Hello

Sorry for this basic question.
I have a structural scan I analyzed in AFNI (anat 1), and I want to co-register it with a structural scan that was obtained in a different scanning session (same patient) using freesurfer (anat 2).
I do not know what I am doing wrong but it does not work. Please help. Details below.


I thought the steps should be:
1. convert freesurfer .mgz to .nii.gz
2. align the two images using align_epi_anat.py.

I tried this, but align_epi_anat was grumpy about anat 1 being oblique, and then crashed.
So I added a new step:
1. convert freesurfer .mgz to .nii.gz
2. de-oblique anat 1 with 3dWarp
3. align the two images using align_epi_anat.py.

This also failed. I must be doing something fundamentally wrong.
Here is the command line history:
align_epi_anat.py -dset1 warped+orig -dset2 brainmask.nii.gz -dset2to1
#++ align_epi_anat version: 1.45
#++ turning off deobliquing tshift, volume registration, resampling
#++ turning off deobliquing tshift, volume registration, resampling
#Script is running (command trimmed):
3dAttribute DELTA ./brainmask.nii.gz
#Script is running (command trimmed):
3dAttribute DELTA ./brainmask.nii.gz
#Script is running (command trimmed):
3dAttribute DELTA ./warped+orig
#++ Multi-cost is lpa
#++ Removing all the temporary files
#Script is running:
\rm -f ./__tt_brainmask.nii.gz*
#Script is running:
\rm -f ./__tt_warped*
#Script is running (command trimmed):
3dcopy ./warped+orig ./__tt_warped
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (Mar 31 2014) [64-bit]
#++ Removing skull from dset1 data
#Script is running (command trimmed):
3dSkullStrip -orig_vol -input ./__tt_warped+orig -prefix ./__tt_warped_ns
#++ using 0th sub-brick because only one found
#Script is running (command trimmed):
3dbucket -prefix ./__tt_brainmask.nii.gz_ts ./brainmask.nii.gz'[0]'
++ 3dbucket: AFNI version=AFNI_2011_12_21_1014 (Mar 31 2014) [64-bit]
** ERROR: Could not 3dTstat epi
#++ removing skull or area outside brain
Traceback (most recent call last):
File "/Users/goldenholzdm/abin/align_epi_anat.py", line 3108, in <module>
ps.process_epi(use_ss=ps.epi_strip_method)
File "/Users/goldenholzdm/abin/align_epi_anat.py", line 2816, in process_epi
skullstrip_o = self.skullstrip_data( e, use_ss, ps.skullstrip_opt, prefix)
File "/Users/goldenholzdm/abin/align_epi_anat.py", line 2599, in skullstrip_data
% (skullstrip_opt, e.input(), n.pp()) , ps.oexec)
AttributeError: 'NoneType' object has no attribute 'input'