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 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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