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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
| April 05, 2021 02:02PM | |
Hello AFNI. I am running the following group comparison without an specific mask:
3dttest++ \
-prefix HighvsLowICG_noCov_noMask \
-prefix_clustsim HighvsLowICG_noCov_noMask \
-tempdir /scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp \
-center SAME\
-Clustsim 24 \
-toz \
-setA HighICG \
-230 r_CBF_GMC_80.nii.gz \
-....
-setB LowICG \
-172 r_CBF_GMC_80.nii.gz \
- ....
It seems that the t-test runs but at the clustSim moment, something is failing, any suggestions of what am I doing wrong?
++ 3dttest++: AFNI version=AFNI_19.3.18 (Dec 27 2019) [64-bit]
++ Authored by: Zhark++
++ Number of -Clustsim threads set to 24
++ option -setA :: processing as LONG form (label label dset label dset ...)
++ have 21 volumes corresponding to option '-setA'
++ option -setB :: processing as LONG form (label label dset label dset ...)
++ have 18 volumes corresponding to option '-setB'
++ no mask ==> processing all 902629 voxels
++ 2-sample test: '-AminusB' option is assumed
++ 2-sample test: results will be HighICG - LowICG
++ loading -setA datasets
^[[7m*+ WARNING:^[[0m 3dttest++ -setA :: 790863 vectors are constant
++ loading -setB datasets
^[[7m*+ WARNING:^[[0m 3dttest++ -setB :: 790863 vectors are constant
++ Memory usage now = 321,648,610 (322 million)
++ t-testing:0123456789.0123456789.0123456789.0123456789.0123456789.!
+ skipped 793799 voxels completely for having constant data
++ ---------- End of analyses -- freeing workspaces ----------
++ Memory usage now = 166,374,694 (166 million)
++ Creating FDR curves in output dataset
^[[7m*+ WARNING:^[[0m Smallest FDR q [1 HighICG-LowICG_Zscr] = 0.164516 ==> few true single voxel detections
++ Smallest FDR q [3 HighICG_Zscr] = 1.02322e-14
++ Smallest FDR q [5 LowICG_Zscr] = 3.17844e-14
+ Added 3 FDR curves to dataset
++ Output dataset ./HighvsLowICG_noCov_noMask.resid.nii
+ 2-sample test: results are HighICG - LowICG
++ ================ Starting -Clustsim calculations ================
+ === temporary files will have prefix HighvsLowICG_noCov_noMask ===
+ === running 24 -randomsign jobs (417 iterations per job) ===
++ 3dttest++: AFNI version=AFNI_19.3.18 (Dec 27 2019) [64-bit]
++ Authored by: Zhark++
++ option -setA :: processing as SHORT form (all values are datasets)
++ have 21 volumes corresponding to option '-setA'
++ option -setB :: processing as SHORT form (all values are datasets)
++ have 18 volumes corresponding to option '-setB'
++ random seeds are 416376842 730536107
++ no mask ==> processing all 902629 voxels
++ 2-sample test: '-AminusB' option is assumed
++ 2-sample test: results will be SetA - SetB
++ loading -setA datasets
^[[7m*+ WARNING:^[[0m 3dttest++ -setA :: 793799 vectors are constant
++ loading -setB datasets
^[[7m*+ WARNING:^[[0m 3dttest++ -setB :: 793799 vectors are constant
++ Memory usage now = 159,195,775 (159 million)
++ t-test randomsign/permute:0123456789.012sh: line 3: 87130 Killed 3dttest++ -DAFNI_AUTOMATIC_FDR=NO -DAFNI_DONT_LOGFILE=YES -randomsign 417 -nomeans -toz -seed 423043748 737203013 -no1sam -permute -setA HighvsLowICG_noCov_noMask.resid.nii'[0..20]' -setB HighvsLowICG_noCov_noMask.resid.nii'[21..$]' -prefix /scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0006.nii &>/dev/null
sh: line 3: 87143 Killed 3dttest++ -DAFNI_AUTOMATIC_FDR=NO -DAFNI_DONT_LOGFILE=YES -randomsign 417 -nomeans -toz -seed 427488352 741647617 -no1sam -permute -setA HighvsLowICG_noCov_noMask.resid.nii'[0..20]' -setB HighvsLowICG_noCov_noMask.resid.nii'[21..$]' -prefix /scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0010.nii &>/dev/null
.
.
.
+ 3dttest++ ===== simulation jobs have finished (7286.4 s elapsed)
+ 3dttest++ ===== starting 3dClustSim A: elapsed = 7291.2 s
++ 3dClustSim: AFNI version=AFNI_19.3.18 (Dec 27 2019) [64-bit]
++ Authored by: RW Cox and BD Ward
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0000.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0001.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0002.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0004.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0005.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0006.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0007.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0008.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0009.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0010.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0012.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0014.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0015.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0016.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0017.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0018.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0019.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0020.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0021.nii': failure to open dataset
^[[7m** FATAL ERROR:^[[0m can't continue after above -inset problems
** Program compile date = Dec 27 2019
^[[7m** FATAL ERROR:^[[0m ===== 3dClustSim command failed
(( =====
** Program compile date = Dec 27 2019
~
3dttest++ \
-prefix HighvsLowICG_noCov_noMask \
-prefix_clustsim HighvsLowICG_noCov_noMask \
-tempdir /scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp \
-center SAME\
-Clustsim 24 \
-toz \
-setA HighICG \
-230 r_CBF_GMC_80.nii.gz \
-....
