Hi, I had an issue with 3dSkullStrip with just one subject out of 30. It seems like 3dSkullStrip is failing on the anatomical. Why might that be?
Josh
align_epi_anat.py -anat2epi -anat mprage+orig -save_skullstrip -suffix _al_junk -epi pb01.jxj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off
#++ align_epi_anat version: 1.44
#++ turning off volume registration
#Script is running (command trimmed):
3dAttribute DELTA ./pb01.jxj.r01.tshift+orig
#Script is running (command trimmed):
3dAttribute DELTA ./pb01.jxj.r01.tshift+orig
#Script is running:
3dAttribute DELTA /raid10/studies/varenicline/subjects/jxj.results/mprage+orig
#++ Multi-cost is lpc
#++ Removing all the temporary files
#Script is running:
\rm -f ./__tt_pb01.jxj.r01.tshift*
#Script is running:
\rm -f ./__tt_mprage*
#Script is running (command trimmed):
3dcopy ./mprage+orig ./__tt_mprage
++ WARNING: file /home/gowinjl/.afni.log is now 135458098 (135 million [mega]) bytes long!
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (Dec 16 2013) [64-bit]
#++ Removing skull from anat data
#Script is running (command trimmed):
3dSkullStrip -orig_vol -input ./__tt_mprage+orig -prefix ./__tt_mprage_ns
/bin/sh: 3dSkullStrip: command not found
** ERROR: Could not strip skull
** ERROR - script failed
