@SSwarper failure

Hello AFNI experts,

I’ve run into a problem with @SSwarper. I use the following command to coregister native T1 images to the MNI template:

@SSwarper 						                                             					                                                 \
-base /Users/katya/abin/MNI152_2009_template_SSW.nii.gz  					                                                         \
-input /Volumes/My_Passport_for_Mac/LwFL_MRI/subject_data/$subj.results/${subj}_T1_MPRAGE_SAG_ISO+orig 	 \
-subid $subj					        					                                                                                         \
-odir $output_dir/warpedT1 							                                            					                 \
-deoblique											                                            					         \
-giant_move											                                            					         \

It works great for about half of my subjects, but for the other half @SSwarper aborts unexpectedly (usually at Steps 6.1-6.3) with the message:

Fatal Signal 11 (SIGSEGV) received
Last STATUS: call Extract_Gradient_Maxima_3D
Bottom of Debug Stack
** AFNI version = AFNI_21.0.08 Compile date = Feb 10 2021
** [[Precompiled binary macos_10.12_local: Feb 10 2021]]
** 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.
** Crash log is appended to file /Users/katya/.afni.crashlog
** ERROR: program failed in Step 6.3b

I followed the advice given by Rick in another thread and dropped OMP_NUM_THREADS down to 1 (out of available 16) to prevent memory overload, but that didn’t help.

Do you have any advice on how it could be remedied?

Thank you,

Hi, Katya-

Hmm, weird.

There should be some initial+intermediate images made—What do the init*.jpg files in the @SSwarper output directory look like?



I’ve updated AFNI from v. 21.0.08 to the most recent v. 21.2.08 and reran @SSwarper with some of the problematic subjects. The alignment was successful in all cases, so it looks like whatever caused the problem was fixed in one of the recent updates!


Hello Paul,

Thank you for your response. Please see my reply in the parent thread - I’ve updated AFNI to the most current version and it fixed the problem.


Hi, Katya-

Good to know, thanks.