-setB LowICG \
-172 r_CBF_GMC_80.nii.gz \
- ....
It seems that the t-test runs but at the clustSim moment, something is failing, any suggestions of what am I doing wrong?
++ 3dttest++: AFNI version=AFNI_19.3.18 (Dec 27 2019) [64-bit]
++ Authored by: Zhark++
++ Number of -Clustsim threads set to 24
++ option -setA :: processing as LONG form (label label dset label dset ...)
++ have 21 volumes corresponding to option '-setA'
++ option -setB :: processing as LONG form (label label dset label dset ...)
++ have 18 volumes corresponding to option '-setB'
++ no mask ==> processing all 902629 voxels
++ 2-sample test: '-AminusB' option is assumed
++ 2-sample test: results will be HighICG - LowICG
++ loading -setA datasets
^[[7m*+ WARNING:^[[0m 3dttest++ -setA :: 790863 vectors are constant
++ loading -setB datasets
^[[7m*+ WARNING:^[[0m 3dttest++ -setB :: 790863 vectors are constant
++ Memory usage now = 321,648,610 (322 million)
++ t-testing:0123456789.0123456789.0123456789.0123456789.0123456789.!
+ skipped 793799 voxels completely for having constant data
++ ---------- End of analyses -- freeing workspaces ----------
++ Memory usage now = 166,374,694 (166 million)
++ Creating FDR curves in output dataset
^[[7m*+ WARNING:^[[0m Smallest FDR q [1 HighICG-LowICG_Zscr] = 0.164516 ==> few true single voxel detections
++ Smallest FDR q [3 HighICG_Zscr] = 1.02322e-14
++ Smallest FDR q [5 LowICG_Zscr] = 3.17844e-14
+ Added 3 FDR curves to dataset
++ Output dataset ./HighvsLowICG_noCov_noMask.resid.nii
+ 2-sample test: results are HighICG - LowICG
++ ================ Starting -Clustsim calculations ================
+ === temporary files will have prefix HighvsLowICG_noCov_noMask ===
+ === running 24 -randomsign jobs (417 iterations per job) ===
++ 3dttest++: AFNI version=AFNI_19.3.18 (Dec 27 2019) [64-bit]
++ Authored by: Zhark++
++ option -setA :: processing as SHORT form (all values are datasets)
++ have 21 volumes corresponding to option '-setA'
++ option -setB :: processing as SHORT form (all values are datasets)
++ have 18 volumes corresponding to option '-setB'
++ random seeds are 416376842 730536107
++ no mask ==> processing all 902629 voxels
++ 2-sample test: '-AminusB' option is assumed
++ 2-sample test: results will be SetA - SetB
++ loading -setA datasets
^[[7m*+ WARNING:^[[0m 3dttest++ -setA :: 793799 vectors are constant
++ loading -setB datasets
^[[7m*+ WARNING:^[[0m 3dttest++ -setB :: 793799 vectors are constant
++ Memory usage now = 159,195,775 (159 million)
++ t-test randomsign/permute:0123456789.012sh: line 3: 87130 Killed 3dttest++ -DAFNI_AUTOMATIC_FDR=NO -DAFNI_DONT_LOGFILE=YES -randomsign 417 -nomeans -toz -seed 423043748 737203013 -no1sam -permute -setA HighvsLowICG_noCov_noMask.resid.nii'[0..20]' -setB HighvsLowICG_noCov_noMask.resid.nii'[21..$]' -prefix /scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0006.nii &>/dev/null
sh: line 3: 87143 Killed 3dttest++ -DAFNI_AUTOMATIC_FDR=NO -DAFNI_DONT_LOGFILE=YES -randomsign 417 -nomeans -toz -seed 427488352 741647617 -no1sam -permute -setA HighvsLowICG_noCov_noMask.resid.nii'[0..20]' -setB HighvsLowICG_noCov_noMask.resid.nii'[21..$]' -prefix /scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0010.nii &>/dev/null
.
.
.
+ 3dttest++ ===== simulation jobs have finished (7286.4 s elapsed)
+ 3dttest++ ===== starting 3dClustSim A: elapsed = 7291.2 s
++ 3dClustSim: AFNI version=AFNI_19.3.18 (Dec 27 2019) [64-bit]
++ Authored by: RW Cox and BD Ward
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0000.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0001.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0002.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0004.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0005.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0006.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0007.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0008.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0009.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0010.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0012.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0014.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0015.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0016.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0017.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0018.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0019.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0020.nii': failure to open dataset
^[[7m** ERROR:^[[0m -inset '/scratch/global/lbohorquez/PCASL_analysis/results_noMask/temp/HighvsLowICG_noCov_noMask.0021.nii': failure to open dataset
^[[7m** FATAL ERROR:^[[0m can't continue after above -inset problems
** Program compile date = Dec 27 2019
^[[7m** FATAL ERROR:^[[0m ===== 3dClustSim command failed
(( =====
** Program compile date = Dec 27 2019
~
| Subject | Author | Posted |
|---|---|---|
|
LuisaBoh | April 05, 2021 02:02PM |
|
RWCox | April 20, 2021 07:04PM |
