What does your matlab script do? Your glmfit cmd looks fine.
On Thu, 15 Oct 2009, Maximilien Chaumon wrote: > Thanks Doug, > I was just a bit confused because I thought the help for mri_glmfit > mentioned an osgm directory that wasn't there. > I was given a matlab script that does that now. > I'm using a command like this: > mri_glmfit --y tal.ces.000.nii --osgm --glmdir tal.rfx.osgm --nii --mask > ../tal.mask.nii > > Thanks > Mx > > 2009/10/15 Doug Greve <gr...@nmr.mgh.harvard.edu> > >> >> isxconcat-sess creates the files that you pass to mri_glmfit (ie, >> multi-frame volumes and/or surfaces where each frame is a >> subject). Something like: >> >> >> AVG08/Analyse_Simple_Confidence/High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor/tal.ces.nii >> >> You can then use this as input to mri_glmfit passing it with >> the --y option. You can get more help from the FS FAST tutorial. Go to >> the wiki, type "isxconcat-sess" in the Search field, then hit the >> "Text" button. >> >> doug >> >> >> >> On Wed, 14 Oct 2009, Maximilien Chaumon wrote: >> >> Hi freesurfers, >>> >>> I've been running isxconcat-sess with this line >>> >>> chaumon[/homes/11/chaumon/data] (nmr-std-env) isxconcat-sess -sf >>> subjlist.txt -analysis Analyse_Simple_Confidence -c >>> High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor -o AVG08 >>> >>> I was expecting to find a directory called osgm in the specified analysis >>> directory with which I could feed data to mri_glmfit, but I can't find it. >>> >>> /homes/11/chaumon/bomba/AVG08/Analyse_Simple_Confidence/High_confidence__Low_confidence_vs_HSF_gabor__LSF_gabor >>> >>> The log file is attached. I don't find "error" in the text. >>> >>> Where am I wrong? >>> Is there any mri_glmfit-sess like script somewhere? It's going to be >>> pretty >>> tough to find each parameter to feed to mri_glmfit... >>> >>> Thanks, >>> Max >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> In order to help us help you, please follow the steps in: >> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
