afni.nimh.nih.gov

Short update: to test what happens when commenting out the lines that delete temporary files, I commented them out.

Now the script runs well until the end; for the tailarach transformation, it says (this is run 08, others are similar):

#Script is running (command trimmed):
3dAllineate -base anat_avg+tlrc -1Dmatrix_apply sr906_frun08_bigal_tlrc_mat.aff12.1D -prefix sr906_frun08_tlrc_bigal+tlrc -input __tt_sr906_frun08_tsh+orig -verb -master SOURCE
++ 3dAllineate: AFNI version=AFNI_2008_07_18_1710 (Nov 5 2008) [32-bit]
++ Authored by: Emperor Zhark
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./__tt_sr906_frun08_tsh+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./__tt_sr906_frun08_tsh+orig.BRIK is 2.567502 degrees from plumb.
++ Loading datasets
++ ========== Applying transformation to 172 sub-bricks ==========
++ ========== sub-brick #0 ==========
++ using -1Dmatrix_apply
++ Computing output image
[...]
++ ========== sub-brick #171 ==========
++ using -1Dmatrix_apply
++ Computing output image
++ Output dataset ./sr906_frun08_tlrc_bigal+orig.BRIK
++ total CPU time = 15.6 sec
++ ###########################################################
#Script is running (command trimmed):
3drefit -deoblique sr906_frun08_tlrc_bigal+tlrc
++ 3drefit: AFNI version=AFNI_2008_07_18_1710 (Nov 5 2008) [32-bit]
++ Authored by: RW Cox
** ERROR: Can't open dataset sr906_frun08_tlrc_bigal+tlrc
++ 3drefit processed 0 datasets

So for some reason (?!) 3dAllineate is doing computations but does not give the output file the +tlrc suffix. I'm really lost now and any help is appreciated