It all looks right (though have not looked at contrasts). The argument to the --y flag is just the input file, it does not need to be named a certain name.
On 07/09/2015 07:56 AM, pablo najt wrote: > Dear Doug, > Thank you very much for your response. I am attaching my g3vo.txt file > -have changed extension now. > I finally manage to make it work but I am not confident if this is the > ideal way of running a design for 3 groups 1 factor 3 levels no > covariates as FS indicate > (https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V). > > This is how I am running it: > > mri_glmfit --glmdir rh.thickness.g3v0.glmdir > --y rh.g3v0.thickness.15B.mgh --fsgd g3v0.txt > --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 > --surf fsaverage rh --cortex > > And run separately for volume and white. > But my question is should I be running it using y.mgh instead (as below)? > mri_glmfit \ > --glmdir g3v0 \ > --y y.mgh \ > --fsgd g3v0.fsgd \ > --C normal-mci.mtx \ > --C normal-ad.mtx \ > --C mci-ad.mtx \ > --C group.effect.mtx \ > --C normal+mci-vs-ad.mtx > But my problem is that I would need to run in Qdec and this is not for > more than 2 group analyses? > Many thanks! > Pablo > > > > > > Date: Wed, 8 Jul 2015 17:35:21 -0400 > > From: gr...@nmr.mgh.harvard.edu > > To: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] 3 Group comparison > > > > 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. > > > > > _______________________________________________ > 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
