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

History of AFNI updates  

Previous Message Next Message
Message List New Topic Print View
|
dante.picchioni
April 10, 2018 06:29PM
Dear Colleagues,

When executing:

align_epi_anat.py \
-anat anat.nii \
-epi "${label_fmri}"_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
Reply Quote
RSS
Subject Author Posted

align_epi_anat.py -tlrc_apar error

dante.picchioni April 10, 2018 06:29PM

Re: align_epi_anat.py -tlrc_apar error

dante.picchioni April 11, 2018 08:35AM

Re: align_epi_anat.py -tlrc_apar error

Daniel Glen April 11, 2018 11:55PM

Re: align_epi_anat.py -tlrc_apar error

dante.picchioni April 12, 2018 09:55AM