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 <greve@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
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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