hcp fix multi-run error
73 views
Skip to first unread message
Austin Cooper
Nov 20, 2025, 5:08:08 PM11/20/25
to HCP-Users
Hello!
I'm noticing that my FIX processing seems to be stopping short in terms of outputting all expected files.
The particular error I'm seeing is:
Fri Oct 10 10:07:23 EDT 2025:hcp_fix_multi_run: Running MELODIC located at: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/fsl/6.0.7.7/bin/melodic
Fri Oct 10 10:07:23 EDT 2025:hcp_fix_multi_run: melodic_cmd: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/fsl/6.0.7.7/bin/melodic -i all_fMRI_data_hp0_vnts -o all_fMRI_data_hp0.ica/filtered_func_data.ica --nobet --report --Oall --tr=0.937000 --vn --dim=328 -m all_fMRI_data_brain_mask
Fri Oct 10 11:03:34 EDT 2025:hcp_fix_multi_run: melodic has been run: return_code = 0
Fri Oct 10 11:03:47 EDT 2025:hcp_fix_multi_run: Running FIX
Fri Oct 10 11:03:47 EDT 2025:hcp_fix_multi_run: using training data file: /project/6001995/coopapap/scripts/HCPpipelines-master/fix/training_files/HCP_Style_Single_Multirun_Dedrift.RData
Fri Oct 10 11:03:47 EDT 2025:hcp_fix_multi_run: fix_cmd: /project/6001995/coopapap/scripts/HCPpipelines-master/fix/fix all_fMRI_data_hp0.ica /project/6001995/coopapap/scripts/HCPpipelines-master/fix/training_files/HCP_Style_Single_Multirun_Dedrift.RData 10
Fri Oct 10 11:03:47 EDT 2025:hcp_fix_multi_run: Check all_fMRI_data_hp0.ica/fix/logMatlab.txt for log output from feature extraction
Fri Oct 10 11:03:47 EDT 2025:hcp_fix_multi_run: Check all_fMRI_data_hp0.ica/.fix_2b_predict.log for log output from component classification
Fri Oct 10 11:03:47 EDT 2025:hcp_fix_multi_run: Check all_fMRI_data_hp0.ica/.fix.log for log output from cleanup stage
FIX Feature extraction for Melodic output directory: all_fMRI_data_hp0.ica
create edge masks
run FAST
registration of standard space masks
extract features
FIX Classifying components in Melodic directory: all_fMRI_data_hp0.ica using training file: /project/6001995/coopapap/scripts/HCPpipelines-master/fix/training_files/HCP_Style_Single_Multirun_Dedrift.RData and threshold 10
No valid labelling file specified
Fri Oct 10 11:50:41 EDT 2025:hcp_fix_multi_run: Done running FIX
Could not find a supported file with prefix "all_fMRI_data_hp0.ica/filtered_func_data_clean"
Fri Oct 10 11:50:41 EDT 2025:hcp_fix_multi_run: While running '/project/6001995/coopapap/scripts/HCPpipelines-master/ICAFIX/hcp_fix_multi_run --fmri-names=/scratch/coopapap/data/MGH/HCPNaming/glaucoma/15_scan1/MNINonLinear/Results/tfMRI_TASK1_AP/tfMRI_TASK1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/15_scan1/MNINonLinear/Results/tfMRI_TASK2_AP/tfMRI_TASK2_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/15_scan1/MNINonLinear/Results/tfMRI_TASK3_AP/tfMRI_TASK3_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/15_scan1/MNINonLinear/Results/tfMRI_TASK4_AP/tfMRI_TASK4_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/15_scan1/MNINonLinear/Results/rfMRI_REST1_AP/rfMRI_REST1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/15_scan1/MNINonLinear/Results/tfMRI_MOVIE1_AP/tfMRI_MOVIE1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/15_scan1/MNINonLinear/Results/tfMRI_MOVIE2_AP/tfMRI_MOVIE2_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/15_scan1/MNINonLinear/Results/tfMRI_MOVIE3_AP/tfMRI_MOVIE3_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/15_scan1/MNINonLinear/Results/tfMRI_MOVIE4_AP/tfMRI_MOVIE4_AP --high-pass=0 --concat-fmri-name=/scratch/coopapap/data/MGH/HCPNaming/glaucoma/15_scan1/MNINonLinear/Results/all_fMRI_data/all_fMRI_data --motion-regression=FALSE --training-file=HCP_Style_Single_Multirun_Dedrift.RData --fix-threshold=10 --delete-intermediates=FALSE --config= --processing-mode=HCPStyleData':
Fri Oct 10 11:50:41 EDT 2025:hcp_fix_multi_run: ERROR: '/cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/fsl/6.0.7.7/bin/immv' command failed with return code: 1
Fri Oct 10 11:50:41 EDT 2025:hcp_fix_multi_run: ERROR: '/cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/fsl/6.0.7.7/bin/immv' command failed with return code: 1
===> ERROR: Command returned with nonzero exit code
---------------------------------------------------
script: hcp_fix_multi_run
stopped at line: 909
call: $FSLDIR/bin/immv ${concatfmrihp}.ica/filtered_func_data_clean ${concatfmrihp}_clean
expanded call: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/fsl/6.0.7.7/bin/immv all_fMRI_data_hp0.ica/filtered_func_data_clean all_fMRI_data_hp0_clean
hostname: rl21703
exit code: 1
---------------------------------------------------
===> Aborting execution!
