Errors with @SSWarper Fatal Signal 11 (SIGSEGV) received

AFNI Message Board
1

When running @SSwarper, I am often getting errors with it, similar to this one I have pasted below. Oddly, it works for some of my subject data, but fails like this for others. I cannot attach my .afni.crashlog as it is not an image, but I have also pasted some of what it displays at the bottom of this.

Please let me know if you need more information.

Thanks!


+++ Command Echo:
   3dQwarp -lite -base /Volumes/Research_Data/Rhoades_Projects/RestingStatefMRI/Masks_Templates/MNI152_2009_template_SSW.nii.gz[0] -source Sub_004_01_anat_warped/junk.SSwarper.WK3Ac5k8M1m_AffSS.nii -iniwarp Sub_004_01_anat_warped/junk.SSwarper.WK3Ac5k8M1m_QQ5_WARP.nii -warpscale 1 -pcl -inilev 6 -maxlev 7 -workhard:6:7 -wtgaus 4.5 -inedge -pblur -nodset -prefix Sub_004_01_anat_warped/junk.SSwarper.WK3Ac5k8M1m_QQ7.nii 

++ 3dQwarp: AFNI version=AFNI_20.1.14 (Jun 10 2020) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
++ Dataset zero-pad: xbot=15 xtop=14  ybot=13 ytop=22  zbot=15 ztop=9 voxels
++ Weightizing the base image: FWHM = 4.5 (vox)
++ +++++++++++ Begin warp optimization:  base=/Volumes/Research_Data/Rhoades_Projects/RestingStatefMRI/Masks_Templates/MNI152_2009_template_SSW.nii.gz  source=/Volumes/Research_Data/Rhoades_Projects/RestingStatefMRI/Raw_Data/Sub_004/Sub_004_01_anat_warped/junk.SSwarper.WK3Ac5k8M1m_AffSS.nii

Fatal Signal 11 (SIGSEGV) received
     IW3D_setup_for_improvement
    IW3D_warpomatic
   IW3D_warp_s2bim
  3dQwarp
 Bottom of Debug Stack
** AFNI version = AFNI_20.1.14  Compile date = Jun 10 2020
** [[Precompiled binary macos_10.12_local: Jun 10 2020]]
** 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/tlab/.afni.crashlog
++ SSW Step 6 ... piece 3a

Here is some of the .afni.crashlog (I was running a foreach loop so I have several errors that are similar, but they are not all the same either):


