Thanks Bob!

I am (g)root on the server and I think I used sudo killall afni.

The GroupIncorr issue:
I am sorry, this might have been incompetence... I just used one subject to create the GroupIncorr.niml/data files. Could that have been an issue? Bad data? We ran it now using 3 subjects and it work! Sorry!

The Instacorr Issue:
Yes! It was probably was the scaling! Is this a problem? Running InstaCorr on pb.volreg/pb.blur or even pb.scale works fine. The masks "masks out" the brain only when using the errts.fanaticor. Is should not be specific to this dataset, I tried with data from another study and the same thing happens for errts.fanaticor. And, I have used this before without problems but the new element here is the scaling block that we added since it was present in the recommended afni_proc.py resting state example. As long as we give our own afni_proc mask (mask_epi_anat - and yes we did run afni_proc =)), are we fine? Or does this indicate some other issue?



Edited 5 time(s). Last edit at 08/31/2021 04:17PM by Robin.