Fatal Signal 11 (SIGSEGV) received when running 3dttest++

AFNI Message Board
1

I see that the command is using the first 12 characters rather than the whole name, but I suspect some other problem is occurring too. I’m new to 3dtest++ and find the necessary syntax of the covariates file and the mapping between the 3dttest++ command unclear.

Here’s the error message:

3dttest++ -setA ‘S??.rest.3dTcorrMap.z+tlrc.BRIK’ -prefix testing -mask clip_group_brainTissueMask_tSNR10_count_no19+tlrc. -covariates covariates_ageTT_no19b.txt
++ 3dttest++: AFNI version=AFNI_16.3.08 (Nov 4 2016) [64-bit]
++ Authored by: Zhark++
++ 123062 voxels in -mask dataset
++ Covariates file: 4 columns, each with 24 rows

  • Covariate column labels: Subject;Age;TT;Labels
  • Found 2 numeric columns: Age TT
  • Found 1 dataset name column: Labels
    ++ loading covariates
    ** ERROR: Can’t find label ‘S08.rest.3dT’ in covariates file
    ** ERROR: Can’t find label ‘S09.rest.3dT’ in covariates file
    ** ERROR: Can’t find label ‘S11.rest.3dT’ in covariates file
    ** ERROR: Can’t find label ‘S13.rest.3dT’ in covariates file
    ** ERROR: Can’t find label ‘S15.rest.3dT’ in covariates file
    ** ERROR: Can’t find label ‘S16.rest.3dT’ in covariates file
    ** ERROR: Can’t find label ‘S18.rest.3dT’ in covariates file
    ** ERROR: Can’t find label ‘S22.rest.3dT’ in covariates file
    ** ERROR: Can’t find label ‘S23.rest.3dT’ in covariates file
    ** ERROR: Can’t find label ‘S24.rest.3dT’ in covariates file
    ** ERROR: Can’t find label ‘S26.rest.3dT’ in covariates file
    ** ERROR: Can’t find label ‘S28.rest.3dT’ in covariates file
    ** ERROR: Can’t find label ‘S30.rest.3dT’ in covariates file
    ** ERROR: Can’t find label ‘S31.rest.3dT’ in covariates file
    ** ERROR: Can’t find label ‘S32.rest.3dT’ in covariates file
    ** ERROR: Can’t find label ‘S33.rest.3dT’ in covariates file
    ** ERROR: Can’t find label ‘S34.rest.3dT’ in covariates file
    ** ERROR: Can’t find label ‘S37.rest.3dT’ in covariates file
    ** ERROR: Can’t find label ‘S39.rest.3dT’ in covariates file
    ** ERROR: Can’t find label ‘S41.rest.3dT’ in covariates file
    ** ERROR: Can’t find label ‘S42.rest.3dT’ in covariates file
    ** ERROR: Can’t find label ‘S44.rest.3dT’ in covariates file
    ** ERROR: Can’t find label ‘S46.rest.3dT’ in covariates file
    ** ERROR: Can’t find label ‘S48.rest.3dT’ in covariates file

Fatal Signal 11 (SIGSEGV) received
THD_delete_3dim_dataset
3dttest++ main
Bottom of Debug Stack
** Command line was:
3dttest++ -setA ‘S??.rest.3dTcorrMap.z+tlrc.BRIK’ -prefix testing -mask clip_group_brainTissueMask_tSNR10_count_no19+tlrc. -covariates covariates_ageTT_no19b.txt
** AFNI version = AFNI_16.3.08 Compile date = Nov 4 2016
** [[Precompiled binary macosx_10.7_Intel_64: Nov 4 2016]]
** Program Death **

2

Well, the first suspect is the labels in the covariates file. What does it look like?

3

The covariates are of the format:
Subject Age TT Labels
S08 30 600 S08.rest.3dTcorrMap.z+tlrc.HEAD
S09…

I’ve also tried:
Subject Age TT Labels
S08 30 600 S08.rest.3dT
S09…

and got:
Analysis_TT_age: 3dttest++ -setA ‘S??.rest.3dTcorrMap.z+tlrc.BRIK’ -prefix testing -mask clip_group_brainTissueMask_tSNR10_count_no19+tlrc. -covariates covariates_ageTT_no19c.txt
++ 3dttest++: AFNI version=AFNI_16.3.08 (Nov 4 2016) [64-bit]
++ Authored by: Zhark++
++ 123062 voxels in -mask dataset
++ Covariates file: 4 columns, each with 24 rows

  • Covariate column labels: Subject;Age;TT;Labels
  • Found 2 numeric columns: Age TT
  • Found 1 dataset name column: Labels
    ++ loading covariates
    ** ERROR: Can’t find label ‘S08.rest.3dT’ in covariates file
    ** ERROR: Can’t find label ‘S09.rest.3dT’ in covariates file
    etc.
    Fatal Signal 11 (SIGSEGV) received
    THD_delete_3dim_dataset
    3dttest++ main
    Bottom of Debug Stack
    ** Command line was:
    3dttest++ -setA ‘S??.rest.3dTcorrMap.z+tlrc.BRIK’ -prefix testing -mask clip_group_brainTissueMask_tSNR10_count_no19+tlrc. -covariates covariates_ageTT_no19c.txt
    ** AFNI version = AFNI_16.3.08 Compile date = Nov 4 2016
    ** [[Precompiled binary macosx_10.7_Intel_64: Nov 4 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 /Users/knutsonk/.afni.crashlog
4

I got rid of the Label and used a covariates file consisting of:
Subject Age TT
S08 30 600
etc.

and that worked with the command:
3dttest++ -setA S
S08 S08.rest.3dTcorrMap.z+tlrc.BRIK
etc.
-prefix Results_ -mask mask+tlrc. -covariates covariates.txt

5

Yes, the Subject column is basically supposed
to be the label. Your final Labels column was
either going to be interpreted as numbers or as
datasets (for voxelwise covariates), either of
which would have failed.

  • rick