*********------ CRASH LOG ------------------------------***********
Fatal Signal 11 (SIGSEGV) received
.......... recent internal history .........................................
+++++++mri_free [7]: {ENTRY (file=mri_free.c line=49) from IW3D_cleanup_improvement {765040 ms}
-------mri_free [7]: EXIT} (file=mri_free.c line=50) to IW3D_cleanup_improvement {765040 ms}
+++++++mri_free [7]: {ENTRY (file=mri_free.c line=49) from IW3D_cleanup_improvement {765040 ms}
-------mri_free [7]: EXIT} (file=mri_free.c line=50) to IW3D_cleanup_improvement {765040 ms}
+++++++mri_free [7]: {ENTRY (file=mri_free.c line=49) from IW3D_cleanup_improvement {765040 ms}
-------mri_free [7]: EXIT} (file=mri_free.c line=50) to IW3D_cleanup_improvement {765040 ms}
+++++++IW3D_destroy [7]: {ENTRY (file=mri_nwarp.c line=935) from IW3D_cleanup_improvement {765040 ms}
-------IW3D_destroy [7]: EXIT} (file=mri_nwarp.c line=942) to IW3D_cleanup_improvement {765040 ms}
+++++++IW3D_destroy [7]: {ENTRY (file=mri_nwarp.c line=935) from IW3D_cleanup_improvement {765040 ms}
-------IW3D_destroy [7]: EXIT} (file=mri_nwarp.c line=942) to IW3D_cleanup_improvement {765040 ms}
+++++++IW3D_destroy [7]: {ENTRY (file=mri_nwarp.c line=935) from IW3D_cleanup_improvement {765040 ms}
-------IW3D_destroy [7]: EXIT} (file=mri_nwarp.c line=942) to IW3D_cleanup_improvement {765040 ms}
+++++++INCOR_destroy [7]: {ENTRY (file=thd_incorrelate.c line=1865) from IW3D_cleanup_improvement {765040 ms}
-------INCOR_destroy [7]: EXIT} (file=thd_incorrelate.c line=1867) to IW3D_cleanup_improvement {765040 ms}
------IW3D_cleanup_improvement [6]: EXIT} (file=mri_nwarp.c line=10220) to IW3D_setup_for_improvement {765040 ms}
++++++mri_to_float [6]: {ENTRY (file=mri_to_float.c line=19) from IW3D_setup_for_improvement {765040 ms}
+++++++mri_new_7D_generic [7]: {ENTRY (file=mri_new.c line=48) from mri_to_float {765040 ms}
-------mri_new_7D_generic [7]: EXIT} (file=mri_new.c line=143) to mri_to_float {765040 ms}
+++++++mri_add_name [7]: {ENTRY (file=mri_add_name.c line=19) from mri_to_float {765065 ms}
-------mri_add_name [7]: EXIT} (file=mri_add_name.c line=24) to mri_to_float {765065 ms}
------mri_to_float [6]: EXIT} (file=mri_to_float.c line=94) to IW3D_setup_for_improvement {765075 ms}
++++++mri_to_float [6]: {ENTRY (file=mri_to_float.c line=19) from IW3D_setup_for_improvement {765075 ms}
+++++++mri_new_7D_generic [7]: {ENTRY (file=mri_new.c line=48) from mri_to_float {765075 ms}
-------mri_new_7D_generic [7]: EXIT} (file=mri_new.c line=143) to mri_to_float {765075 ms}
+++++++mri_add_name [7]: {ENTRY (file=mri_add_name.c line=19) from mri_to_float {765100 ms}
-------mri_add_name [7]: EXIT} (file=mri_add_name.c line=24) to mri_to_float {765100 ms}
------mri_to_float [6]: EXIT} (file=mri_to_float.c line=94) to IW3D_setup_for_improvement {765110 ms}
++++++mri_maxabs [6]: {ENTRY (file=mri_max.c line=98) from IW3D_setup_for_improvement {765110 ms}
------mri_maxabs [6]: EXIT} (file=mri_max.c line=129) to IW3D_setup_for_improvement {765122 ms}
++++++mri_new_7D_generic [6]: {ENTRY (file=mri_new.c line=48) from IW3D_setup_for_improvement {765122 ms}
------mri_new_7D_generic [6]: EXIT} (file=mri_new.c line=143) to IW3D_setup_for_improvement {765122 ms}
............................................................................
     IW3D_setup_for_improvement
    IW3D_warpomatic
   IW3D_warp_s2bim
  3dQwarp
** AFNI compile date = Jun 10 2020
** [[Precompiled binary macos_10.12_local: Jun 10 2020]]
** Program Crash **