Fri Oct 10 10:07:23 EDT 2025:hcp_fix_multi_run: melodic_cmd: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/fsl/6.0.7.7/bin/melodic -i all_fMRI_data_hp0_vnts -o all_fMRI_data_hp0.ica/filtered_func_data.ica --nobet --report --Oall --tr=0.937000 --vn --dim=328 -m all_fMRI_data_brain_mask
Fri Oct 10 11:03:34 EDT 2025:hcp_fix_multi_run: melodic has been run: return_code = 0
Fri Oct 10 11:03:47 EDT 2025:hcp_fix_multi_run: Running FIX
Fri Oct 10 11:03:47 EDT 2025:hcp_fix_multi_run: using training data file: /project/6001995/coopapap/scripts/HCPpipelines-master/fix/training_files/HCP_Style_Single_Multirun_Dedrift.RData
Fri Oct 10 11:03:47 EDT 2025:hcp_fix_multi_run: fix_cmd: /project/6001995/coopapap/scripts/HCPpipelines-master/fix/fix all_fMRI_data_hp0.ica /project/6001995/coopapap/scripts/HCPpipelines-master/fix/training_files/HCP_Style_Single_Multirun_Dedrift.RData 10
Fri Oct 10 11:03:47 EDT 2025:hcp_fix_multi_run: Check all_fMRI_data_hp0.ica/fix/logMatlab.txt for log output from feature extraction
Fri Oct 10 11:03:47 EDT 2025:hcp_fix_multi_run: Check all_fMRI_data_hp0.ica/.fix_2b_predict.log for log output from component classification
Fri Oct 10 11:03:47 EDT 2025:hcp_fix_multi_run: Check all_fMRI_data_hp0.ica/.fix.log for log output from cleanup stage
FIX Feature extraction for Melodic output directory: all_fMRI_data_hp0.ica
create edge masks
run FAST
registration of standard space masks
extract features
FIX Classifying components in Melodic directory: all_fMRI_data_hp0.ica using training file: /project/6001995/coopapap/scripts/HCPpipelines-master/fix/training_files/HCP_Style_Single_Multirun_Dedrift.RData and threshold 10
No valid labelling file specified
Fri Oct 10 11:50:41 EDT 2025:hcp_fix_multi_run: Done running FIX
Could not find a supported file with prefix "all_fMRI_data_hp0.ica/filtered_func_data_clean"
Fri Oct 10 11:50:41 EDT 2025:hcp_fix_multi_run: While running '/project/6001995/coopapap/scripts/HCPpipelines-master/ICAFIX/hcp_fix_multi_run --fmri-names=/scratch/coopapap/data/MGH/HCPNaming/glaucoma/15_scan1/MNINonLinear/Results/tfMRI_TASK1_AP/tfMRI_TASK1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/15_scan1/MNINonLinear/Results/tfMRI_TASK2_AP/tfMRI_TASK2_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/15_scan1/MNINonLinear/Results/tfMRI_TASK3_AP/tfMRI_TASK3_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/15_scan1/MNINonLinear/Results/tfMRI_TASK4_AP/tfMRI_TASK4_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/15_scan1/MNINonLinear/Results/rfMRI_REST1_AP/rfMRI_REST1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/15_scan1/MNINonLinear/Results/tfMRI_MOVIE1_AP/tfMRI_MOVIE1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/15_scan1/MNINonLinear/Results/tfMRI_MOVIE2_AP/tfMRI_MOVIE2_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/15_scan1/MNINonLinear/Results/tfMRI_MOVIE3_AP/tfMRI_MOVIE3_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/15_scan1/MNINonLinear/Results/tfMRI_MOVIE4_AP/tfMRI_MOVIE4_AP --high-pass=0 --concat-fmri-name=/scratch/coopapap/data/MGH/HCPNaming/glaucoma/15_scan1/MNINonLinear/Results/all_fMRI_data/all_fMRI_data --motion-regression=FALSE --training-file=HCP_Style_Single_Multirun_Dedrift.RData --fix-threshold=10 --delete-intermediates=FALSE --config= --processing-mode=HCPStyleData':
Fri Oct 10 11:50:41 EDT 2025:hcp_fix_multi_run: ERROR: '/cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/fsl/6.0.7.7/bin/immv' command failed with return code: 1
Fri Oct 10 11:50:41 EDT 2025:hcp_fix_multi_run: ERROR: '/cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/fsl/6.0.7.7/bin/immv' command failed with return code: 1
===> ERROR: Command returned with nonzero exit code
---------------------------------------------------
script: hcp_fix_multi_run
stopped at line: 909
call: $FSLDIR/bin/immv ${concatfmrihp}.ica/filtered_func_data_clean ${concatfmrihp}_clean
expanded call: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/fsl/6.0.7.7/bin/immv all_fMRI_data_hp0.ica/filtered_func_data_clean all_fMRI_data_hp0_clean
hostname: rl21703
exit code: 1
---------------------------------------------------
===> Aborting execution!
