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

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Lauren L
July 13, 2017 12:32PM
Hello AFNI gurus,

I am running afni_proc.py on a remote server, and it exited before finishing with the following error: 

3dNwarpApply -source s160427_NTD015_2_T1_MEMPRAGE+orig -master anat_final.s160427_NTD015_2+tlrc -ainterp wsinc5 -nwarp anat.un.aff.qw_WARP.nii anat.un.aff.Xat.1D s160427_NTD015_2_T1_MEMPRAGE_al_keep_mat.aff12.1D -prefix anat_w_skull_warped
++ 3dNwarpApply: AFNI version=AFNI_17.0.18 (Mar 29 2017) [64-bit]
++ Authored by: Zhark the Warped
*+ WARNING:   If you are performing spatial transformations on an oblique dset, 
  such as ./s160427_NTD015_2_T1_MEMPRAGE+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:./s160427_NTD015_2_T1_MEMPRAGE+orig.BRIK is 15.402659 degrees from plumb.
++ opened source dataset 's160427_NTD015_2_T1_MEMPRAGE+orig'
++ -master dataset is 'anat_final.s160427_NTD015_2+tlrc'
++ Processing -nwarp 
Fatal Signal 11 (SIGSEGV) received
       THD_open_nifti
      THD_open_one_dataset
     THD_open_dataset
    CW_read_dataset_warp
   IW3D_read_nwarp_catlist
  3dNwarpApply
 Bottom of Debug Stack
** Command line was:
3dNwarpApply -source s160427_NTD015_2_T1_MEMPRAGE+orig -master anat_final.s160427_NTD015_2+tlrc -ainterp wsinc5 -nwarp anat.un.aff.qw_WARP.nii anat.un.aff.Xat.1D s160427_NTD015_2_T1_MEMPRAGE_al_keep_mat.aff12.1D -prefix anat_w_skull_warped
** AFNI version = AFNI_17.0.18  Compile date = Mar 29 2017
** [[Precompiled binary linux_openmp_64: Mar 29 2017]]
** Program Death **

I ran the exact same afni_proc.py script on this exact dataset on my own iMAC, and it ran successfully and didn't throw this error - so I don't believe it is something with the data itself, but I could be wrong.

Thank you for your time and help!
Best,
Lauren
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Subject Author Posted

3dNwarpApply fatal signal 11 (SIGSEGV)

Lauren L July 13, 2017 12:32PM

Re: 3dNwarpApply fatal signal 11 (SIGSEGV)

rick reynolds July 28, 2017 09:26AM