Dear AFNI experts,

I am trying to run 3dGroupInCorr in batch mode. Other than the -help output from 3dGroupInCorr, is there a PDF document with more details?

Thank you,


Hi Isabelle,

That topic starts on slide 20 of the class handout afni20_instastuff.pdf.

Also, see the “RESTING STATE NOTE” section from afni_proc.py -help,
starting with “step 2” (or just search for 3dGroupInCorr). The
batch mode comments come later than that.

Assuming you have run 3dSetupGroupInCorr already,
also consider this example using batch mode with an
ROI mask:

3dGroupInCorr                           \
   -setA ic.A_cats.grpincorr.niml       \
   -setB ic.B_dogs.grpincorr.niml       \
   -labelA A_cats -labelB B_dogs        \
   -covariates covary.paw.size.txt      \
   -center SAME -donocov                \
   -batch MASKAVE "gic.cats.vs.dogs.LAMY left_amyg_mask+tlrc"
  • rick