Hi. I’m trying to determine voxel-level correlation between 2 image types using 3dtest++ with voxel-level covariate. Both image types are in 2mm MNI space. The program crashes with no useful information (for me). What’s wrong?
Here is the script:
SUVdir=/autofs/cluster/stroke/PSF/PET/SUV
MRdir=/autofs/cluster/stroke/PSF/MR
mkdir -p $SUVdir/ttests_covar/P8_suvr-gfa_3dttest
outdir=$SUVdir/ttests_covar/P8_suvr-gfa_3dttest
cd $SUVdir/SUVR-wb_nl_MNI
3dttest++
-prefix $outdir/P8_suvr-gfa
-DAFNI_DEBUG_TABLE=YES
-setA
PSF_001.nii.gz
PSF_002.nii.gz
PSF_003.nii.gz
PSF_005.nii.gz
PSF_006.nii.gz
PSF_008.nii.gz
PSF_009.nii.gz
PSF_010.nii.gz
-mask $MRdir/composite_lesion/MNI152_T1_2mm_brain_no-LV-Lesion_bin.nii.gz
-covariates /autofs/cluster/stroke/PSF/scripts/covarfile_gfa
Here is the covariate file - covarfile_gfa:
subj GFA
PSF_001 /autofs/cluster/stroke/PSF/PET/SUV/SUVR-wb_nl_MNI/PSF_001_gfa.nii.gz
PSF_002 /autofs/cluster/stroke/PSF/PET/SUV/SUVR-wb_nl_MNI/PSF_002_gfa.nii.gz
PSF_003 /autofs/cluster/stroke/PSF/PET/SUV/SUVR-wb_nl_MNI/PSF_003_gfa.nii.gz
PSF_005 /autofs/cluster/stroke/PSF/PET/SUV/SUVR-wb_nl_MNI/PSF_005_gfa.nii.gz
PSF_006 /autofs/cluster/stroke/PSF/PET/SUV/SUVR-wb_nl_MNI/PSF_006_gfa.nii.gz
PSF_008 /autofs/cluster/stroke/PSF/PET/SUV/SUVR-wb_nl_MNI/PSF_008_gfa.nii.gz
PSF_009 /autofs/cluster/stroke/PSF/PET/SUV/SUVR-wb_nl_MNI/PSF_009_gfa.nii.gz
PSF_010 /autofs/cluster/stroke/PSF/PET/SUV/SUVR-wb_nl_MNI/PSF_010_gfa.nii.gz
Here is the terminal output:
++ 3dttest++: AFNI version=AFNI_17.2.05 (Jul 27 2017) [64-bit]
++ Authored by: Zhark++
++ option -setA :: processing as SHORT form (all values are datasets)
++ 212204 voxels in -mask dataset
++ Mixed Table: processing file /autofs/cluster/stroke/PSF/scripts/covarfile_gfa
- first line = ‘subj GFA’
- found 2 labels in first line
- processing row #0 = ‘PSF_001 /autofs/cluster/stroke/PSF/PET/SUV/SUVR-wb_nl_MNI/PSF_001_gfa.nii.gz’
- deciding format of 1 columns
- – col#1 is string
- processing row #1 = ‘PSF_002 /autofs/cluster/stroke/PSF/PET/SUV/SUVR-wb_nl_MNI/PSF_002_gfa.nii.gz’
