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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
| July 26, 2016 03:02PM | |
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:
but it's failing with the following messages (for some reason it's doubling up on the tempdir in filenames:
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.
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 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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
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.
| Subject | Author | Posted |
|---|---|---|
|
Colm Connolly | July 26, 2016 03:02PM |
|
Colm Connolly | July 27, 2016 02:17PM |
|
rick reynolds | July 28, 2016 04:07PM |
