3dttest++

AFNI Message Board
1

Dear AFNI experts,
I take the liberty of writing you regarding some trouble I’m encountering with my 3dttest++ script. I would like to perform a 3dttest++ to investigate the effect of self-reported variables (quantitative measures evaluated with self-reported questionnaires) on functional connectivity among healthy subjects for one specific ROI.

Currently I’m getting an error message that says the following:

/data1/YAIROD/resting_state/results/23subjects> tcsh -xef 3dttest.22subjects_NAcc_withCov.WithCentering2.csh
set findir = /data1/YAIROD/resting_state/results/23subjects
set groupMask = /data1/YAIROD/resting_state/results/23subjects/groupMask
3dttest++ -prefix /data1/YAIROD/resting_state/results/23subjects/3dttest.22subjects_NAcc_withCov.WithCentering -DAFNI_DEBUG_TABLE=YES -mask /data1/YAIROD/resting_state/results/23subjects/groupMask/final_groupMask_23subjs+tlrc. -covariates /data1/YAIROD/resting_state/results/23subjects/3dttest.NAcc.22subjects.covariates.txt -center DIFF -setA /data1/YAIROD/resting_state/subjects/DH803/DH803.results.withFS/seed_connectivity_maps/zMapDH803LR_NAcc+tlrc.HEAD /data1/YAIROD/resting_state/subjects/DH804/DH804.results.withFS/seed_connectivity_maps/zMapDH804LR_NAcc+tlrc.HEAD /data1/YAIROD/resting_state/subjects/DH807/DH807.results.withFS/seed_connectivity_maps/zMapDH807LR_NAcc+tlrc.HEAD /data1/YAIROD/resting_state/subjects/DH808/DH808.results.withFS/seed_connectivity_maps/zMapDH808LR_NAcc+tlrc.HEAD /data1/YAIROD/resting_state/subjects/DH809/DH809.results.withFS/seed_connectivity_maps/zMapDH809LR_NAcc+tlrc.HEAD /data1/YAIROD/resting_state/subjects/DH810/DH810.results.withFS/seed_connectivity_maps/zMapDH810LR_NAcc+tlrc.HEAD /data1/YAIROD/resting_state/subjects/DH811/DH811.results.withFS/seed_connectivity_maps/zMapDH811LR_NAcc+tlrc.HEAD /data1/YAIROD/resting_state/subjects/DH813/DH813.results.withFS/seed_connectivity_maps/zMapDH813LR_NAcc+tlrc.HEAD /data1/YAIROD/resting_state/subjects/DH814/DH814.results.withFS/seed_connectivity_maps/zMapDH814LR_NAcc+tlrc.HEAD /data1/YAIROD/resting_state/subjects/DH815/DH815.results.withFS/seed_connectivity_maps/zMapDH815LR_NAcc+tlrc.HEAD /data1/YAIROD/resting_state/subjects/DH819/DH819.results.withFS/seed_connectivity_maps/zMapDH819LR_NAcc+tlrc.HEAD /data1/YAIROD/resting_state/subjects/DH823/DH823.results.withFS/seed_connectivity_maps/zMapDH823LR_NAcc+tlrc.HEAD /data1/YAIROD/resting_state/subjects/DH828/DH828.results.withFS/seed_connectivity_maps/zMapDH828LR_NAcc+tlrc.HEAD /data1/YAIROD/resting_state/subjects/DH833/DH833.results.withFS/seed_connectivity_maps/zMapDH833LR_NAcc+tlrc.HEAD /data1/YAIROD/resting_state/subjects/DH834/DH834.results.withFS/seed_connectivity_maps/zMapDH834LR_NAcc+tlrc.HEAD /data1/YAIROD/resting_state/subjects/DH835/DH835.results.withFS/seed_connectivity_maps/zMapDH835LR_NAcc+tlrc.HEAD /data1/YAIROD/resting_state/subjects/DH836/DH836.results.withFS/seed_connectivity_maps/zMapDH836LR_NAcc+tlrc.HEAD /data1/YAIROD/resting_state/subjects/DH837/DH837.results.withFS/seed_connectivity_maps/zMapDH837LR_NAcc+tlrc.HEAD /data1/YAIROD/resting_state/subjects/DH839/DH839.results.withFS/seed_connectivity_maps/zMapDH839LR_NAcc+tlrc.HEAD /data1/YAIROD/resting_state/subjects/DH841/DH841.results.withFS/seed_connectivity_maps/zMapDH841LR_NAcc+tlrc.HEAD /data1/YAIROD/resting_state/subjects/DH844/DH844.results.withFS/seed_connectivity_maps/zMapDH844LR_NAcc+tlrc.HEAD /data1/YAIROD/resting_state/subjects/DH846/DH846.results.withFS/seed_connectivity_maps/zMapDH846LR_NAcc+tlrc.HEAD
++ 3dttest++: AFNI version=AFNI_18.1.24 (Jun 3 2018) [64-bit]
++ Authored by: Zhark++
++ 70622 voxels in -mask dataset
++ Mixed Table: processing file /data1/YAIROD/resting_state/results/23subjects/3dttest.NAcc.22subjects.covariates.txt

