afni.nimh.nih.gov

Hi,

I'm experimenting with 3dttest++ to explore teh new resid and clustsim options but have run into a problem with it not working.

I'm running 3dttest++ as follows:

cd /data/sanDiego/rsfcGraphAnalysis/data//Group.results ; mkdir tmp.resid.clustsim.L_whole_amygdala.3mm ; 3dttest++ -resid new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid \
-CLUSTSIM \
-prefix_clustsim resid.CStemp.L_whole_amygdala.3mm \
-tempdir tmp.resid.clustsim.L_whole_amygdala.3mm \
-mask mask.grey.mddAndCtrl.union.masked+tlrc.HEAD \
-prefix new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried \
-center NONE \
-setA MDD 106_A /data/sanDiego/rsfcGraphAnalysis//data/106_A/rsfc/L_whole_amygdala.3mm/L_whole_amygdala.3mm.z-score+tlrc.HEAD \
111_A /data/sanDiego/rsfcGraphAnalysis//data/111_A/rsfc/L_whole_amygdala.3mm/L_whole_amygdala.3mm.z-score+tlrc.HEAD \
112_A /data/sanDiego/rsfcGraphAnalysis//data/112_A/rsfc/L_whole_amygdala.3mm/L_whole_amygdala.3mm.z-score+tlrc.HEAD \
113_A /data/sanDiego/rsfcGraphAnalysis//data/113_A/rsfc/L_whole_amygdala.3mm/L_whole_amygdala.3mm.z-score+tlrc.HEAD \
[trimmed] \
-setB NCL 108_A /data/sanDiego/rsfcGraphAnalysis//data/108_A/rsfc/L_whole_amygdala.3mm/L_whole_amygdala.3mm.z-score+tlrc.HEAD \
109_A /data/sanDiego/rsfcGraphAnalysis//data/109_A/rsfc/L_whole_amygdala.3mm/L_whole_amygdala.3mm.z-score+tlrc.HEAD \
116_A /data/sanDiego/rsfcGraphAnalysis//data/116_A/rsfc/L_whole_amygdala.3mm/L_whole_amygdala.3mm.z-score+tlrc.HEAD \
121_A /data/sanDiego/rsfcGraphAnalysis//data/121_A/rsfc/L_whole_amygdala.3mm/L_whole_amygdala.3mm.z-score+tlrc.HEAD \
[trimmed] \
-covariates /data/sanDiego/rsfcGraphAnalysis/data//Group.data/3dttest.covariates.mddAndCtrl.L_whole_amygdala.3mm.txt

but it's failing with the following messages (for some reason it's doubling up on the tempdir in filenames:

