Hi AFNI!

I ran into some trouble with a dataset where the anatomical and functional datasets were separated by a great distance (at least 60 mm). This caused me to get warping errors:

Linear warp: Script completed but parts of the brain were cropped out
NL warp: Script crashed due to memory corruption. Error message:

++ 3dNwarpApply: AFNI version=AFNI_16.0.05 (Feb 10 2016) [64-bit]
++ Authored by: Zhark the Warped
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./MACS_002_WIP_MPRAGE_SENSE_4_1+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:./MACS_002_WIP_MPRAGE_SENSE_4_1+orig.BRIK is 8.115999 degrees from plumb.
*** Error in `3dNwarpApply': malloc(): memory corruption: 0x000000000168d1e0 ***

Fatal Signal 6 (SIGABRT) received
3dNwarpApply
Bottom of Debug Stack
** AFNI version = AFNI_16.0.05 Compile date = Feb 10 2016
** [[Precompiled binary linux_openmp_64: Feb 10 2016]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.


Since I got a warning message about the datasets beeing very far appart I thought that this was causing the above errors and I was hinted to use some kind of centering for the warping. I looked arround on the message board and found similar questions. But neihter ginormous move or align_centers yes worked. What did work (for affine warping), however, was to add the option -tlrc_opts_at -init_xform CENTER to the afni proc command. For the Linear warping this worked (toghter with giant move), the cropping dissapeard and I was happy. So this centering is not default?


But I want to preform a non linear warp (tlrc_NL_warp). When I use -tlrc_NL_warp I get the error above and when I try to add the same option as above (-init_xform CENTER) I run into trouble. As it seems the non linear warping is run before the affine warping when using the -tlrc_NL_warp option. When setting the same option as above: "-tlrc_opts_at -init_xform CENTER" it is passed to the function auto_warp.py instead of @auto_tlrc and that is not a valid option for this function. So this gives me another error message:

# Finished alignment successfully
auto_warp.py -base TT_N27+tlrc -input T1_al_keep+orig -skull_strip_input no -init_xform CENTER (or AUTO_CENTER)

#++ auto_warp.py version: 0.03
** error: unknown trailing arguments : ['-init_xform', 'CENTER']
** ERROR - script failed

What can I do to get this centering done for -tlrc_NL_warp just like I did for linear warping with -tlrc_opts_at -init_xform CENTER?

Any why is this a problem? Should'nt "align" take care of the data sets beeing far appart since it is run before the tlrc block?

My afni_proc.py command is below:

afni_proc.py -subj_id $sub_id \
-dsets $fmri_data \
-copy_anat $T1_data \
-blocks despike tshift align tlrc volreg blur mask regress \
-tcat_remove_first_trs 0 \
-align_opts_aea \
-giant_move \
-volreg_align_to MIN_OUTLIER \
-volreg_tlrc_warp \
-tlrc_NL_warp \
-tlrc_opts_at \
-init_xform CENTER (or AUTO_CENTER) (with and without this tlrc_ops since it causes the memory error)
-regress_censor_motion 0.3 \
-regress_censor_outliers 0.1 \
-regress_apply_mot_types demean deriv \
etc...



Edited 6 time(s). Last edit at 04/11/2016 03:26PM by Robin.