Dimon Deaths

AFNI Message Board
1

Dear Colleagues,

With the help of many, I am performing all-night fMRI sleep studies. As a result, the study necessitates being able to convert, manipulate, and analyze data from very long scans. When running Dimon, it has occasionally crashed and died when converting dicom images to AFNI files. See below for the error message associated with a death that occurred with a run with 6003 sub-bricks. This also happened with three other runs with 3216, 3537, and 3614 sub-bricks.

Sincerely,

Dante Picchioni

Fatal Signal 11 (SIGSEGV) received
mri_read_file
T3D_read_images
to3d:main
Bottom of Debug Stack
** Command line was:
to3d -prefix func08 -time:zt 50 6003 3.0sec FROM_IMAGE …/…/[pii_redacted]/mr_0016/amri_ep2d_bold_sleep_8_gt-00001.dcm …/…/[pii_redacted]/20160518-4000424849/mr_0016/amri_ep2d_bold_sleep_8_gt-00001_v00002.dcm …/…/[pii_redacted]/20160518-4000424849/mr_0016/amri_ep2d_bold_sleep_8_gt-00001_v00003.dcm … …/…/[pii_redacted]/20160518-4000424849/mr_0016/amri_ep2d_bold_sleep_8_gt-00001_v06002.dcm …/…/[pii_redacted]/20160518-4000424849/mr_0016/amri_ep2d_bold_sleep_8_gt-00001_v06003.dcm
** AFNI version = AFNI_16.0.16 Compile date = Mar 24 2016
** [[Precompiled binary linux_openmp_64: Mar 24 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.
** Crash log is appended to file /home/picchionid/.afni.crashlog

2

Hi Dante,

Since to3d is crashing just once in a while, and presumably
because of having so much data, that suggests you are just
running out of RAM. How much RAM do you have, and how
big are the resulting BRIK files?

Are the datasets all basically the same size? If so, then you
might just be careful to shut down some other program that
might be using a lot of your RAM.

Of course, any analysis you try to do with such datasets
will have even bigger problems, since most programs will
store an extra copy of each dataset for computations. Is
that a shared computer?

  • rick
3

Rick,

While we were troubleshooting this problem, we updated AFNI, and the problem apparently resolved itself. Thanks for your time and patience.

Sincerely,

Dante

4

Hmmm, then I suspect the fix from March 26
did the trick. See:

afni_history -program to3d | tail

  • rick
1 Like