- processing row #2 = ‘PSF_003 /autofs/cluster/stroke/PSF/PET/SUV/SUVR-wb_nl_MNI/PSF_003_gfa.nii.gz’
- processing row #3 = ‘PSF_005 /autofs/cluster/stroke/PSF/PET/SUV/SUVR-wb_nl_MNI/PSF_005_gfa.nii.gz’
- processing row #4 = ‘PSF_006 /autofs/cluster/stroke/PSF/PET/SUV/SUVR-wb_nl_MNI/PSF_006_gfa.nii.gz’
- processing row #5 = ‘PSF_008 /autofs/cluster/stroke/PSF/PET/SUV/SUVR-wb_nl_MNI/PSF_008_gfa.nii.gz’
- processing row #6 = ‘PSF_009 /autofs/cluster/stroke/PSF/PET/SUV/SUVR-wb_nl_MNI/PSF_009_gfa.nii.gz’
- processing row #7 = ‘PSF_010 /autofs/cluster/stroke/PSF/PET/SUV/SUVR-wb_nl_MNI/PSF_010_gfa.nii.gz’
- checking for duplicate labels
- Table element follows::
<AFNI_table
ni_type=“2*String”
ni_dimen=“8”
Labels=“subj;GFA” >
“PSF_001” “/autofs/cluster/stroke/PSF/PET/SUV/SUVR-wb_nl_MNI/PSF_001_gfa.nii.gz”
“PSF_002” “/autofs/cluster/stroke/PSF/PET/SUV/SUVR-wb_nl_MNI/PSF_002_gfa.nii.gz”
“PSF_003” “/autofs/cluster/stroke/PSF/PET/SUV/SUVR-wb_nl_MNI/PSF_003_gfa.nii.gz”
“PSF_005” “/autofs/cluster/stroke/PSF/PET/SUV/SUVR-wb_nl_MNI/PSF_005_gfa.nii.gz”
“PSF_006” “/autofs/cluster/stroke/PSF/PET/SUV/SUVR-wb_nl_MNI/PSF_006_gfa.nii.gz”
“PSF_008” “/autofs/cluster/stroke/PSF/PET/SUV/SUVR-wb_nl_MNI/PSF_008_gfa.nii.gz”
“PSF_009” “/autofs/cluster/stroke/PSF/PET/SUV/SUVR-wb_nl_MNI/PSF_009_gfa.nii.gz”
“PSF_010” “/autofs/cluster/stroke/PSF/PET/SUV/SUVR-wb_nl_MNI/PSF_010_gfa.nii.gz”
</AFNI_table>
++ Covariates file: 2 columns, each with 8 rows
- Covariate column labels: subj;GFA
- Found 1 dataset name column: GFA
++ loading covariates
Fatal Signal 11 (SIGSEGV) received
3dttest++ main
Bottom of Debug Stack
** Command line was:
3dttest++ -prefix /autofs/cluster/stroke/PSF/PET/SUV/ttests_covar/P8_suvr-gfa_3dttest/P8_suvr-gfa -setA PSF_001.nii.gz PSF_002.nii.gz PSF_003.nii.gz PSF_005.nii.gz PSF_006.nii.gz PSF_008.nii.gz PSF_009.nii.gz PSF_010.nii.gz -mask /autofs/cluster/stroke/PSF/MR/composite_lesion/MNI152_T1_2mm_brain_no-LV-Lesion_bin.nii.gz -covariates /autofs/cluster/stroke/PSF/scripts/covarfile_gfa
