Hello AFNI experts,

I encountered a problem with the align_epi_anat.py script, that seems to remove one of the transformation matrices when running the script.

Input files are:

- anat_avg+orig; average anatomical volume [oblique]
- anat_avg+tlrc; tailarached version (@auto_tlrc)
- sr906_frun??+orig: functional runs [oblique]

and I would like to transform the functional runs to tailarach space while retaining their original resolution (2x2x3 mm^3)

When running the script with the following parameters

align_epi_anat.py -epi sr906_frun05+orig -anat anat_avg+orig \
-child_epi sr906_frun01+orig sr906_frun02+orig sr906_frun03+orig \
sr906_frun04+orig sr906_frun05+orig sr906_frun06+orig sr906_frun07+orig \
sr906_frun08+orig -epi_base 0 -tshift on -volreg on -volreg_opts '-verb \
-dfile mcparams.txt' -suffix _bigal -big_move -epi2anat -tlrc_apar \
anat_avg+tlrc -master_tlrc SOURCE

then first it aligns the anatomical to the epi (as far as I can tell), and a file called __tt_anat_avg_ns_obla2e_mat.1D is created by the script. When preparing processing the child-epis, the script mentions

#++ Removing all the temporary files
#Script is running:
rm -f __tt_sr906_frun05*
#Script is running:
rm -f __tt_anat_avg*

which also removes the __tt_anat_avg_ns_obla2e_mat.1D file. When creating the tailarached version of the functional runs, it complaints that

#++ Inverting anat to epi matrix
#Script is running:
cat_matvec -ONELINE __tt_anat_avg_ns_obla2e_mat.1D anat_avg_bigal_e2a_only_mat.aff12.1D -I > sr906_frun01_bigal_mat.aff12.1D
** ERROR: THD_read_dvecmat: can't read matrix+vector from '__tt_anat_avg_ns_obla2e_mat.1D'
** FATAL ERROR: Can't read matrix from '__tt_anat_avg_ns_obla2e_mat.1D'

and of course on the tlrc versions of the functional runs cannot be created.

Do I do something wrong here? Why is the __tt_anat_avg_ns_obla2e_mat.1D file deleted if the script seems to need this file later on?

thanks,
Nick