Hi there!

I've been trying to use align_epi_anat.py (version 1.44) to coregister two nifti volumes, though the script seems to run into the following issues.

If the epi file is not in AFNI format (and attempting to skull strip):
++ 3dbucket: AFNI version=AFNI_2011_12_21_1014 (Mar 12 2014) [64-bit]
** ERROR: Could not 3dTstat epi
#++ removing skull or area outside brain
Traceback (most recent call last):
File "/usr/local/apps/afni/current/linux_openmp_64/align_epi_anat.py", line 3105, in ?
ps.epi_ts, ps.epi_vr, ps.epi_ns = \
File "/usr/local/apps/afni/current/linux_openmp_64/align_epi_anat.py", line 2814, in process_epi
skullstrip_o = self.skullstrip_data( e, use_ss, ps.skullstrip_opt, prefix)
File "/usr/local/apps/afni/current/linux_openmp_64/align_epi_anat.py", line 2595, in skullstrip_data
com = shell_com( \
AttributeError: 'NoneType' object has no attribute 'input'

whereas this is handled fine with an AFNI-formatted file.

Also, if the structural scan is not in AFNI format, the script saves the resulting output image (with the -anat2epi flag and named by suffix) as follows:

input: struct.nii
output: struct.nii_2epi+orig.nii

Thanks for all your work!