executing 3dREMLfit with afni_proc.py

Hi AFNI Gurus,

I would like to run 3dREMLfit using afni_proc.py and have added the the options to do s (-regress_3dD_stop -regress_reml_exec), but I am unclear on which additional options need to be set. For example, using -regress_opts_reml do I need to provide the -matrix option or does afni_proc.py already pass the matrix file to to 3dREMLfit? Similarly, do I need to designate a mask file with -mask and set the -Rvar and -Rbeta for it to output these files or does afni_proc.py set these things already?

Thanks for your help!

Hi Lauren,

You should not need to pass any extra options to 3dREMLfit,
with the possible exception of -GOFORIT, if that is needed for
some reason. When running 3dDeconvolve to generate the
X-matrix, 3dDeconvolve also generates a 3dREMLfit script,
which is then used by afni_proc.py.

Actually, it is easy to see what would happen because the
3dREMfit script is surely already being generated with your
current afni_proc.py analysis, it is just not being run.

Anyway, so you should not expect to have to do anything

Is there some problem that you are running into?

  • rick

Hi Rick,

Got it - nope no problems as of yet. Thank you!