3dREMLfit Command Not Found

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1

AFNI version info (afni -ver): 23.0.7

I am using afni_proc.py to analyze task-based fMRI. The script runs correctly until it gets to 3dREMLfit. In the output file, it just states "3dREMLfit Command not found". I am using a computing cluster and have worked with our research IT but we cannot find a solution. We have confirmed that the path is correct to the afni module directory and 3dREMLfit is there.

Here is the code lines where the script stops (bolded):

tcsh -x stats.REML_cmd -GOFORIT 99
3dREMLfit -matrix X.xmat.1D -input pb05.sub-016.r01.scale+tlrc.HEAD pb05.sub-016.r02.scale+tlrc.HEAD pb05.sub-016.r03.scale+tlrc.HEAD pb05.sub-016.r04.scale+tlrc.HEAD -fout -tout -Rbuck stats.sub-016_REML -Rvar stats.sub-016_REMLvar -Rerrts errts.sub-016_REML -verb -GOFORIT 99
3dREMLfit: Command not found.

Thank you for your help!

2

Hello, I still have not found a solution to this issue. Does anyone have suggestions?

Thank you!

3

Howdy-

Sorry, missed this earlier.

Do you have the output* text file that we usually try to create when running afni_proc.py? That might shed light on, perhaps, an earlier error/failure that leads to this. I will send you a message with my email, for sending the output* file, since it typically too large to post here.

-pt

4

It looks like the $PATH is being messed up when switching to tcsh, which is used to execute the script. If on your own you were to run:

tcsh
3dREMLfit -help
exit

Then I would expect "3dREMLfit -help" to fail. In that case you should be able to run it using 'bash', instead.

Give that a try.

  • rick