AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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_durai_
November 19, 2013 01:16AM
Hi afni experts,

I am trying to register a T2W partial structural image to a whole brain T1 MPRAGE. Both are skull stripped and the T2W was resampled to the same dimensions as the T1 prior to using the following command. I used this command as I read that align_api_anat can do intramodality alignment as well.

align_epi_anat.py -dset1 t5_MP_ns.nii -dset2 t5_tse_ns_rsmp.nii -dset2to1 -cost nmi -suffix aeap_nmi -AddEdge -giant_move -partial_coronal -anat_has_skull no -volreg off

but I am getting the following error...any help is appreciated!

#++ align_epi_anat version: 1.44
#++ turning off volume registration
#++ turning off deobliquing tshift, volume registration, resampling
#++ turning off deobliquing tshift, volume registration, resampling
#Script is running (command trimmed):
3dAttribute DELTA ./t5_tse_ns_rsmp.nii
#Script is running (command trimmed):
3dAttribute DELTA ./t5_tse_ns_rsmp.nii
#Script is running (command trimmed):
3dAttribute DELTA ./t5_MP_ns.nii
#++ Multi-cost is nmi
#++ Removing all the temporary files
#Script is running:
\rm -f ./__tt_t5_tse_ns_rsmp.nii*
#Script is running:
\rm -f ./__tt_t5_MP_ns.nii*
#Script is running (command trimmed):
3dcopy ./t5_MP_ns.nii ./__tt_t5_MP_ns.nii
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (Oct 18 2013) [64-bit]
#++ using 0th sub-brick because only one found
#Script is running (command trimmed):
3dbucket -prefix ./__tt_t5_tse_ns_rsmp.nii_ts ./t5_tse_ns_rsmp.nii'[0]'
++ 3dbucket: AFNI version=AFNI_2011_12_21_1014 (Oct 18 2013) [64-bit]
** ERROR: Could not 3dTstat epi
#++ removing skull or area outside brain
Traceback (most recent call last):
File "/home/owner/Desktop/fmri/afni/abin/align_epi_anat.py", line 3106, in <module>
ps.process_epi(use_ss=ps.epi_strip_method)
File "/home/owner/Desktop/fmri/afni/abin/align_epi_anat.py", line 2814, in process_epi
skullstrip_o = self.skullstrip_data( e, use_ss, ps.skullstrip_opt, prefix)
File "/home/owner/Desktop/fmri/afni/abin/align_epi_anat.py", line 2597, in skullstrip_data
% (skullstrip_opt, e.input(), n.pp()) , ps.oexec)
AttributeError: 'NoneType' object has no attribute 'input'
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Subject Author Posted

partial T2 structural to T1 structural

_durai_ November 19, 2013 01:16AM

Re: partial T2 structural to T1 structural

Daniel Glen November 19, 2013 09:06AM

Re: partial T2 structural to T1 structural

_durai_ November 19, 2013 01:31PM

Re: partial T2 structural to T1 structural

Daniel Glen November 19, 2013 01:52PM

Re: partial T2 structural to T1 structural

_durai_ November 19, 2013 02:50PM

Re: partial T2 structural to T1 structural

Daniel Glen November 19, 2013 06:49PM