  • first line = ‘subj BDI CERQnonAdaptER CERQrum’
  • found 4 labels in first line
  • processing row #0 = ‘zMapDH803LR_NAcc 4 11 15’
  • deciding format of 3 columns
  • – col#1 is numeric
  • – col#2 is numeric
  • – col#3 is numeric
  • processing row #1 = ‘zMapDH804LR_NAcc 1 6.5 9’
  • processing row #2 = ‘zMapDH807LR_NAcc 2 7 11’
  • processing row #3 = ‘zMapDH808LR_NAcc 6 6.75 14’
  • processing row #4 = ‘zMapDH809LR_NAcc 9 11.5 15’
  • processing row #5 = ‘zMapDH810LR_NAcc 0 5 4’
  • processing row #6 = ‘zMapDH811LR_NAcc 7 7.5 9’
  • processing row #7 = ‘zMapDH813LR_NAcc 1 6.25 8’
  • processing row #8 = ‘zMapDH814LR_NAcc 1 10.75 14’
  • processing row #9 = ‘zMapDH815LR_NAcc 19 11 15’
  • processing row #10 = ‘zMapDH819LR_NAcc 2 10.25 12’
  • processing row #11 = ‘zMapDH823LR_NAcc 1 9 11’
  • processing row #12 = ‘zMapDH828LR_NAcc 7 8.25 8’
  • processing row #13 = ‘zMapDH833LR_NAcc 5 5.5 8’
  • processing row #14 = ‘zMapDH834LR_NAcc 5 11 17’
  • processing row #15 = ‘zMapDH835LR_NAcc 5 10 13’
  • processing row #16 = ‘zMapDH836LR_NAcc 4 7 7’
  • processing row #17 = ‘zMapDH837LR_NAcc 16 6.75 10’
  • processing row #18 = ‘zMapDH839LR_NAcc 7 9 18’
  • processing row #19 = ‘zMapDH841LR_NAcc 1 6.25 10’
  • processing row #20 = ‘zMapDH844LR_NAcc 1 8.75 10’
  • processing row #21 = ‘zMapDH846LR_NAcc 1 10.5 14’
  • checking for duplicate labels
  • Table element follows::
    <AFNI_table
    ni_type=“String,3*float”
    ni_dimen=“22”
    Labels=“subj;BDI;CERQnonAdaptER;CERQrum” >
    “zMapDH803LR_NAcc” 4 11 15
    “zMapDH804LR_NAcc” 1 6.5 9
    “zMapDH807LR_NAcc” 2 7 11
    “zMapDH808LR_NAcc” 6 6.75 14
    “zMapDH809LR_NAcc” 9 11.5 15
    “zMapDH810LR_NAcc” 0 5 4
    “zMapDH811LR_NAcc” 7 7.5 9
    “zMapDH813LR_NAcc” 1 6.25 8
    “zMapDH814LR_NAcc” 1 10.75 14
    “zMapDH815LR_NAcc” 19 11 15
    “zMapDH819LR_NAcc” 2 10.25 12
    “zMapDH823LR_NAcc” 1 9 11
    “zMapDH828LR_NAcc” 7 8.25 8
    “zMapDH833LR_NAcc” 5 5.5 8
    “zMapDH834LR_NAcc” 5 11 17
    “zMapDH835LR_NAcc” 5 10 13
    “zMapDH836LR_NAcc” 4 7 7
    “zMapDH837LR_NAcc” 16 6.75 10
    “zMapDH839LR_NAcc” 7 9 18
    “zMapDH841LR_NAcc” 1 6.25 10
    “zMapDH844LR_NAcc” 1 8.75 10
    “zMapDH846LR_NAcc” 1 10.5 14
    </AFNI_table>

