afni.nimh.nih.gov
AFNI Message Board
Dear AFNI users-
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
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
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
| August 07, 2016 10:31PM | |
Hi,
I use the new -clustsim option of 3dttest++ recently.
I always meet the error message below.
++ t-test randomsign:sh: 1: Syntax error: Bad fd number
sh: 1: Syntax error: Bad fd number
Although the error message is displayed, the 3dttest++ continues and finally with results.
Is this a potential problem need further care?
The output information for the -clustsim section:
++ ================ Starting -clustsim calculations ================
+ ===== temporary files will have prefix TT.4sAVd179k2U =====
+ ===== running 4 -randomsign jobs (2501 iterations per job) =====
+ #0 jobs command:
3dttest++ -DAFNI_AUTOMATIC_FDR=NO -DAFNI_DONT_LOGFILE=YES -randomsign 2501 -nomeans -toz -no1sam -mask /media/sf_DataAna/tdcs_reana/group/AB/statfolder/ana/TT_mask_rs+tlrc -paired -setA TT.4sAVd179k2U.resid.nii'[0..31]' -setB TT.4sAVd179k2U.resid.nii'[32..$]' -prefix .//TT.4sAVd179k2U.000.nii
sh: 1: Syntax error: Bad fd number
++ 3dttest++: AFNI version=AFNI_16.2.06 (Jul 25 2016) [64-bit]
++ Authored by: Zhark++
++ 92165 voxels in -mask dataset
++ 2-sample test: '-AminusB' option is assumed
++ paired test: results will be SetA - SetB
++ loading input datasets
++ Memory usage now = 26,511,204 (27 million [mega])
++ t-test randomsign:sh: 1: Syntax error: Bad fd number
sh: 1: Syntax error: Bad fd number
0123456789.0123456789.0123456789.0123456789.0123456789.!
++ ---------- End of analyses -- freeing workspaces ----------
++ Memory usage now = 2,920,635,820 (2.9 billion [giga])
++ Output dataset .//TT.4sAVd179k2U.000.nii
+ paired test: results are SetA - SetB
+ ===== jobs have finished (596.01 s elapsed) =====
+ ===== starting 3dClustSim =====
3dClustSim -DAFNI_DONT_LOGFILE=YES -inset .//TT.4sAVd179k2U.???.nii -prefix TT.4sAVd179k2U.CSim -LOTS -both -nodec -cmd TT.4sAVd179k2U.CSim.cmd -mask /media/sf_DataAna/tdcs_reana/group/AB/statfolder/ana/TT_mask_rs+tlrc
++ 3dClustSim: AFNI version=AFNI_16.2.06 (Jul 25 2016) [64-bit]
++ Authored by: RW Cox and BD Ward
++ 92165 voxels in mask (31.58% of total)
+ loading -inset './/TT.4sAVd179k2U.000.nii' with 2501 volumes
++ -inset had 2501 volumes = new '-niter' value
++ Startup clock time = 13.2 s
++ Using 4 OpenMP threads
Simulating:0123456789.0123456789.0123456789.0123456789.01234567!
++ Clock time now = 71.2 s
++ Clock time now = 72.6 s
++ Command fragment to put cluster results into a dataset header;
+ (also echoed to file TT.4sAVd179k2U.CSim.cmd for your scripting pleasure)
+ Append the name of the datasets to be patched to this command:
3drefit -atrstring AFNI_CLUSTSIM_NN1_1sided file:TT.4sAVd179k2U.CSim.NN1_1sided.niml -atrstring AFNI_CLUSTSIM_MASK file:TT.4sAVd179k2U.CSim.mask -atrstring AFNI_CLUSTSIM_NN2_1sided file:TT.4sAVd179k2U.CSim.NN2_1sided.niml -atrstring AFNI_CLUSTSIM_NN3_1sided file:TT.4sAVd179k2U.CSim.NN3_1sided.niml -atrstring AFNI_CLUSTSIM_NN1_2sided file:TT.4sAVd179k2U.CSim.NN1_2sided.niml -atrstring AFNI_CLUSTSIM_NN2_2sided file:TT.4sAVd179k2U.CSim.NN2_2sided.niml -atrstring AFNI_CLUSTSIM_NN3_2sided file:TT.4sAVd179k2U.CSim.NN3_2sided.niml -atrstring AFNI_CLUSTSIM_NN1_bisided file:TT.4sAVd179k2U.CSim.NN1_bisided.niml -atrstring AFNI_CLUSTSIM_NN2_bisided file:TT.4sAVd179k2U.CSim.NN2_bisided.niml -atrstring AFNI_CLUSTSIM_NN3_bisided file:TT.4sAVd179k2U.CSim.NN3_bisided.niml
+ ===== 3drefit-ing 3dClustSim results into ./ana/groupttest_015+tlrc.HEAD =====
++ 3drefit: AFNI version=AFNI_16.2.06 (Jul 25 2016) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset ./ana/groupttest_015+tlrc.HEAD
++ applying attributes
++ 3drefit processed 1 datasets
+ ===== deleting temp files TT.4sAVd179k2U.*.nii TT.4sAVd179k2U.*.niml =====
+ =============== -clustsim work is finished
===============
Thanks a lot!
lzy
I use the new -clustsim option of 3dttest++ recently.