*********------ CRASH LOG ------------------------------***********
Fatal Signal 11 (SIGSEGV) received
.......... recent internal history .........................................
+++++++mri_free [7]: {ENTRY (file=mri_free.c line=49) from IW3D_cleanup_improvement {2290 ms}
-------mri_free [7]: EXIT} (file=mri_free.c line=50) to IW3D_cleanup_improvement {2290 ms}
+++++++mri_free [7]: {ENTRY (file=mri_free.c line=49) from IW3D_cleanup_improvement {2290 ms}
-------mri_free [7]: EXIT} (file=mri_free.c line=50) to IW3D_cleanup_improvement {2290 ms}
+++++++mri_free [7]: {ENTRY (file=mri_free.c line=49) from IW3D_cleanup_improvement {2290 ms}
-------mri_free [7]: EXIT} (file=mri_free.c line=50) to IW3D_cleanup_improvement {2290 ms}
+++++++IW3D_destroy [7]: {ENTRY (file=mri_nwarp.c line=935) from IW3D_cleanup_improvement {2290 ms}
-------IW3D_destroy [7]: EXIT} (file=mri_nwarp.c line=942) to IW3D_cleanup_improvement {2290 ms}
+++++++IW3D_destroy [7]: {ENTRY (file=mri_nwarp.c line=935) from IW3D_cleanup_improvement {2290 ms}
-------IW3D_destroy [7]: EXIT} (file=mri_nwarp.c line=942) to IW3D_cleanup_improvement {2290 ms}
+++++++IW3D_destroy [7]: {ENTRY (file=mri_nwarp.c line=935) from IW3D_cleanup_improvement {2290 ms}
-------IW3D_destroy [7]: EXIT} (file=mri_nwarp.c line=942) to IW3D_cleanup_improvement {2290 ms}
+++++++INCOR_destroy [7]: {ENTRY (file=thd_incorrelate.c line=1865) from IW3D_cleanup_improvement {2290 ms}
-------INCOR_destroy [7]: EXIT} (file=thd_incorrelate.c line=1867) to IW3D_cleanup_improvement {2291 ms}
------IW3D_cleanup_improvement [6]: EXIT} (file=mri_nwarp.c line=10220) to IW3D_setup_for_improvement {2291 ms}
++++++mri_to_float [6]: {ENTRY (file=mri_to_float.c line=19) from IW3D_setup_for_improvement {2291 ms}
+++++++mri_new_7D_generic [7]: {ENTRY (file=mri_new.c line=48) from mri_to_float {2291 ms}
-------mri_new_7D_generic [7]: EXIT} (file=mri_new.c line=143) to mri_to_float {2295 ms}
+++++++mri_add_name [7]: {ENTRY (file=mri_add_name.c line=19) from mri_to_float {2301 ms}
-------mri_add_name [7]: EXIT} (file=mri_add_name.c line=24) to mri_to_float {2301 ms}
------mri_to_float [6]: EXIT} (file=mri_to_float.c line=94) to IW3D_setup_for_improvement {2311 ms}
++++++mri_to_float [6]: {ENTRY (file=mri_to_float.c line=19) from IW3D_setup_for_improvement {2311 ms}
+++++++mri_new_7D_generic [7]: {ENTRY (file=mri_new.c line=48) from mri_to_float {2311 ms}
-------mri_new_7D_generic [7]: EXIT} (file=mri_new.c line=143) to mri_to_float {2315 ms}
+++++++mri_add_name [7]: {ENTRY (file=mri_add_name.c line=19) from mri_to_float {2325 ms}
-------mri_add_name [7]: EXIT} (file=mri_add_name.c line=24) to mri_to_float {2325 ms}
------mri_to_float [6]: EXIT} (file=mri_to_float.c line=94) to IW3D_setup_for_improvement {2334 ms}
++++++mri_maxabs [6]: {ENTRY (file=mri_max.c line=98) from IW3D_setup_for_improvement {2334 ms}
------mri_maxabs [6]: EXIT} (file=mri_max.c line=129) to IW3D_setup_for_improvement {2346 ms}
++++++mri_new_7D_generic [6]: {ENTRY (file=mri_new.c line=48) from IW3D_setup_for_improvement {2346 ms}
------mri_new_7D_generic [6]: EXIT} (file=mri_new.c line=143) to IW3D_setup_for_improvement {2351 ms}
............................................................................
     IW3D_setup_for_improvement
    IW3D_warpomatic
   IW3D_warp_s2bim
  3dQwarp
** AFNI compile date = Jun 10 2020
** [[Precompiled binary macos_10.12_local: Jun 10 2020]]
** Program Crash **

