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  

|
December 09, 2015 01:11PM
Dear AFNI Experts,

When trying to re-order briks in a existing bucket image, I'm using this command:

3dbucket -fbuc -prefix ${subj}_LS-S_reord ${subj}_LS-S+orig'[1dcat reorder.1D]'

Where "reorder.1D" is a simple text file with 287 entries in a single column. Here's the error message I'm getting:

++ 3dbucket: AFNI version=AFNI_2011_12_21_1014 (Dec 8 2015) [64-bit]

Fatal Signal 11 (SIGSEGV) received
3dbucket main
Bottom of Debug Stack
** AFNI version = AFNI_2011_12_21_1014 Compile date = Dec 8 2015
** [[Precompiled binary linux_openmp_64: Dec 8 2015]]
** 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 /home/wgraves/.afni.crashlog


And here's the "CRASH LOG":
*********------ CRASH LOG ------------------------------***********
Fatal Signal 11 (SIGSEGV) received
.......... recent internal history .........................................
++++mri_new_7D_generic [4]: {ENTRY (file=mri_new.c line=48) from EDIT_substitute_brick
----mri_new_7D_generic [4]: EXIT} (file=mri_new.c line=140) to EDIT_substitute_brick
++++mri_free [4]: {ENTRY (file=mri_free.c line=49) from EDIT_substitute_brick
mri_free -- call killpurge
+++++mri_killpurge [5]: {ENTRY (file=mri_purger.c line=259) from mri_free
mri_killpurge -- check if im==NULL ptr=0x2a22750
mri_killpurge -- can't killpurge NULL fname!
-----mri_killpurge [5]: EXIT} (file=mri_purger.c line=270) to mri_free
mri_free -- free im
----mri_free [4]: EXIT} (file=mri_free.c line=66) to EDIT_substitute_brick
---EDIT_substitute_brick [3]: EXIT} (file=edt_substbrick.c line=67) to 3dbucket main
+++EDIT_dset_items [3]: {ENTRY (file=edt_dsetitems.c line=125) from 3dbucket main
---EDIT_dset_items [3]: EXIT} (file=edt_dsetitems.c line=964) to 3dbucket main
+++EDIT_dset_items [3]: {ENTRY (file=edt_dsetitems.c line=125) from 3dbucket main
---EDIT_dset_items [3]: EXIT} (file=edt_dsetitems.c line=964) to 3dbucket main
+++EDIT_substitute_brick [3]: {ENTRY (file=edt_substbrick.c line=33) from 3dbucket main
++++mri_new_7D_generic [4]: {ENTRY (file=mri_new.c line=48) from EDIT_substitute_brick
----mri_new_7D_generic [4]: EXIT} (file=mri_new.c line=140) to EDIT_substitute_brick
++++mri_free [4]: {ENTRY (file=mri_free.c line=49) from EDIT_substitute_brick
mri_free -- call killpurge
+++++mri_killpurge [5]: {ENTRY (file=mri_purger.c line=259) from mri_free
mri_killpurge -- check if im==NULL ptr=0x2a22800
mri_killpurge -- can't killpurge NULL fname!
-----mri_killpurge [5]: EXIT} (file=mri_purger.c line=270) to mri_free
mri_free -- free im
----mri_free [4]: EXIT} (file=mri_free.c line=66) to EDIT_substitute_brick
---EDIT_substitute_brick [3]: EXIT} (file=edt_substbrick.c line=67) to 3dbucket main
+++EDIT_dset_items [3]: {ENTRY (file=edt_dsetitems.c line=125) from 3dbucket main
---EDIT_dset_items [3]: EXIT} (file=edt_dsetitems.c line=964) to 3dbucket main
+++EDIT_dset_items [3]: {ENTRY (file=edt_dsetitems.c line=125) from 3dbucket main
---EDIT_dset_items [3]: EXIT} (file=edt_dsetitems.c line=964) to 3dbucket main
............................................................................
3dbucket main
** AFNI compile date = Dec 8 2015
** [[Precompiled binary linux_openmp_64: Dec 8 2015]]
** Program Crash **


Also, when I run the exact same command but using the "-dry" option, it runs as expected.

Thanks in advance for any help you can give with this!

Best,
Will
Subject Author Posted

3dbucket crash

wgraves December 09, 2015 01:11PM

Re: 3dbucket crash

wgraves December 09, 2015 01:41PM

Re: 3dbucket crash

rick reynolds December 09, 2015 08:43PM

Re: 3dbucket crash

wgraves December 11, 2015 09:42AM

Re: 3dbucket crash

rick reynolds December 14, 2015 09:33AM

Re: 3dbucket crash

rick reynolds January 04, 2016 01:11PM

Re: 3dbucket crash

jkeidel December 14, 2015 08:41AM