I’m using align_epi_anat.py to align a subject’s anatomical to their resting state epi (for later TMS targeting) but it keeps failing at the skull strip step. Both are deobliqued, and the epi has also been slice time corrected, despiked, and bandpassed.
align_epi_anat.py -anat2epi -anat deobl.MPRAGE+orig -save_orig_skullstrip _strip -suffix _al_junk -epi bp+orig -epi_base 2 -volreg off -tshift off -resample off -ginormous_move -Allineate_opts ‘-warp aff -twofirst’
#++ align_epi_anat version: 1.55
#++ turning off volume registration
#++ turning off resampling
#Script is running:
3dAttribute DELTA /projects/b1033/dervishrs_kw/YA/01DY/AR.results/bp+orig
#Script is running:
3dAttribute DELTA /projects/b1033/dervishrs_kw/YA/01DY/AR.results/bp+orig
#Script is running (command trimmed):
3dAttribute DELTA ./deobl.MPRAGE+orig
#++ Multi-cost is lpc
#++ Removing all the temporary files
#Script is running:
\rm -f ./__tt_bp*
#Script is running:
\rm -f ./__tt_deobl.MPRAGE*
#Script is running (command trimmed):
3dcopy ./deobl.MPRAGE+orig ./__tt_deobl.MPRAGE+orig
++ 3dcopy: AFNI version=AFNI_16.2.12 (Aug 23 2016) [64-bit]
#++ Removing skull from anat data
#Script is running (command trimmed):
3dSkullStrip -orig_vol -input ./__tt_deobl.MPRAGE+orig -prefix ./__tt_deobl.MPRAGE_ns
#Script is running (command trimmed):
3dinfo ./__tt_deobl.MPRAGE_ns+orig | \grep ‘Data Axes Tilt:’|\grep ‘Oblique’
#++ Dataset /projects/b1033/dervishrs_kw/YA/01DY/AR.results/__tt_deobl.MPRAGE_ns+orig is not oblique
#Script is running (command trimmed):
3dinfo ./bp+orig | \grep ‘Data Axes Tilt:’|\grep ‘Oblique’
#++ Dataset /projects/b1033/dervishrs_kw/YA/01DY/AR.results/bp+orig is not oblique
#Script is running (command trimmed):
3dAttribute DELTA ./__tt_deobl.MPRAGE_ns+orig
#++ Spacing for anat to oblique epi alignment is 1.000000
#Script is running (command trimmed):
3dcopy ./__tt_deobl.MPRAGE_ns+orig ./__tt_deobl.MPRAGE_ns_ob; @Align_Centers -base ./bp+orig -dset ./__tt_deobl.MPRAGE_ns_ob+orig -no_cp
++ 3dcopy: AFNI version=AFNI_16.2.12 (Aug 23 2016) [64-bit]
++ 3drefit: AFNI version=AFNI_16.2.12 (Aug 23 2016) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset ./__tt_deobl.MPRAGE_ns_ob+orig
++ 3drefit processed 1 datasets
#Script is running (command trimmed):
cat_matvec ./__tt_deobl.MPRAGE_ns_ob_shft.1D -I > ./__tt_deobl.MPRAGE_ns_shft_I.1D
#++ Creating representative epi sub-brick
#Script is running (command trimmed):
3dbucket -prefix ./__tt_bp_ts ./bp+orig’[2]’
++ 3dbucket: AFNI version=AFNI_16.2.12 (Aug 23 2016) [64-bit]
#++ removing skull or area outside brain
#Script is running (command trimmed):
3dSkullStrip -orig_vol -input ./__tt_bp_ts+orig -prefix ./__tt_bp_ts_ns
Fatal Signal 11 (SIGSEGV) received
SUMA_SurfGridIntersect
SUMA_FindVoxelsInSurface
3dSkullStrip
Bottom of Debug Stack
** AFNI version = AFNI_16.2.12 Compile date = Aug 23 2016
** [[Precompiled binary linux_openmp_64: Aug 23 2016]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Memory usage: chunks=245 bytes=61699156
** ERROR: Could not strip skull
** ERROR - script failed