[colmconn@kryten scripts]$ export OMP_NUM_THREADS=40
[colmconn@kryten scripts]$ bash   new-07-ttest.withCovariates.mddAndCtrl.L_whole_amygdala.3mm.sh
++ 3dttest++: AFNI version=AFNI_16.2.05 (Jul 22 2016) [64-bit]
++ Authored by: Zhark++
++ Number of -clustsim threads set to 40
++ 67116 voxels in -mask dataset
++ Covariates file: 2 columns, each with 101 rows
 + Covariate column labels: subject;Full
 + Found 1 numeric column: Full 
++ running 3dClustSim --> changed '-resid' prefix to NIFTI form: new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii
++ 2-sample test: '-AminusB' option is assumed
++ 2-sample test: results will be MDD - NCL
++ loading covariates
++ Two samples: t-testing fixed covariates for similarity between groups
 +  Full: mean of setA-setB=-9.504717 ; 2-sided p-value=0.0001
++ loading input datasets
++ Memory usage now = 60,513,316 (61 million [mega])
++ t-testing:0123456789.0123456789.0123456789.0123456789.0123456789.!
 + skipped 39 voxels completely for having constant data
++ ---------- End of analyses -- freeing workspaces ----------
++ Memory usage now = 124,757,340 (125 million [mega])
++ Creating FDR curves in output dataset
*+ WARNING: Smallest FDR q [1 MDD-NCL_Zscr] = 0.677335 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [3 MDD-NCL_Full_Zscr] = 0.999898 ==> few true single voxel detections
++ Smallest FDR q [5 MDD_Zscr] = 4.14588e-14
*+ WARNING: Smallest FDR q [7 MDD_Full_Zscr] = 0.930404 ==> few true single voxel detections
++ Smallest FDR q [9 NCL_Zscr] = 4.92629e-14
*+ WARNING: Smallest FDR q [11 NCL_Full_Zscr] = 0.961098 ==> few true single voxel detections
 + Added 6 FDR curves to dataset
*+ WARNING: Over-writing dataset ./new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried+tlrc.HEAD
*+ WARNING: Over-writing dataset ./new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii.gz
++ Output dataset ./new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii.gz
 + 2-sample test: results are MDD - NCL
++ ================ Starting -clustsim calculations ================
 + ===== temporary files will have prefix resid.CStemp.L_whole_amygdala.3mm =====
 + ===== running 40 -randomsign jobs (251 iterations per job) =====
 + #0 jobs command:
   3dttest++ -DAFNI_AUTOMATIC_FDR=NO -DAFNI_DONT_LOGFILE=YES -randomsign 251 -nomeans -toz -no1sam -mask mask.grey.mddAndCtrl.union.masked+tlrc.HEAD -nocov -covariates /data/sanDiego/rsfcGraphAnalysis/data//Group.data/3dttest.covariates.mddAndCtrl.L_whole_amygdala.3mm.txt -center NONE -setA rAAA 106_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[0]' 111_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[1]' 112_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[2]' 113_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[3]' 118_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[4]' 120_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[5]' 133_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[6]' 134_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[7]' 136_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[8]' 137_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[9]' 140_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[10]' 144_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[11]' 147_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[12]' 154_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[13]' 158_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[14]' 160_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[15]' 164_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[16]' 167_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[17]' 301_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[18]' 304_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[19]' 310_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[20]' 313_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[21]' 330_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[22]' 331_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[23]' 332_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[24]' 335_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[25]' 336_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[26]' 339_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[27]' 342_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[28]' 343_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[29]' 351_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[30]' 353_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[31]' 355_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[32]' 356_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[33]' 358_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[34]' 359_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[35]' 360_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[36]' 362_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[37]' 363_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[38]' 364_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[39]' 366_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[40]' 368_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[41]' 371_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[42]' 373_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[43]' 378_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[44]' 389_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[45]' 390_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[46]' 393_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[47]' -setB rBBB 108_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[48]' 109_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[49]' 116_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[50]' 121_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[51]' 122_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[52]' 123_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[53]' 124_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[54]' 126_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[55]' 127_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[56]' 131_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[57]' 138_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[58]' 139_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[59]' 141_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[60]' 142_A 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new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[87]' 397_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[88]' 400_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[89]' 402_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[90]' 403_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[91]' 406_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[92]' 409_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[93]' 413_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[94]' 414_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[95]' 417_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[96]' 419_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[97]' 421_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[98]' 422_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[99]' 423_A new.ttest.mddAndCtrl.L_whole_amygdala.3mm.covaried.resid.nii'[100]' -prefix tmp.resid.clustsim.L_whole_amygdala.3mm/resid.CStemp.L_whole_amygdala.3mm.000.nii
++ 3dttest++: AFNI version=AFNI_16.2.05 (Jul 22 2016) [64-bit]
++ Authored by: Zhark++
++ 67116 voxels in -mask dataset
++ Covariates file: 2 columns, each with 101 rows
 + Covariate column labels: subject;Full
 + Found 1 numeric column: Full 
++ 2-sample test: '-AminusB' option is assumed
++ 2-sample test: results will be rAAA - rBBB
++ loading covariates
++ Two samples: t-testing fixed covariates for similarity between groups
 +  Full: mean of setA-setB=-9.504717 ; 2-sided p-value=0.0001
++ loading input datasets
++ Memory usage now = 32,633,595 (33 million [mega])
++ t-test randomsign:0123456789.0123456789.0123456789.0123456789.0123456789.!
++ ---------- End of analyses -- freeing workspaces ----------
++ Memory usage now = 276,352,523 (276 million [mega])
** ERROR (nifti_image_write_hdr_img2): cannot open output file 'tmp.resid.clustsim.L_whole_amygdala.3mm/tmp.resid.clustsim.L_whole_amygdala.3mm/resid.CStemp.L_whole_amygdala.3mm.000.nii.gz'
 + 2-sample test: results are rAAA - rBBB
 + ===== jobs have finished (358.92 s elapsed) =====
 + ===== starting 3dClustSim =====
   3dClustSim -DAFNI_DONT_LOGFILE=YES -inset tmp.resid.clustsim.L_whole_amygdala.3mm/resid.CStemp.L_whole_amygdala.3mm.???.nii -prefix resid.CStemp.L_whole_amygdala.3mm.CSim -LOTS -both -nodec -cmd resid.CStemp.L_whole_amygdala.3mm.CSim.cmd -mask mask.grey.mddAndCtrl.union.masked+tlrc.HEAD
++ 3dClustSim: AFNI version=AFNI_16.2.05 (Jul 22 2016) [64-bit]
++ Authored by: RW Cox and BD Ward
** ERROR: -inset 'tmp.resid.clustsim.L_whole_amygdala.3mm/resid.CStemp.L_whole_amygdala.3mm.???.nii': failure to open dataset
** FATAL ERROR: no valid datasets opened after -inset 
** Program compile date = Jul 22 2016
** FATAL ERROR: ===== 3dClustSim command failed (( =====
** Program compile date = Jul 22 2016
[colmconn@kryten scripts]$

Is the cause of this error the command line or a bug in3dttest++.


Thanks,

Colm.



Edited 1 time(s). Last edit at 07/27/2016 01:20PM by Colm Connolly.