and I do notice that the subjects I have successfully processed in the past had a file named "prefiltered_func_data_mcf_conf_hp_clean.nii.gz" in their .../MNINonLinear/Results/all_fMRI_data/all_fMRI_data_hp0.ica/mc folder, whilst this subject does not have that file.
I wonder if this file's absence is to do with the "No valid labelling file specified" that I see in the output log?
A glimpse into the parameters I have set for this processing step are:
fMRINames="tfMRI_TASK1_AP@tfMRI_TASK2_AP@tfMRI_TASK3_AP@tfMRI_TASK4_AP@rfMRI_REST1_AP@tfMRI_MOVIE1_AP@tfMRI_MOVIE2_AP@tfMRI_MOVIE3_AP@tfMRI_MOVIE4_AP"
ConcatNames="all_fMRI_data"
bandpass=0 #changed from 2000 to 0 since it apparently reduces the computational load
domot=FALSE
MRTrainingData=HCP_Style_Single_Multirun_Dedrift.RData
SRTrainingData=HCP_hp2000.RData
I wonder if this is enough information for you to provide a pointer/solution?
Tim Coalson
Nov 21, 2025, 5:20:07 PM11/21/25
to hcp-...@humanconnectome.org
We recommend using pyfix instead of legacy fix when feasible (use a recent version of FSL 6 and leave FSL_FIXDIR unset). "No valid labelling file specified" may mean that legacy R-based fix failed at an earlier step, and it tends to put the actual error message into some other log file instead of reporting it to the user.
Tim
--
You received this message because you are subscribed to the Google Groups "HCP-Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to hcp-users+...@humanconnectome.org.
To view this discussion visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/34f4ed84-b210-4dd6-b4a0-e00c7fddbb41n%40humanconnectome.org.
Message has been deleted
Austin Cooper
Nov 24, 2025, 7:09:21 AM11/24/25
to HCP-Users, tim.c...@gmail.com
Thanks Tim. The FSL module I'm using is fsl/6.0.7.18 with r/4.3.1. I also have easy access to fsl/6.0.7.7. I believe I used fsl/6.0.1 when running this with another compute cluster, and perhaps this module is more adept for this pipeline? Any insights?
Next, I see that
FSL_FIXDIR is set to FSL_FIXDIR=$HCPPIPEDIR/fix in the setupHCPPipeline script... should I remove this line?
I also see this type of warning come up in many different locations of the output text file:
Detected locale "C" with character encoding "ANSI_X3.4-1968", which is not UTF-8.
Qt depends on a UTF-8 locale, and has switched to "C.UTF-8" instead.
If this causes problems, reconfigure your locale. See the locale(1) manual for more information.
Qt depends on a UTF-8 locale, and has switched to "C.UTF-8" instead.
If this causes problems, reconfigure your locale. See the locale(1) manual for more information.
Any pointers regarding these would be greatly appreciated!
Tim Coalson
Nov 24, 2025, 4:41:07 PM11/24/25
to Austin Cooper, HCP-Users
Commenting out the FSL_FIXDIR line should switch to python fix, yes.
That warning is harmless. QT6 apparently disagrees with "LC_ALL=C", which we have set for reproducibility purposes. We may change that to "LC_ALL=C.UTF-8" at some point to reduce the warning messages.
Tim
Austin Cooper
Jan 16, 2026, 1:21:57 PM (2 days ago) Jan 16
to HCP-Users, tim.c...@gmail.com, HCP-Users, Austin Cooper
Hey Time!
I'm still having issues with this problem specific to the FSL_FIXDIR.
