There is not a --meas option for mri_glmfit, you need to give it a --y option explicity, though it may be trying to read a yfile if you have one in the FSGD. How did you make g3v0.fsgd? Can you send it? The second command looks like you are doing the right thing, you just need to tell mri_glmfit that this is surface data by adding --surface fsaverage hemi
where hemi is lh or rh doug On 07/07/2015 06:45 AM, pablo najt wrote: > Dear FS experts, > I am trying to run a 3 group comparison with FS. > I have run preproc ( script from ENIGMA Cortical protocol) on my first > fsgd file. > > As I have three groups I have prepared my second fsgd file as g3v0.fsgd > and all my desired contrasts, rather than using QDEC. > > I run this second stage as follows: > mri_glmfit \ > --glmdir g3v0 \ > --meas thickness ../SURF/lh.thickness.mgh \ > --fsgd g3v0.fsgd \ > --C HC-BD_fam.mtx \ > --C HC-BD.mtx \ > --C BD-BD_fam.mtx \ > --C group.effect.mtx \ > --C HC+BD-vs-BD_fam.mtx > > and I get: > > Loading y from /Volumes/NEW_VOLUME/Familial_FS_Final/FSGD/y.mgh > > mghRead(/Volumes/NEW_VOLUME/Familial_FS_Final/FSGD/y.mgh, -1): could > not open file > > ERROR: loading y /Volumes/NEW_VOLUME/Familial_FS_Final/FSGD/y.mgh > > > As far as I understand y.mgh is a stack data that is made after using > QDEC is run. But I have been prompted to not use QDEC, so I am now > wondering how I am supposed to run my glm design. > > Also I tried to change the y.mgh to any of the outputs of the > mris_preproc (lh.white.mgh, lh.volume.mgh, lh.thickness.mgh, etc), and > it says: > > Creating output directory g3v0 > > Loading y from /Volumes/NEW_VOLUME/Familial_FS_Final/SURF/rh.white.mgh > > ERROR: you must use '--surface subject hemi' with surface data > > Any suggestion would be greatly appreciated. > Thanks a lot. > Pablo > > > _______________________________________________ > 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.
