By the way, I hope you don't mind if I quickly ask about a different thing,
This sequence:
3dAllineate -base $MPRAGE_file \
-input ${MDfile_u}+orig \
-prefix $MDfile_alMP_u \
-cost lpa \
-1Dmatrix_save tmp \
-automask \
-source_automask \
-cmass \
-maxrot 45
#convert transform into 3x4 format for further cat_matvec
cat_matvec tmp.aff12.1d > ${MD_MP_lin_Xfm}.1d
rm tmp.aff12.1d
works fine on Ubuntu on my laptop, but fails on CentOS Biowulf. Both cat_matvec and rm claim that tmp.aff12.1d is not there. If I check after the script finished, I see tmp.aff12.1d in the folder.
This looks like an HPC issue (because it runs fine on Ubuntu), and I have a ticket open with them, but just in case it's actually an AFNI thing, I am asking here as well. (I believe AFNI versions might be slightly different, on Ubuntu I have 22.0.01 and HPC is on AFNI_22.0.04)
