Dear FS experts following to my query below I run into further errors. If anyone could advice it would be great help.Regards,Pablomri_glmfit \ --y lh.g3v0.thickness.10B.mgh \ --fsgd g3v0.fsgd dods\ --C HC-BD_fam.mtx \ --surf fsaverage lh \ --cortex \ --glmdir lh.g3v0.glmdir? --y lh.g3v0.thickness.10B.mgh \? --fsgd g3v0.fsgd dods\? --C HC-BD_fam.mtx \ gdfReadHeader: reading g3v0.fsgdINFO: gd2mtx_method is dodsERROR: must specify GLM output dir[pablo:/Volumes/NEW_VOLUME/Familial_FS_Final] pablonajt% --surf fsaverage lh \? --cortex \? --glmdir lh.g3v0.glmdir--surf: Command not found.[pablo:/Volumes/NEW_VOLUME/Familial_FS_Final] pablonajt% mri_glmfit \ --y lh.g3v0.thickness.10B.mgh \ --fsgd g3v0.fsgd dods \ --C HC-BD_fam.mtx \ --surf fsaverage lh \ --cortex \ --glmdir lh.g3v0.glmdir? --y lh.g3v0.thickness.10B.mgh \ --fsgd g3v0.fsgd dods \ --C HC-BD_fam.mtx \ --surf fsaverage lh \ --cortex \ --glmdir lh.g3v0.glmdirERROR: Option --fsgd unknown[pablo:/Volumes/NEW_VOLUME/Familial_FS_Final] pablonajt% [pablo:/Volumes/NEW_VOLUME/Familial_FS_Final] pablonajt% mri_glmfit \ --glmdir g3v0 \ --y h.g3v0.thickness.10B.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.mtxERROR: Option --glmdir unknown[pablo:/Volumes/NEW_VOLUME/Familial_FS_Final] pablonajt% mri_glmfit \ --glmdir g3v0 \ --y y.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.mtxERROR: Option --glmdir unknown[pablo:/Volumes/NEW_VOLUME/Familial_FS_Final] pablonajt% Previous message begin here------------------------------------------------------------------------------------------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.mghmghRead(/Volumes/NEW_VOLUME/Familial_FS_Final/FSGD/y.mgh, -1): could not open fileERROR: 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 g3v0Loading y from /Volumes/NEW_VOLUME/Familial_FS_Final/SURF/rh.white.mghERROR: you must use '--surface subject hemi' with surface dataAny 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 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 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.
