Hi,

To make the mask:

mri_binarize --i aseg.mgz --match 17 --o Lhipp.mgh

Run glmfit:

cmdline mri_glmfit.bin --osgm --glmdir lh.testretest.volume-rate.fwhm10_LHipp --y lh.testretest.volume-spc-10.stack.mgh --mask fsaverage/mri/Lhipp.mgh --surf fsaverage lh

sysname Linux

FixVertexAreaFlag = 1

UseMaskWithSmoothing 1

OneSampleGroupMean 1

y /storage/affective/ume2/confined/Amir/FS/lh.testretest.volume-spc-10.stack.mgh

logyflag 0

usedti 0

mask fsaverage/mri/Lhipp.mgh

maskinv 0

glmdir lh.testretest.volume-rate.fwhm10_LHipp

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory lh.testretest.volume-rate.fwhm10_LHipp

Loading y from /storage/affective/ume2/confined/Amir/FS/lh.testretest.volume-spc-10.stack.mgh

... done reading.

Saving design matrix to lh.testretest.volume-rate.fwhm10_LHipp/Xg.dat

Computing normalized matrix

Normalized matrix condition is 1

Matrix condition is 1

ERROR: dimension mismatch 1 between y and mask

Best regards,
Amirhossein Manzouri

On Thu, Feb 15, 2018 at 7:49 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Can you send your glmfit command line and terminal output?

On 02/15/2018 07:21 AM, amirhossein manzouri wrote:

Hi ,
I did longitudinal analysis and now I made masks for Hippocampus and amygdala masks from fsavergae/mri/aseg.mgz using mri_binarize .I use the masks with mri_glmfit for volume_rate_stack but I get "dimensions mismatch 1 between y and mask" error .
I wonder:
1) How can I run analysis in subcortical volumes?
2) Is it possible to run mri_glmfit on the whole brain not lh and rh separately ?

Best regards,
Amirhossein Manzouri

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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/

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.