** AFNI version = AFNI_17.2.05 Compile date = Jul 27 2017
** [[Precompiled binary linux_openmp_64: Jul 27 2017]]
** 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.
** Memory usage: chunks=243 bytes=8880971
** Crash log is appended to file /homes/5/judith/.afni.crashlog
Here is the crashlog:
------ CRASH LOG ------------------------------**
Fatal Signal 11 (SIGSEGV) received
… recent internal history …
-----THD_load_datablock [5]: EXIT} (file=thd_loaddblk.c line=150) to THD_extract_many_arrays
----THD_extract_many_arrays [4]: EXIT} (file=thd_dsetto1D.c line=638) to THD_dset_to_vectim
THD_dset_to_vectim – setting parameters in vectim header
THD_dset_to_vectim – VECTIM_scan()
—THD_dset_to_vectim [3]: EXIT} (file=thd_dset_to_vectim.c line=117) to 3dttest++ main
+++THD_dset_to_vectim [3]: {ENTRY (file=thd_dset_to_vectim.c line=26) from 3dttest++ main
++++THD_load_datablock [4]: {ENTRY (file=thd_loaddblk.c line=133) from THD_dset_to_vectim
+++++THD_load_nifti [5]: {ENTRY (file=thd_niftiread.c line=774) from THD_load_datablock
THD_load_nifti – purging existing data bricks (if any)
++++++THD_purge_datablock [6]: {ENTRY (file=thd_purgedblk.c line=15) from THD_load_nifti
THD_purge_datablock – MEM_MALLOC: clearing sub-bricks
+++++++mri_killpurge [7]: {ENTRY (file=mri_purger.c line=259) from THD_purge_datablock
mri_killpurge – check if im==NULL ptr=0x1a4e028 OK
mri_killpurge – can’t killpurge NULL fname!
-------mri_killpurge [7]: EXIT} (file=mri_purger.c line=270) to THD_purge_datablock
------THD_purge_datablock [6]: EXIT} (file=thd_purgedblk.c line=39) to THD_load_nifti
THD_load_nifti – calling nifti_image_read_bricks
THD_load_nifti – copying brick pointers directly
THD_load_nifti – doing floatscan
THD_load_nifti – free-ing NBL
-----THD_load_nifti [5]: EXIT} (file=thd_niftiread.c line=945) to THD_load_datablock
----THD_load_datablock [4]: EXIT} (file=thd_loaddblk.c line=272) to THD_dset_to_vectim
THD_dset_to_vectim – create index list
THD_dset_to_vectim – ignore==0 → extracting all at once
++++THD_extract_many_arrays [4]: {ENTRY (file=thd_dsetto1D.c line=551) from THD_dset_to_vectim
+++++THD_load_datablock [5]: {ENTRY (file=thd_loaddblk.c line=133) from THD_extract_many_arrays
-----THD_load_datablock [5]: EXIT} (file=thd_loaddblk.c line=150) to THD_extract_many_arrays
----THD_extract_many_arrays [4]: EXIT} (file=thd_dsetto1D.c line=638) to THD_dset_to_vectim
THD_dset_to_vectim – setting parameters in vectim header
THD_dset_to_vectim – VECTIM_scan()
—THD_dset_to_vectim [3]: EXIT} (file=thd_dset_to_vectim.c line=117) to 3dttest++ main
…
** Command line was:
3dttest++ -prefix /autofs/cluster/stroke/PSF/PET/SUV/ttests_covar/P8_suvr-gfa_3dttest/P8_suvr-gfa -setA PSF_001.nii.gz PSF_002.nii.gz PSF_
003.nii.gz PSF_005.nii.gz PSF_006.nii.gz PSF_008.nii.gz PSF_009.nii.gz PSF_010.nii.gz -mask /autofs/cluster/stroke/PSF/MR/composite_lesion
/MNI152_T1_2mm_brain_no-LV-Lesion_bin.nii.gz -covariates /autofs/cluster/stroke/PSF/scripts/covarfile_gfa
…
3dttest++ main
** Command line was:
3dttest++ -prefix /autofs/cluster/stroke/PSF/PET/SUV/ttests_covar/P8_suvr-gfa_3dttest/P8_suvr-gfa -setA PSF_001.nii.gz PSF_002.nii.gz PSF_
003.nii.gz PSF_005.nii.gz PSF_006.nii.gz PSF_008.nii.gz PSF_009.nii.gz PSF_010.nii.gz -mask /autofs/cluster/stroke/PSF/MR/composite_lesion
/MNI152_T1_2mm_brain_no-LV-Lesion_bin.nii.gz -covariates /autofs/cluster/stroke/PSF/scripts/covarfile_gfa
** AFNI compile date = Jul 27 2017
** [[Precompiled binary linux_openmp_64: Jul 27 2017]]
** Program Crash **
.