I updated the files and now here is what I get.
[jgowin@muso ~]$ grep AFNI_COMPRESSOR ~/.afnirc ~/.cshrc ~/.bash*
/home/jgowin/.afnirc:AFNI_COMPRESSOR = NONE
/home/jgowin/.cshrc:setenv AFNI_COMPRESSOR NONE
/home/jgowin/.bashrc:AFNI_COMPRESSOR=NONE
/home/jgowin/.bashrc:export AFNI_COMPRESSOR
Now, most of my files are saving uncompressed as .BRIK files. However, at the @auto_tlrc stage, it is still saving as .nii.gz and failing to find base.nii since only base.nii.gz exists.
Do I need to edit my rc files?