Fsl dual_regression error

Summary of what happened:

Hello, everyone! I’m learning dual regression of the fsl course and keep getting an error.

Command used (and if a helper script was used, a link to the helper script or the command generated):

dual_regression groupICA15/melodic_IC 1 design/unpaired_ttest.mat design/unpaired_ttest.con 5000 groupICA15.dr `cat inputlist_new.txt`

Version:

fsl 6.0.7.6

Environment (Docker, Singularity, custom installation):

wsl ubuntu 20.04 & macOS 11

Data formatted according to a validatable standard? Please provide the output of the validator:

Relevant log outputs (up to 20 lines):

ired_ttest.con 5000 groupICA15zty.dr 'cat inputlist_new.txt' creating common mask
Error submitting job - Errors occured when running array task in shell plugin: Task 1 failed executing: /home/tianyu/fsl /bin/fslmaths CON_417/CON_417_resting.feat/filtered_func_data_clean_standard -Tstd -bin groupICA15zty.dr/mask_00000 -odt char () Task 2 failed executing: /home/tianyu/fsl/bin/fslmaths CON_425/CON_425_resting.feat/filtered_func_data_clean_standard -T std -bin groupICA15zty.dr/mask_00001 -odt char ()
Task 3 failed executing: /home/tianyu/fsl/bin/fslmaths CON_428/CON_428_resting.feat/filtered_func_data_clean_standard -T std -bin groupICA15zty.dr/mask_00002 -odt char ()
Task 4 failed executing: /home/tianyu/fsl/bin/fslmaths CON_430/CON_430_resting.feat/filtered_func_data_clean_standard -T std -bin groupICA15zty.dr/mask_00003 -odt char ()
Task 5 failed executing: /home/tianyu/fsl/bin/fslmaths CON_449/CON_449_resting.feat/filtered_func_data_clean_standard -T std -bin groupICA15zty.dr/mask_00004 -odt char ()
Task 6 failed executing: /home/tianyu/fsl/bin/fslmaths CON_453/CON_453_resting.feat/filtered_func_data_clean_standard -T std -bin groupICA15zty.dr/mask_00005 -odt char ()
Task 7 failed executing: /home/tianyu/fsl/bin/fslmaths TUM_401/TUM_401_resting.feat/filtered_func_data_clean_standard -T std -bin groupICA15zty.dr/mask_00006 -odt char ()
Task 9 failed executing: /home/tianyu/fsl/bin/fslmaths TUM_405/TUM_405_resting.feat/filtered_func_data_clean_standard -T std -bin groupICA15zty.dr/mask_00008 -odt char ()
Task 10 failed executing: /home/tianyu/fsl/bin/fslmaths TUM_421/TUM_421_resting.feat/filtered_func_data_clean_standard – Tstd -bin groupICA15zty.dr/mask_00009 -odt char ()
Task 11 failed executing: /home/tianyu/fsl/bin/fslmaths TUM_422/TUM_422_resting.feat/filtered_func_data_clean_standard - Tstd -bin groupICA15zty.dr/mask_00010 -odt char ()

and

usage: fsl_sub [-h] [-a ARCH] [-c COPROCESSOR]
[--coprocessor_multi COPROCESSOR_MULTI] [--coprocessor_class COPROCESSOR_CLASS] [--coprocessor_class_strict]
[--coprocessor_toolkit COPROCESSOR_TOOLKIT] [-F] [-j JOBHOLD] [--not_requeueable] [--array_hold ARRAY_HOLD] [-1 LOGDIR] [-m MAILOPTIONS] [-M MAILTO] [-n] [-N NAME] [-P PRIORITY] [-q QUEUE] [-r RESOURCE] [--delete_job DELETE_JOB] [--extra EXTRA] [-R GB] [-s PARALLELENV, THREADS]
[-t ARRAY_TASK] [--array_native ARRAY_NATIVE] [-X NUMBER] [--keep_jobscript] [--has_coprocessor COPROCESSOR_NAME] [--has_queues] [--project PROJECT] [-S] [-T MINUTES] [--show_config] [-v] [-v] [-z file]
fsl_sub: error: argument -j/--jobhold: expected one argument doing the dual regressions
usage: fsl_sub [-h] [-a ARCH] [-C COPROCESSOR]
[--coprocessor_multi COPROCESSOR_MULTI] [--coprocessor_class COPROCESSOR_CLASS] [--coprocessor_class_strict]
[--coprocessor_toolkit COPROCESSOR_TOOLKIT] [-F] [-j JOBHOLD] [--not_requeueable] [--array_hold ARRAY_HOLD] [-1 LOGDIR] [-m MAILOPTIONS] [-M MAILTO] [-n] [-N NAME] [-p PRIORITY] [-q QUEUE] [-r RESOURCE] [--delete_job DELETE_JOB] [--extra EXTRA] [-R GB] [-s PARALLELENV, THREADS] [-t ARRAY_TASK] [--array_native ARRAY_NATIVE] [-x NUMBER] [--keep_jobscript] [--has_coprocessor COPROCESSOR_NAME] [--has_queues] [--project PROJECT] [-S] [-T MINUTES]

Screenshots / relevant information:


Hi @Shulk, there may be some informative error messages in the files contained within the groupICA.dr/scripts+logs directory - try running:

cat groupICA.dr/scripts+logs/*.e*
cat groupICA.dr/scripts+logs/*.o*

Thank you very much! However, the output was nothing and all these files are 0 KB.


I guess some issues happened while reading filtered_func_data_clean_standard.nii.gz, but it worked just fine when I ran melodic. It was really strange that I only got two mask_*.nii.gz.
mask

How much RAM does your computer have? The FSL commands may be running out of RAM. There is also a chance that fsl_sub is trying to run too many jobs simultaneously, which is causing your computer to run out of RAM. Can you try running this:

export FSLSUB_PARALLEL=1

and then re-running dual regression in the same terminal?

@paulmccarthy
It worked!
I’m truly grateful for your help!