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  

|
August 19, 2020 02:42PM
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 **




.
Subject Author Posted

3dtest++ with per voxel covariate

judithschaechter August 19, 2020 02:42PM