align_epi_anat.py -tlrc_apar error

AFNI Message Board
1

Dear Colleagues,

When executing:

align_epi_anat.py \
-anat anat.nii \
-epi "${label_fmri[i]}"_f1_f2_v1_am_r1_r2_st_v2_tr.nii \
-epi_base 0 \
-epi2anat \
-Allineate_opts -warp shift_rotate \
-giant_move \
-anat_has_skull yes \
-suffix _al \
-tlrc_apar anat_tl.nii

I received:

#Script is running (command trimmed):
3drefit -deoblique ./20161028_0406_f1_f2_v1_am_r1_r2_st_v2_tr_tlrc_al
++ 3drefit: AFNI version=AFNI_18.0.25 (Mar 7 2018) [64-bit]
++ Authored by: RW Cox
[7m** ERROR: [0m Can’t open dataset ./20161028_0406_f1_f2_v1_am_r1_r2_st_v2_tr_tlrc_al
++ 3drefit processed 0 datasets

Before this point, the deobliquing seemed to work as it should when being applied to the dataset that was only allineated:

#Script is running (command trimmed):
3drefit -deoblique ././20161028_0406_f1_f2_v1_am_r1_r2_st_v2_tr_al+orig
++ 3drefit: AFNI version=AFNI_18.0.25 (Mar 7 2018) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset ././20161028_0406_f1_f2_v1_am_r1_r2_st_v2_tr_al+orig

  • deoblique
    ++ 3drefit processed 1 datasets

Is the +tlrc missing from the trimmed command? I may be missing something that makes this moot, but I thought I would post it to be certain.

Sincerely,

Dante

2

Dear Colleagues,

I neglected to mention a couple of things.

  1. I was using AFNI version=AFNI_18.0.25 (Mar 7 2018) [64-bit].

  2. I really like this feature of align_epi_anat.py. It is fitting like a glove with my needs and is a very convenient way to minimize data interpolation.

Sincerely,

Dante

3

This looks like a bug. I’ve updated the source, so it should be good with the next release. Thanks for letting me know.

1 Like
4

Thanks!