Error with align_epi_anat.py

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1

Hello AFNI community,

I am trying the align_api_anat.py program

OS: Mac Hihg Sierra,
Verion: AFNI_18.1.23 (May 30 2018)

align_epi_anat.py -anat 0003/T1/T1.nii -epi 0003/FMRI/do_stc_ds_tc_BOLD.nii -epi_base 10 -AddEdge -giant_move -anat_has_skull yes -epi_strip none -volreg_method 3dAllineate

I got an error that my dataset was oblique and I should use 3dWarp -deoblique. After that I got an error as below:
#++ resampling epi to match anat data
#Script is running (command trimmed):
3dresample -master ./__tt_T1_ns_ob+orig -prefix ./__tt_stc_ds_tc_BOLD.nii_rs_in -inset ./__tt_stc_ds_tc_BOLD_ts+orig’’ -rmode Cu
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./__tt_stc_ds_tc_BOLD_ts+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./__tt_stc_ds_tc_BOLD_ts+orig.BRIK is 10.046100 degrees from plumb.
** ERROR: Could not resample

This error want away when I removed the AddEdge option.

Can you help me understand why my command did not work?

Thanks!
Swati

2

It seems the AddEdge option still has problems with NIFTI datasets. You can wait for me to figure this out when I get some time, or you can convert the datasets to AFNI format.

3

Thanks, Daniel. I will see if I can use the data in AFNI format.

Swati