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 <gr...@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 > 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/ > > > > 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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