afni.nimh.nih.gov

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

Claudie