*********------ CRASH LOG ------------------------------***********
Fatal Signal 11 (SIGSEGV) received
.......... recent internal history .........................................
+++++++mri_free [7]: {ENTRY (file=mri_free.c line=49) from IW3D_cleanup_improvement {2575 ms}
-------mri_free [7]: EXIT} (file=mri_free.c line=50) to IW3D_cleanup_improvement {2575 ms}
+++++++mri_free [7]: {ENTRY (file=mri_free.c line=49) from IW3D_cleanup_improvement {2575 ms}
-------mri_free [7]: EXIT} (file=mri_free.c line=50) to IW3D_cleanup_improvement {2575 ms}
+++++++mri_free [7]: {ENTRY (file=mri_free.c line=49) from IW3D_cleanup_improvement {2575 ms}
-------mri_free [7]: EXIT} (file=mri_free.c line=50) to IW3D_cleanup_improvement {2575 ms}
+++++++IW3D_destroy [7]: {ENTRY (file=mri_nwarp.c line=935) from IW3D_cleanup_improvement {2575 ms}
-------IW3D_destroy [7]: EXIT} (file=mri_nwarp.c line=942) to IW3D_cleanup_improvement {2575 ms}
+++++++IW3D_destroy [7]: {ENTRY (file=mri_nwarp.c line=935) from IW3D_cleanup_improvement {2575 ms}
-------IW3D_destroy [7]: EXIT} (file=mri_nwarp.c line=942) to IW3D_cleanup_improvement {2575 ms}
+++++++IW3D_destroy [7]: {ENTRY (file=mri_nwarp.c line=935) from IW3D_cleanup_improvement {2575 ms}
-------IW3D_destroy [7]: EXIT} (file=mri_nwarp.c line=942) to IW3D_cleanup_improvement {2575 ms}
+++++++INCOR_destroy [7]: {ENTRY (file=thd_incorrelate.c line=1865) from IW3D_cleanup_improvement {2575 ms}
-------INCOR_destroy [7]: EXIT} (file=thd_incorrelate.c line=1867) to IW3D_cleanup_improvement {2575 ms}
------IW3D_cleanup_improvement [6]: EXIT} (file=mri_nwarp.c line=10220) to IW3D_setup_for_improvement {2575 ms}
++++++mri_to_float [6]: {ENTRY (file=mri_to_float.c line=19) from IW3D_setup_for_improvement {2575 ms}
+++++++mri_new_7D_generic [7]: {ENTRY (file=mri_new.c line=48) from mri_to_float {2575 ms}
-------mri_new_7D_generic [7]: EXIT} (file=mri_new.c line=143) to mri_to_float {2579 ms}
+++++++mri_add_name [7]: {ENTRY (file=mri_add_name.c line=19) from mri_to_float {2586 ms}
-------mri_add_name [7]: EXIT} (file=mri_add_name.c line=24) to mri_to_float {2586 ms}
------mri_to_float [6]: EXIT} (file=mri_to_float.c line=94) to IW3D_setup_for_improvement {2595 ms}
++++++mri_to_float [6]: {ENTRY (file=mri_to_float.c line=19) from IW3D_setup_for_improvement {2595 ms}
+++++++mri_new_7D_generic [7]: {ENTRY (file=mri_new.c line=48) from mri_to_float {2595 ms}
-------mri_new_7D_generic [7]: EXIT} (file=mri_new.c line=143) to mri_to_float {2599 ms}
+++++++mri_add_name [7]: {ENTRY (file=mri_add_name.c line=19) from mri_to_float {2610 ms}
-------mri_add_name [7]: EXIT} (file=mri_add_name.c line=24) to mri_to_float {2610 ms}
------mri_to_float [6]: EXIT} (file=mri_to_float.c line=94) to IW3D_setup_for_improvement {2619 ms}
++++++mri_maxabs [6]: {ENTRY (file=mri_max.c line=98) from IW3D_setup_for_improvement {2619 ms}
------mri_maxabs [6]: EXIT} (file=mri_max.c line=129) to IW3D_setup_for_improvement {2632 ms}
++++++mri_new_7D_generic [6]: {ENTRY (file=mri_new.c line=48) from IW3D_setup_for_improvement {2632 ms}
------mri_new_7D_generic [6]: EXIT} (file=mri_new.c line=143) to IW3D_setup_for_improvement {2636 ms}
............................................................................
     IW3D_setup_for_improvement
    IW3D_warpomatic
   IW3D_warp_s2bim
  3dQwarp
** AFNI compile date = Jun 10 2020
** [[Precompiled binary macos_10.12_local: Jun 10 2020]]
** Program Crash **
2