++ Covariates file: 4 columns, each with 22 rows

  • Covariate column labels: subj;BDI;CERQnonAdaptER;CERQrum
  • Found 3 numeric columns: BDI CERQnonAdaptER CERQrum
    ++ option -setA :: processing as LONG form (label label dset label dset …)
    *+ WARNING: -setA: LONG form group label ‘/data1/YAIROD/resting_state/subjects/DH803/DH803.results.withFS/seed_connectivity_maps/zMapDH803LR_NAcc+tlrc.HEAD’ looks like a dataset name but isn’t – is this OK ?!?
    *+ WARNING: -setA: LONG form dataset label ‘/data1/YAIROD/resting_state/subjects/DH804/DH804.results.withFS/seed_connectivity_maps/zMapDH804LR_NAcc+tlrc.HEAD’ looks like a dataset name – is this OK ?!?
    ** FATAL ERROR: Option -setA: can’t open dataset ‘/data1/YAIROD/resting_state/subjects/DH807/DH807.results.withFS/seed_connectivity_maps/zMapDH807LR_NAcc+tlrc.HEAD’

Please find below my 3dttest++ script as well as my covariates’ file:

set data directories and file names

set findir = /data1/YAIROD/resting_state/results/23subjects
set groupMask = /data1/YAIROD/resting_state/results/23subjects/groupMask

3dttest++
-prefix $findir/3dttest.22subjects_NAcc_withCov.WithCentering
-DAFNI_DEBUG_TABLE=YES
-mask $groupMask/final_groupMask_23subjs+tlrc.
-covariates $findir/3dttest.NAcc.22subjects.covariates.txt
-center DIFF
-setA
/data1/YAIROD/resting_state/subjects/DH803/DH803.results.withFS/seed_connectivity_maps/zMapDH803LR_NAcc+tlrc’[0]’
/data1/YAIROD/resting_state/subjects/DH804/DH804.results.withFS/seed_connectivity_maps/zMapDH804LR_NAcc+tlrc’[0]’
/data1/YAIROD/resting_state/subjects/DH807/DH807.results.withFS/seed_connectivity_maps/zMapDH807LR_NAcc+tlrc’[0]’
/data1/YAIROD/resting_state/subjects/DH808/DH808.results.withFS/seed_connectivity_maps/zMapDH808LR_NAcc+tlrc’[0]’
/data1/YAIROD/resting_state/subjects/DH809/DH809.results.withFS/seed_connectivity_maps/zMapDH809LR_NAcc+tlrc’[0]’
/data1/YAIROD/resting_state/subjects/DH810/DH810.results.withFS/seed_connectivity_maps/zMapDH810LR_NAcc+tlrc’[0]’
/data1/YAIROD/resting_state/subjects/DH811/DH811.results.withFS/seed_connectivity_maps/zMapDH811LR_NAcc+tlrc’[0]’
/data1/YAIROD/resting_state/subjects/DH813/DH813.results.withFS/seed_connectivity_maps/zMapDH813LR_NAcc+tlrc’[0]’
/data1/YAIROD/resting_state/subjects/DH814/DH814.results.withFS/seed_connectivity_maps/zMapDH814LR_NAcc+tlrc’[0]’
/data1/YAIROD/resting_state/subjects/DH815/DH815.results.withFS/seed_connectivity_maps/zMapDH815LR_NAcc+tlrc’[0]’
/data1/YAIROD/resting_state/subjects/DH819/DH819.results.withFS/seed_connectivity_maps/zMapDH819LR_NAcc+tlrc’[0]’
/data1/YAIROD/resting_state/subjects/DH823/DH823.results.withFS/seed_connectivity_maps/zMapDH823LR_NAcc+tlrc’[0]’
/data1/YAIROD/resting_state/subjects/DH828/DH828.results.withFS/seed_connectivity_maps/zMapDH828LR_NAcc+tlrc’[0]’
/data1/YAIROD/resting_state/subjects/DH833/DH833.results.withFS/seed_connectivity_maps/zMapDH833LR_NAcc+tlrc’[0]’
/data1/YAIROD/resting_state/subjects/DH834/DH834.results.withFS/seed_connectivity_maps/zMapDH834LR_NAcc+tlrc’[0]’
/data1/YAIROD/resting_state/subjects/DH835/DH835.results.withFS/seed_connectivity_maps/zMapDH835LR_NAcc+tlrc’[0]’
/data1/YAIROD/resting_state/subjects/DH836/DH836.results.withFS/seed_connectivity_maps/zMapDH836LR_NAcc+tlrc’[0]’
/data1/YAIROD/resting_state/subjects/DH837/DH837.results.withFS/seed_connectivity_maps/zMapDH837LR_NAcc+tlrc’[0]’
/data1/YAIROD/resting_state/subjects/DH839/DH839.results.withFS/seed_connectivity_maps/zMapDH839LR_NAcc+tlrc’[0]’
/data1/YAIROD/resting_state/subjects/DH841/DH841.results.withFS/seed_connectivity_maps/zMapDH841LR_NAcc+tlrc’[0]’
/data1/YAIROD/resting_state/subjects/DH844/DH844.results.withFS/seed_connectivity_maps/zMapDH844LR_NAcc+tlrc’[0]’
/data1/YAIROD/resting_state/subjects/DH846/DH846.results.withFS/seed_connectivity_maps/zMapDH846LR_NAcc+tlrc’[0]’

