Thank you for your response. I ran the mri_glmfit with the aseg table rather than --y as you suggested. I am interested in visualizing the results of the mri_glmfit analysis in the form of "blobs" indicating the brain regions in which groups differ (as possible with freeview or tksurfer in surface-based mri_glmfit when overlaying the specific contrasts onto fsaverage). Is there a way of doing this for subcortical regions without being limited to the pre-set subcortical segmentation boundaries? Thank you Jonathan ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, October 04, 2016 3:42 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Input file in subcortical analysis using mri_glmfit
Use the --table to spec the input instead of --y
On 10/03/2016 12:38 PM, Greenberg, Jonathan wrote:
Dear FS users
I am trying to compare subcortical volumes of 3 groups (and no co-variates) pre and post an intervention using mri_glmfit in Paired-Analysis.
My question pertains to which file I should specify as the input (--y) in the mri_glmfit command. The examples in the Wikis use either a preprocessed and smoothed surface file (e.g. “--y lh.paried-diff.thickness.sm05.MGH”) or “y.mgh”. The surface examples seem irrelevant since I am interested in subcortical volumes. When I try to follow the y.mgh example
mri_glmfit \
--glmdir rh.paired-diff \
--y y.mgh \
--fsgd paired-diff.fsgd \
--C n-vs-w.mtx \
--C n+h-vs-w.mtx \
--C n-vs-h.mtx \
it seems it cannot locate the y.mgh file, and the following message is displayed
…loading y from /autofs/space/jizo_001/Users/jonathan-bhi-SUBJECTS_DIR/qdec/y.mgh
mghRead (/autofs/space/jizo_001/Users/jonathan-bhi-SUBJECTS_DIR/qdec/y.mgh -1): could not open file
ERROR: loading y /autofs/space/jizo_001/Users/jonathan-bhi-SUBJECTS_DIR/qdec/y.mgh
Should something be done to create y.mgh prior to running this command (given that qdec is not used)? Should a different input file be used instead?
Thank you
Jonathan
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