Now to do some actual work after the installation..
it appears that I do not have a 3dSkullStrip:
$align_epi_anat.py -anat Datasets/Imagination/MPRAGEco.nii.gz -epi Datasets/Imagination/Imagination.nii.gz -epi_base 5 -epi2anat
#++ align_epi_anat version: 1.50
#Script is running:
3dAttribute DELTA Datasets/Imagination/Imagination.nii.gz
#Script is running:
3dAttribute DELTA Datasets/Imagination/Imagination.nii.gz
#Script is running:
3dAttribute DELTA Datasets/Imagination/MPRAGEco.nii.gz
#++ Multi-cost is lpc
#++ Removing all the temporary files
#Script is running:
\rm -f ./__tt_Imagination*
#Script is running:
\rm -f ./__tt_MPRAGEco*
#Script is running (command trimmed):
3dcopy Datasets/Imagination/MPRAGEco.nii.gz ./__tt_MPRAGEco+orig
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (Mar 25 2015) [64-bit]
#++ Removing skull from anat data
#Script is running (command trimmed):
3dSkullStrip -orig_vol -input ./__tt_MPRAGEco+orig -prefix ./__tt_MPRAGEco_ns
/bin/sh: 3dSkullStrip: command not found
** ERROR: Could not strip skull
** ERROR - script failed
Why is 3dSkullStrip not created?
Many thanks,
Ranjan