Covariates’ file:

subj BDI CERQnonAdaptER CERQrum
zMapDH803LR_NAcc 4 11 15
zMapDH804LR_NAcc 1 6.5 9
zMapDH807LR_NAcc 2 7 11
zMapDH808LR_NAcc 6 6.75 14
zMapDH809LR_NAcc 9 11.5 15
zMapDH810LR_NAcc 0 5 4
zMapDH811LR_NAcc 7 7.5 9
zMapDH813LR_NAcc 1 6.25 8
zMapDH814LR_NAcc 1 10.75 14
zMapDH815LR_NAcc 19 11 15
zMapDH819LR_NAcc 2 10.25 12
zMapDH823LR_NAcc 1 9 11
zMapDH828LR_NAcc 7 8.25 8
zMapDH833LR_NAcc 5 5.5 8
zMapDH834LR_NAcc 5 11 17
zMapDH835LR_NAcc 5 10 13
zMapDH836LR_NAcc 4 7 7
zMapDH837LR_NAcc 16 6.75 10
zMapDH839LR_NAcc 7 9 18
zMapDH841LR_NAcc 1 6.25 10
zMapDH844LR_NAcc 1 8.75 10
zMapDH846LR_NAcc 1 10.5 14

So far I tried to change the label of the subj variable without any success.

Many thanks a lot for your kind attention and help !

Claudie

2

Hi Claudie,

That format looks okay to me. Maybe there is a typo and
one or more dataset names is not correct. Maybe
gen_group_command.py would help. Just as a test, run:

gen_group_command.py -command 3dttest++ \
  -dsets /data1/YAIROD/resting_state/subjects/DH*/DH*.results.withFS/seed_connectivity_maps/zMapDH*LR_NAcc+tlrc.HEAD

Does that find any datasets? Or even the same command,
but just using ‘ls’…

  • rick
3

Hi Rick,

Thanks a lot for your precious guidance ! I run the command that you recommended me and indeed, it found a very ‘basic’ typo error.
Everything went then perfectly once I could correct for it.

Just a last question about how to interpret correctly the map that I got with the inclusion of the covariates. If I select a contrast with one of my covariate, let’s say the BDI score which is a score of the severity of the symptoms characterizing depression and which has been centered, I get a deactivation between the Nucleus Accumbens (NAcc) and the PCC. I am wondering whether the right interpretation in this case is (1) once we control for the severity of depression symptoms (characterized by the score at the BDI questionnaire), we get this connectivity map, (2) the higher the BDI score, the lower the connectivity between the NAcc and the PCC or (3) the lower the BDI score, the lower the connectivity the connectivity between the NAcc and the PCC ?

Thanks so much !

Best wishes,

Claudie