freesurfer/subjects/fsaverage/label/ROI_test.label
> >
> > I intend to define a new label (ROI) on fsaverage and then use the
> > mri_labe2label command to copy it on my desired structural MRI image.
> > But it does not work for me.
> How are you doing this? What tool are you using? What steps with the
> tool are you executing?
> >
> > My second problem is that when I define a new label on my subject's
> > MRI image and I run the mri_anatomical_stats with the label of my
> > subject, it does not give me any output and this is what I get:
> >
> > bash-3.2$ mris_anatomical_stats -l anon/label/lh.test.label anon lh
> > limiting computations to label anon/label/lh.test.label.
> > reading volume
> > /Applications/freesurfer/experimental_data/TG//anon/mri/wm.mgz...
> > reading input surface
> > /Applications/freesurfer/experimental_data/TG//anon/surf/lh.white...
> > reading input pial surface
> > /Applications/freesurfer/experimental_data/TG//anon/surf/lh.pial...
> > reading input white surface
> > /Applications/freesurfer/experimental_data/TG//anon/surf/lh.white...
> >
> > and the error is that it could not find the file lh.test.label,
> > however I can see it in the label folder.
> Use the -b or -f flags to specify an output
> >
> > Please guide me with this issue.
> >
> > Best Regards,
> > Mahtab.
> >
> >
> > ___
> > 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.
>
>
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[Freesurfer] Defining ROI and Finding the Cortical Thickness

[Mahtab Farahbakhsh]

Dear freeSurfer,

I have problems with defining new labels for my brain scan or even of
fsaverage. I need to define a new label (ROI) to be able to find the grey
matter thickness for that specific region.

My first problem is that when I define a new label on fsaverage, it does
not save it for me and it gives me the following error:

mghRead(/Applications/freesurfer/experimental_data/TG/fsaverage/mri/wm.mgz,
-1): could not open file
/Applications/freesurfer/Freeview.app/Contents/MacOS/Freeview: could not
open label file
/Applications/freesurfer/subjects/fsaverage/label/ROI_test.label

I intend to define a new label (ROI) on fsaverage and then use the
mri_labe2label command to copy it on my desired structural MRI image. But
it does not work for me.

My second problem is that when I define a new label on my subject's MRI
image and I run the mri_anatomical_stats with the label of my subject, it
does not give me any output and this is what I get:

bash-3.2$ mris_anatomical_stats -l anon/label/lh.test.label anon lh
limiting computations to label anon/label/lh.test.label.
reading volume
/Applications/freesurfer/experimental_data/TG//anon/mri/wm.mgz...
reading input surface
/Applications/freesurfer/experimental_data/TG//anon/surf/lh.white...
reading input pial surface
/Applications/freesurfer/experimental_data/TG//anon/surf/lh.pial...
reading input white surface
/Applications/freesurfer/experimental_data/TG//anon/surf/lh.white...

and the error is that it could not find the file lh.test.label, however I
can see it in the label folder.

Please guide me with this issue.

Best Regards,
Mahtab.
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Re: [Freesurfer] Cortical Thickness of a Volume-defined ROI

[Mahtab Farahbakhsh]

Dear freeSurfer,

Thank you. I can use mris_anatomical_stats for the labels that are already
defined, but when I want to define a new label, it does not work.

My first problem is that when I define a new label on fsaverage, it does
not save it for me and it gives me the following error:

mghRead(/Applications/freesurfer/experimental_data/TG/fsaverage/mri/wm.mgz,
-1): could not open file
/Applications/freesurfer/Freeview.app/Contents/MacOS/Freeview: could not
open label file
/Applications/freesurfer/subjects/fsaverage/label/ROI_test.label

I intend to define a new label (ROI) on fsaverage and then use the
mri_labe2label command to copy it on my desired structural MRI image. But
it does not work for me.

My second problem is that when I define a new label on my subject's MRI
image and I run the mri_anatomical_stats with the label of my subject, it
does not give me any output and this is what I get:

bash-3.2$ mris_anatomical_stats -l anon/label/lh.test.label anon lh
limiting computations to label anon/label/lh.test.label.
reading volume
/Applications/freesurfer/experimental_data/TG//anon/mri/wm.mgz...
reading input surface
/Applications/freesurfer/experimental_data/TG//anon/surf/lh.white...
reading input pial surface
/Applications/freesurfer/experimental_data/TG//anon/surf/lh.pial...
reading input white surface
/Applications/freesurfer/experimental_data/TG//anon/surf/lh.white...

and the error is that it could not find the file lh.test.label, however I
can see it in the label folder.


Please guide me with this issue.

Best Regards,
Mahtab.



On 6 May 2016 at 16:45, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote:

> If you have a label, then you can use mris_anatomical_stats with the -l
> option
> doug
>
> On 05/06/2016 10:01 AM, Mahtab Farahbakhsh wrote:
> > Dear FreeSurfer,
> >
> > I am trying to find the cortical thickness of my ROI which is the
> > perisylvian region of the left hemisphere. What I did was to define a
> > label based on the anatomical area of this region and tried to define
> > a ROI based on this label and the command -mri_label2volume. Howevere,
> > I am using freeview and the tutorial that I found about this issue was
> > based on tkmedit. Would you please guide me how I should get this done?
> >
> > Best Regards,
> > Mahtab Farahbakhsh.
> >
> >
> >
> > ___
> > 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.
>
>
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[Freesurfer] Cortical Thickness of a Volume-defined ROI

[Mahtab Farahbakhsh]

Dear FreeSurfer,

I am trying to find the cortical thickness of my ROI which is the
perisylvian region of the left hemisphere. What I did was to define a label
based on the anatomical area of this region and tried to define a ROI based
on this label and the command -mri_label2volume. Howevere, I am using
freeview and the tutorial that I found about this issue was based on
tkmedit. Would you please guide me how I should get this done?

Best Regards,
Mahtab Farahbakhsh.
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Cortical Thickness of a Volume-defined ROI

[Mahtab Farahbakhsh]

Dear FreeSurfer,

I am trying to find the cortical thickness of my ROI which is the
perisylvian region of the left hemisphere. What I did was to define a label
based on the anatomical area of this region and tried to define a ROI based
on this label and the command -mri_label2volume. Howevere, I am using
freeview and the tutorial that I found about this issue was based on
tkmedit. Would you please guide me how I should get this done?

Best Regards,
Mahtab Farahbakhsh.
___
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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
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but does not contain patient information, please contact the sender and properly
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