I always meet the error message below.
++ t-test randomsign:sh: 1: Syntax error: Bad fd number
sh: 1: Syntax error: Bad fd number
Although the error message is displayed, the 3dttest++ continues and finally with results.
Is this a potential problem need further care?
The output information for the -clustsim section:
++ ================ Starting -clustsim calculations ================
+ ===== temporary files will have prefix TT.4sAVd179k2U =====
+ ===== running 4 -randomsign jobs (2501 iterations per job) =====
+ #0 jobs command:
3dttest++ -DAFNI_AUTOMATIC_FDR=NO -DAFNI_DONT_LOGFILE=YES -randomsign 2501 -nomeans -toz -no1sam -mask /media/sf_DataAna/tdcs_reana/group/AB/statfolder/ana/TT_mask_rs+tlrc -paired -setA TT.4sAVd179k2U.resid.nii'[0..31]' -setB TT.4sAVd179k2U.resid.nii'[32..$]' -prefix .//TT.4sAVd179k2U.000.nii
sh: 1: Syntax error: Bad fd number
++ 3dttest++: AFNI version=AFNI_16.2.06 (Jul 25 2016) [64-bit]
++ Authored by: Zhark++
++ 92165 voxels in -mask dataset
++ 2-sample test: '-AminusB' option is assumed
++ paired test: results will be SetA - SetB
++ loading input datasets
++ Memory usage now = 26,511,204 (27 million [mega])
++ t-test randomsign:sh: 1: Syntax error: Bad fd number
sh: 1: Syntax error: Bad fd number
0123456789.0123456789.0123456789.0123456789.0123456789.!
++ ---------- End of analyses -- freeing workspaces ----------
++ Memory usage now = 2,920,635,820 (2.9 billion [giga])
++ Output dataset .//TT.4sAVd179k2U.000.nii
+ paired test: results are SetA - SetB
+ ===== jobs have finished (596.01 s elapsed) =====
+ ===== starting 3dClustSim =====
3dClustSim -DAFNI_DONT_LOGFILE=YES -inset .//TT.4sAVd179k2U.???.nii -prefix TT.4sAVd179k2U.CSim -LOTS -both -nodec -cmd TT.4sAVd179k2U.CSim.cmd -mask /media/sf_DataAna/tdcs_reana/group/AB/statfolder/ana/TT_mask_rs+tlrc
++ 3dClustSim: AFNI version=AFNI_16.2.06 (Jul 25 2016) [64-bit]
++ Authored by: RW Cox and BD Ward
++ 92165 voxels in mask (31.58% of total)
+ loading -inset './/TT.4sAVd179k2U.000.nii' with 2501 volumes
++ -inset had 2501 volumes = new '-niter' value
++ Startup clock time = 13.2 s
++ Using 4 OpenMP threads
Simulating:0123456789.0123456789.0123456789.0123456789.01234567!
++ Clock time now = 71.2 s
++ Clock time now = 72.6 s
++ Command fragment to put cluster results into a dataset header;
+ (also echoed to file TT.4sAVd179k2U.CSim.cmd for your scripting pleasure)
+ Append the name of the datasets to be patched to this command:
3drefit -atrstring AFNI_CLUSTSIM_NN1_1sided file:TT.4sAVd179k2U.CSim.NN1_1sided.niml -atrstring AFNI_CLUSTSIM_MASK file:TT.4sAVd179k2U.CSim.mask -atrstring AFNI_CLUSTSIM_NN2_1sided file:TT.4sAVd179k2U.CSim.NN2_1sided.niml -atrstring AFNI_CLUSTSIM_NN3_1sided file:TT.4sAVd179k2U.CSim.NN3_1sided.niml -atrstring AFNI_CLUSTSIM_NN1_2sided file:TT.4sAVd179k2U.CSim.NN1_2sided.niml -atrstring AFNI_CLUSTSIM_NN2_2sided file:TT.4sAVd179k2U.CSim.NN2_2sided.niml -atrstring AFNI_CLUSTSIM_NN3_2sided file:TT.4sAVd179k2U.CSim.NN3_2sided.niml -atrstring AFNI_CLUSTSIM_NN1_bisided file:TT.4sAVd179k2U.CSim.NN1_bisided.niml -atrstring AFNI_CLUSTSIM_NN2_bisided file:TT.4sAVd179k2U.CSim.NN2_bisided.niml -atrstring AFNI_CLUSTSIM_NN3_bisided file:TT.4sAVd179k2U.CSim.NN3_bisided.niml
+ ===== 3drefit-ing 3dClustSim results into ./ana/groupttest_015+tlrc.HEAD =====
++ 3drefit: AFNI version=AFNI_16.2.06 (Jul 25 2016) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset ./ana/groupttest_015+tlrc.HEAD
++ applying attributes
++ 3drefit processed 1 datasets
+ ===== deleting temp files TT.4sAVd179k2U.*.nii TT.4sAVd179k2U.*.niml =====
+ =============== -clustsim work is finished
===============
Thanks a lot!
lzy
| Subject | Author | Posted |
|---|---|---|
|
lzhyoung | August 07, 2016 10:31PM |
|
Bob Cox | August 08, 2016 10:49AM |
