AFNI crash switching tlrc to orig

AFNI version info (afni -ver): AFNI_23.2.04

I used to generate a preprocessing script, and then ran the script (this all ran successfully). The directory includes the MPRAGE_ns in both +orig and +tlrc space. I want to toggle between the two. I open the afni gui, load the MPRAGE_ns, but when I go to switch to the orig view, it crashes. I get the following errors on the terminal:

Fatal Signal 11 (SIGSEGV) received
Bottom of Debug Stack

Please advise. Thanks!


Would you be able to provide some extra details? Given your mention of MPRAGE_ns, I assume that was being used as the underlay.

Exactly how was the +tlrc version of MPRAGE_ns created (was it by, or something done outside)?
What were the underlay and overlay datasets before the switch to +orig space?
How was the switch achieved (by selecting an +orig dataset, or clicking on Origiinal view)?

Thanks, and sorry for the trouble.

  • rick

Thank you for the response.

MPRAGE_ns+orig and MPRAGE_nc+tlrc were created via

I am not loading an overlay, just selecting MPRAGE_ns as the underlay. Sometimes it default loads in orig space, sometimes in tlrc (seemingly depends on the space of the previous underlay???).

Then, I try to switch spaces in the gui (orig-to-tlrc or tlrc-to-orig), and it crashes.

output from >> -check_all

-------------------------------- general ---------------------------------
architecture: 64bit
cpu type: x86_64
system: Linux
release: 4.18.0-372.32.1.el8_6.x86_64
version: #1 SMP Tue Oct 25 05:53:57 EDT 2022
distribution: AlmaLinux 8.6 Sky Tiger
number of CPUs: 24
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /gpfs/research/software/afni/abin/afni
afni version : Precompiled binary linux_openmp_64: Aug 9 2023
: AFNI_23.2.04 'Marcus Didius Severus Julianus'
AFNI_version.txt : AFNI_23.2.04, linux_openmp_64, Aug 09 2023, official
which python : /usr/local/bin/python3/python
python version : 3.6.8
which R : /opt/rcc/gnu/R/4.1.0/bin/R
R version : R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"

instances of various programs found in PATH:
afni : 1 (/gpfs/research/software/afni/abin/afni)
R : 2
python : 1 (/usr/libexec/platform-python3.6)
python2 : 2
python3 : 2

testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success : success
3dMVM : success

------------------------ dependent program tests -------------------------
checking for dependent programs...

which tcsh : /usr/bin/tcsh
which Xvfb : /usr/bin/Xvfb

checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE

    oo Warning: 
       These packages are not installed on the computer: afex!
    These packages are not installed on the computer: phia!
    These packages are not installed on the computer: snow!
    These packages are not installed on the computer: lmerTest!
    These packages are not installed on the computer: paran!
    These packages are not installed on the computer: psych!
    These packages are not installed on the computer: brms!
    These packages are not installed on the computer: corrplot!
    These packages are not installed on the computer: metafor!

R RHOME : /opt/rcc/gnu/R/4.1.0/lib64/R

------------------------------ python libs -------------------------------

++ module loaded: matplotlib.pyplot
module file : /usr/lib64/python3.6/site-packages/matplotlib/
matplotlib version : 3.0.3

-- python binaries under /usr/local/bin:

-------------------------------- env vars --------------------------------
PATH = /gpfs/research/software/afni/abin:/opt/rcc/gnu/R/4.1.0/bin:/usr/local/bin/python3:/gpfs/research/software/gsl/1.15/gsl-1.15_build/bin:/gpfs/research/software/gsl/1.15/gsl-1.15_build/include:/opt/rcc/gnu/share/gromacs/top/martini.ff/martini_v3.0.0_proteins/force_fields/martini3001:/opt/rcc/gnu/share/gromacs/top/martini.ff:/opt/rcc/gnu/share/gromacs/top:/gpfs/research/software/hpc/gnu/mvapich2/bin:/opt/rcc/gnu/bin:/gpfs/home/msh23m/.local/bin:/gpfs/home/msh23m/bin:/opt/rcc/precompiled/bin/wombat:/opt/rcc/precompiled/bin:/gpfs/research/software/matlab/r2022b/bin:/usr/share/Modules/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin

R_LIBS = /opt/rcc/gnu/R/4.1.0/share/R/library:/opt/rcc/gnu/R/4.1.0/share/R/library

LD_LIBRARY_PATH = /opt/rcc/gnu/R/4.1.0/lib64:/opt/rcc/gnu/lib64:/gpfs/research/software/gsl/1.15/gsl-1.15_build/lib:/opt/rcc/gnu/lib64/hdf:/gpfs/research/software/hpc/gnu/lib64:/opt/rcc/precompiled/lib64


----------------------------- eval dot files -----------------------------

----------- AFNI $HOME files -----------

.afnirc                   : missing
.sumarc                   : missing
.afni/help/all_progs.COMP : missing

--------- shell startup files ----------

-- no .tcshrc, will create one as a follower of .cshrc
-- considered operations: path, flatdir, apsearch
(not on a mac, should skip flatdir)

-- note: followers should not need edits, so edit flags should be 0
(have 1 follower(s), which can be ignored)

dot file test : want 4 modifications across 3 files:

  file             path  flatdir  apsearch        follower
  ---------------  ----  -------  --------        --------
  .cshrc           1     0        1               0     
  .tcshrc          0     0        0               1     
  .bashrc          1     0        1               0     

------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under .

------------------------------ OS specific -------------------------------
which dnf : /usr/bin/dnf
dnf version : 4.7.0
which yum : /usr/bin/yum
yum version : 4.7.0

========================= summary, please fix: =========================

  • just be aware: login shell 'bash', but our code examples use 'tcsh'
  • missing R packages (see rPkgsInstall)
  • please run: cp /gpfs/research/software/afni/abin/AFNI.afnirc ~/.afnirc
  • please run: "suma -update_env" for .sumarc
  • please run: apsearch -update_all_afni_help
  • dot file test : want 4 modifications across 3 files:
  • insufficient data for AFNI bootcamp
    (see "Prepare for Bootcamp" on install pages)

Thanks for the details, @msh23m, this is fixed now.

I will run a build soon, so updated binaries should be available in about 3 hours. You are welcome to update your package after that. In the meanwhile, avoid using that _ns dataset when switching views. To switch view, change the underlay to either an +orig or +tlrc dataset. After that you can switch back to the _ns underlay. This is just temporary, to avoid the problem.

Please let me know if you have any questions about this.
Thanks a lot for letting us know!

  • rick

Just for the record, the updated binaries are available. If you want to get them:

@update.afni.binaries -d

Thanks again,

  • rick

Excellent - it is now working. Thank you so much for addressing this!!!