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In the FSGD file I have one subject pair (timepoint 1 and timepoint 2), and it is the only group. However, I removed --fsgd and replaced it with --osgm upon your reccomendation, and am still getting the error.

I am also having an issue visualizing the output of mri_preproc in freeview - isnt this mgh file supposed to be a volume? Is there a way to center the freeview cursor to the middle of the current volume?
 
Thanks,
Ken



‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On Thursday, April 30, 2020 2:16 PM, Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

how many subjects are there in your fsgd? How many groups in your fsgd file? Also, you should not use --osgm and --fsgd


On 4/30/2020 1:09 PM, KennethSPrice wrote:

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Hello Freesurfer friends!

I'm going through the "paired analysis" tutorial and am running into an issue with the mri_glmfit. I am running on just one subject pair. https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis#Runmriglmfit

I ran mris_preproc on my 2 timepoints and am getting an error at mri_glmfit
  mris_preproc --target fsaverage --hemi lh \
   --meas thickness --out lh.paired-diff.thickness.mgh \
   --fsgd pairs.fsgd --paired-diff


mri_glmfit \
 --glmdir lh.paired-diff \
 --y lh.paired-diff.thickness.sm05.mgh \
 --fsgd paired-diff.fsgd \

--osgm \

--surf fsaverage lh


I am getting an ERROR: DOF = 0.

MRI's have been put through recon-all and are in there own directories within SUBJECTS_DIR.

What is the cause of the error?

Thanks,

Ken

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