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:
- How can I run analysis in subcortical volumes?
- 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
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