Hmm, what is the output of:


3dinfo -o3 DSET_NAME

for the dset DSET_NAME you input?

Also, what is the output of


3dCM DSET_NAME

?

–pt

3

Sure, assuming I understand correctly that the dset is the same as my input data set to @SSwarper:


3dinfo -o3 Sub_004_01_anat+orig.
-118.359001	-161.014999	-70.319000



3dCM  Sub_004_01_anat+orig.
2.58212  -33.4768  0.161026
4

Yes, that is the correct dset to use.

Soo, I think the center of mass might be a bit far from center, and memory is getting used up expanding the grid to encapulsate it…

Would you mind uploading the dset and I can take a look more closely?

–pt

5

Sure, thank you. I uploaded it (KeithDodd.tgz), and I included the anatomy and resting state files for one of the subjects where I am getting the error (same one we have been discussing). Thanks again!

6

OK, got it, thanks.

And could I please have the exact command that you ran, too?

thanks,
pt

7

Absolutely. I uploaded the script I ran as a .txt in my files – Create_Run_Preprocess_Script_11b_SSwarp – (I assume/hope you have access to that?). The script is roughly running example 11b from afni_proc.py to process my resting state data with my anatomical but I have it running @SSwarper first to skull strip and put in MNI space and then using those warp files for the afni_proc.py.

The relevant lines for the @SSwarper would be:


@SSwarper -input ${sid}_${series}_anat+orig        \
        -subid ${sid}_${series}                  \
        -odir  ${sid}_${series}_anat_warped      \
        -base  ${template}

The given variables are set in the following ways earlier in the script:


set template = "/home/keith/abin/MNI152_2009_template_SSW.nii.gz"
foreach id(004) # a foreach loop to go through each subject
# 001 002 003 004... etc.
     set sid = "Sub_${id}"
     set series = "01" # there was only ever 1 scan per subject
     #### Everything else including the @SSwarper commands and then afni_proc.py ######
end

Thanks!

8

Sooooooo, oddly enough it ran fine for me, and the results look pretty good overall (see attached image).

I just ran essentially the same exact command as you did:


@SSwarper \
    -input ./Sub_004_01_anat+orig. \
   -odir TEST1 \
   -base ~/REF_TEMPLATES/MNI152_2009_template_SSW.nii.gz \
   -subid TEST1

I wonder if there was a memory thing, possibly depending on how many CPUs you were using or other things running on your computer system? My OMP_NUM_THREADS = 6. I just ran this on my Ubuntu laptop, which is not particularly powerful, and my “afni -ver” output is:


Precompiled binary linux_ubuntu_12_64: Jun  3 2020 (Version AFNI_20.1.13 'Otho')

… which is also quite similar to yours.

