HI,

I am sorry: this may be a straightforward question but I can not figure out why 3dinfo is crashing with a segmentation fault.

This file is an activation map obtained by the FAST-fMRI algorithm in our R package (RFASTfMRI). What RFASTfMRI does is creates an activation map and as an array. We have multiplied the activation map with the Z map to only have the Z map wherever there is activation, it is 0 otherwise. We convert it do nifti using the R package oro.nifti.

However, I get:

$ 3dinfo -verb Bstand2-int-FAST-death-negative.nii.gz 
++ 3dinfo: AFNI version=AFNI_20.1.07 (May 21 2020) [64-bit]

Fatal Signal 11 (SIGSEGV) received
     THD_open_nifti
    THD_open_one_dataset
   THD_open_dataset
  3dinfo main
 Bottom of Debug Stack
** AFNI version = AFNI_20.1.07  Compile date = May 21 2020
** [[Precompiled binary linux_openmp_64: May 21 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 .afni.crashlog

The AFNI crash log file is here:

$ m ~/.afni.crashlog 

*********------ CRASH LOG ------------------------------***********
Fatal Signal 11 (SIGSEGV) received
.......... recent internal history .........................................
++3dinfo main [2]: {ENTRY (file=3dinfo.c line=340) from Bottom of Debug Stack {0
 ms}
+++AFNI_process_environ [3]: {ENTRY (file=afni_environ.c line=155) from 3dinfo m
ain {0 ms}
++++AFNI_suck_file [4]: {ENTRY (file=afni_environ.c line=64) from AFNI_process_e
nviron {0 ms}
----AFNI_suck_file [4]: EXIT} (file=afni_environ.c line=84) to AFNI_process_envi
ron {0 ms}
---AFNI_process_environ [3]: EXIT} (file=afni_environ.c line=240) to 3dinfo main
 {1 ms}
+++THD_open_dataset [3]: {ENTRY (file=thd_mastery.c line=31) from 3dinfo main {1
 ms}
++++THD_open_one_dataset [4]: {ENTRY (file=thd_opendset.c line=149) from THD_ope
n_dataset {1 ms}
+++++THD_open_nifti [5]: {ENTRY (file=thd_niftiread.c line=49) from THD_open_one
_dataset {1 ms}
............................................................................
     THD_open_nifti
    THD_open_one_dataset
   THD_open_dataset
  3dinfo main
** AFNI compile date = May 21 2020
** [[Precompiled binary linux_openmp_64: May 21 2020]]
** Program Crash *

Now, this may not be relevant, but the oro.nifti package in R reads the file as I intend it to be:

readNIfTI(fname = "Bstand2-int-FAST-death-negative.nii.gz")
  NIfTI-1 format
  Type            : nifti
  Data Type       : 16 (FLOAT32)
  Bits per Pixel  : 32
  Slice Code      : 0 (Unknown)
  Intent Code     : 5 (Zscore)
  Qform Code      : 4 (MNI_152)
  Sform Code      : 4 (MNI_152)
  Dimension       : 50 x 61 x 23
  Pixel Dimension : 3.5 x 3.5 x 6
  Voxel Units     : mm
  Time Units      : Unknown

Is there something that is not right in the saving for this segmentation fault to happen?

One issue that is bothersome and may be relevant is that oro.nifti in R appears to work with NIfTI-1 format. Is this the issue?
Btw, given a 3D or 4D array, is it possible to convert it into nifti format using afni tools?

Many thanks for your help and suggestions.
Ranjan