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