Maybe you could try running it again, and perhaps grab the stdout/stderr output, in case things break again? The easiest way is if you are running some COMMAND (which can have one or more options, or even better be the execution of a script file running all your commands), then:


# in bash terminal
COMMAND 2>&1 | tee o.output_text.txt
# in tcsh terminal
COMMAND |& tee o.output_text.txt

–pt

QC_anatQQ.TEST1.jpg
QC_anatQQ.TEST1.jpg3102×1384 704 KB

9

Thanks for doing that. It is odd. The mac I am using (I remote serve into my lab’s Mac with TeamViewer) has 64GB ram I think, or at least 32GB. OMP_NUM_THREADS=20 is what showed… it worked throughout most of yesterday, and then of course, after I stopped watching it last night, it errored out with the same type errors on later subjects. To me then, this seems like some sort of bizarre issue with the Mac system… the power settings are set to never sleep, just turn off display, so I do not know what would be causing this issue with 3dQwarp. I also do not believe anyone else is using this computer either.

The oddest part is that it just keeps happening, and once it starts on one subject, it tends to keep happening to the next few… always with 3dQwarp. The first subject it tries to run almost always seems to go OK.

Do you by chance have any ideas on that? At the very least, it seems to get through a few subjects before running into problems, so I can just keep rerunning it.

Thanks again!

10

Yeah, it’s a little weird, because my laptop is not super powerful (7.5GB RAM, 8x1.6GHz Intel i5 CPUs), so… odd. It is possible someone else started using the computer, and that took up resources from beneath your feet?

I don’t know enough about the deeper aspects of memory consumption and clearing caches to comment… I will ping Bob and Rick to see if he has any suggestions.

–pt

11

Have you tracked RAM usage while it ran?

Consider setting OMP_NUM_THREADS to 4, say, and running it again. It is possible that RAM usage scales linearly with CPUs, though I do not recall evaluating 3dQwarp in that regard.

  • rick
12

OK, thank you. I tried setting OMP_NUM_THREADS to 4 with


set OMP_NUM_THREADS = 4

in my script. When I run @SSwarper, it still gives the output of


Default OMP_NUM_THREADS is 20

Do I need to set it differently?

After several passes of this script, I am finally down to one last subject with this issue, but this issue keeps happening to them regardless.


++ 3dQwarp: replacing source dataset with 3dAllineate result Sub_019_01_anat_warped/junk.SSwarper.EBdyxzaeQEc_TAL5_Allin.nii
++ Dataset zero-pad: xbot=15 xtop=14  ybot=13 ytop=22  zbot=15 ztop=9 voxels
++ +++++++++++ Begin warp optimization:  base=/Volumes/Research_Data/Rhoades_Projects/RestingStatefMRI/Masks_Templates/MNI152_2009_template_SSW.nii.gz  source=/Volumes/Research_Data/Rhoades_Projects/RestingStatefMRI/Raw_Data/Sub_019/Sub_019_01_anat_warped/junk.SSwarper.EBdyxzaeQEc_TAL5_Allin.nii

Fatal Signal 11 (SIGSEGV) received
     IW3D_setup_for_improvement
    IW3D_warpomatic
   IW3D_warp_s2bim
  3dQwarp
 Bottom of Debug Stack

Thanks

13

Yes, set it as an environment variable, which will propagate to child shells.

setenv OMP_NUM_THREADS 4

  • rick
14

Thank you very much for all the help, I will give that a try now.

There is only 1 other issue I am getting for a few subjects:


3dAllineate -base final_epi_vr_base_min_outlier+tlrc -allcostX -input anat_final.Sub_016_01.11b.SSwarper.rest+tlrc
tee out.allcostX.txt
++ 3dAllineate: AFNI version=AFNI_20.1.14 (Jun 10 2020) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./anat_final.Sub_016_01.11b.SSwarper.rest+tlrc.HEAD
++ Base dataset:   ./final_epi_vr_base_min_outlier+tlrc.HEAD
++ Loading datasets into memory
++ Local correlation: blok type = 'RHDD(12.915)'
*+ WARNING: center of mass shifts (-cmass) are turned off, but would be TERRIBLY large!
*+ WARNING:   - at least one is more than 50% of search range
 +        -cmass x y z shifts =    6.008   56.231   31.226
 +  shift search range is +/- =   60.669   71.904   69.657
 +                                  9.9%    78.2%    44.8%
*+ WARNING: No output dataset will be calculated

which then seems to propagate to creating some sort of mask of all zeroes.


3dpc -mask mask_inter_Svent+tlrc -pcsave 3 -prefix rm.ROIPC.Svent.r01 rm.det_pcin_r01+tlrc
++ 3dpc: AFNI version=AFNI_20.1.14 (Jun 10 2020) [64-bit]
** FATAL ERROR: mask is all zeros!

Or alternatively ends with:


3dAllineate -base final_epi_vr_base_min_outlier+tlrc -allcostX -input anat_final.Sub_028_01.11b.SSwarper.rest+tlrc
tee out.allcostX.txt
++ 3dAllineate: AFNI version=AFNI_20.1.14 (Jun 10 2020) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./anat_final.Sub_028_01.11b.SSwarper.rest+tlrc.HEAD
++ Base dataset:   ./final_epi_vr_base_min_outlier+tlrc.HEAD
++ Loading datasets into memory
** FATAL ERROR: 3dAllineate fails :: base image has 0 nonzero voxels (< 100)
** Program compile date = Jun 10 2020

I plan to add -cmass to this specific 3dAllineate command and hope that fixes it.

I am simply unsure since that would be editing the script created by afni_proc.py and wondered if maybe the error comes from elsewhere or a setting I had in my afni_proc.py command. Most of my other subjects do not show such an issue.

15

Hello,

I tried what you suggested, but I am still getting the same Fatal Signal Errors which stops SSwarper from working. I have confirmed that the OpenMP thread count was reduced to 4.


+++ Command Echo:
   3dQwarp -lite -base /Volumes/Research_Data/Rhoades_Projects/RestingStatefMRI/Masks_Templates/MNI152_2009_template_SSW.nii.gz[0] -source Sub_037_01_anat_warped/junk.SSwarper.PUsdWbXzVbV_AffSS.nii -iniwarp Sub_037_01_anat_warped/junk.SSwarper.PUsdWbXzVbV_TAL5_AWARP.nii -warpscale 1 -lpa -inilev 1 -maxlev 5 -wtgaus 4.5 -inedge -pblur -workhard:5:5 -nodset -prefix Sub_037_01_anat_warped/junk.SSwarper.PUsdWbXzVbV_QQ5.nii 

++ SSW Step 6 ... piece 2
++ OpenMP thread count = 4
++ 3dQwarp: AFNI version=AFNI_20.1.14 (Jun 10 2020) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
++ Dataset zero-pad: xbot=15 xtop=14  ybot=13 ytop=22  zbot=15 ztop=9 voxels
++ Weightizing the base image: FWHM = 4.5 (vox)
++ +++++++++++ Begin warp optimization:  base=/Volumes/Research_Data/Rhoades_Projects/RestingStatefMRI/Masks_Templates/MNI152_2009_template_SSW.nii.gz  source=/Volumes/Research_Data/Rhoades_Projects/RestingStatefMRI/Raw_Data/Sub_037/Sub_037_01_anat_warped/junk.SSwarper.PUsdWbXzVbV_AffSS.nii

Fatal Signal 11 (SIGSEGV) received
     IW3D_setup_for_improvement
    IW3D_warpomatic
   IW3D_warp_s2bim
  3dQwarp
 Bottom of Debug Stack

Again, this doesn’t happen to every subject, but it does happen to most subjects. Often to the same ones (but not always).

Thanks again!

Note: I think it might be related/limited to Mac, which I believe is Catalina… maybe in a way it allocates memory? I tried a subject I was having problems with on a weaker dell laptop with less RAM, and it worked without an issue. I just wish I could solve the issue on the Mac since it has a much stronger processesor, GPU, and a lot more memory.