I'm getting an error saying that the environment variable must be set (see highlighted below):
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /home/coopapap/.local/easybuild/software/2023/x86-64-v3/Core/freesurfer/6.0.1
FSFAST_HOME /home/coopapap/.local/easybuild/software/2023/x86-64-v3/Core/freesurfer/6.0.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /home/coopapap/.local/easybuild/software/2023/x86-64-v3/Core/freesurfer/6.0.1/subjects
MNI_DIR /home/coopapap/.local/easybuild/software/2023/x86-64-v3/Core/freesurfer/6.0.1/mni
FSL_DIR /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/fsl/6.0.7.7
the subject being processed is 17
##############################################################
##############################################################
##############################################################
############## running IcaFixProcessingBatch.sh ##############
##############################################################
##############################################################
##############################################################
-- IcaFixProcessingBatch.sh: Specified Command-Line Options: -- Start --
StudyFolder: /scratch/coopapap/data/MGH/HCPNaming/glaucoma
Subjlist: 17
EnvironmentScript: /project/6001995/coopapap/scripts/HCPpipelines-master/Examples/glaucoma_scripts/SetUpHCPPipeline.sh
FixDir: /project/6001995/coopapap/scripts/HCPpipelines-master/fix
RunLocal: FALSE
-- IcaFixProcessingBatch.sh: Specified Command-Line Options: -- End --
17
InputFile: /scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK1_AP/tfMRI_TASK1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK2_AP/tfMRI_TASK2_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK3_AP/tfMRI_TASK3_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK4_AP/tfMRI_TASK4_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/rfMRI_REST1_AP/rfMRI_REST1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE1_AP/tfMRI_MOVIE1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE2_AP/tfMRI_MOVIE2_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE3_AP/tfMRI_MOVIE3_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE4_AP/tfMRI_MOVIE4_AP
About to run: /project/6001995/coopapap/scripts/HCPpipelines-master/ICAFIX/hcp_fix_multi_run --fmri-names=/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK1_AP/tfMRI_TASK1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK2_AP/tfMRI_TASK2_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK3_AP/tfMRI_TASK3_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK4_AP/tfMRI_TASK4_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/rfMRI_REST1_AP/rfMRI_REST1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE1_AP/tfMRI_MOVIE1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE2_AP/tfMRI_MOVIE2_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE3_AP/tfMRI_MOVIE3_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE4_AP/tfMRI_MOVIE4_AP --high-pass=0 --concat-fmri-name=/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/all_fMRI_data/all_fMRI_data --motion-regression=FALSE --training-file=HCP_Style_Single_Multirun_Dedrift.RData --fix-threshold=10 --delete-intermediates=FALSE --config= --processing-mode=HCPStyleData
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: arguments: --fmri-names=/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK1_AP/tfMRI_TASK1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK2_AP/tfMRI_TASK2_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK3_AP/tfMRI_TASK3_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK4_AP/tfMRI_TASK4_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/rfMRI_REST1_AP/rfMRI_REST1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE1_AP/tfMRI_MOVIE1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE2_AP/tfMRI_MOVIE2_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE3_AP/tfMRI_MOVIE3_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE4_AP/tfMRI_MOVIE4_AP --high-pass=0 --concat-fmri-name=/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/all_fMRI_data/all_fMRI_data --motion-regression=FALSE --training-file=HCP_Style_Single_Multirun_Dedrift.RData --fix-threshold=10 --delete-intermediates=FALSE --config= --processing-mode=HCPStyleData
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: fmrilist: /scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK1_AP/tfMRI_TASK1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK2_AP/tfMRI_TASK2_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK3_AP/tfMRI_TASK3_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK4_AP/tfMRI_TASK4_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/rfMRI_REST1_AP/rfMRI_REST1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE1_AP/tfMRI_MOVIE1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE2_AP/tfMRI_MOVIE2_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE3_AP/tfMRI_MOVIE3_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE4_AP/tfMRI_MOVIE4_AP
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: hp: 0
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: ConcatName: /scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/all_fMRI_data/all_fMRI_data
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: doMotionRegression: FALSE
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: TrainingData: HCP_Style_Single_Multirun_Dedrift.RData
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: FixThresh: 10
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: DeleteIntermediates: FALSE
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: RewishartThresh: 0
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: volwisharts: 2
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: ciftiwisharts: 3
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: icadimmode: default
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: ProcessingMode: HCPStyleData
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: HCPPIPEDIR: /project/6001995/coopapap/scripts/HCPpipelines-master
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: CARET7DIR: /cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/Compiler/gcccore/connectomeworkbench/2.0.1/bin
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: FSLDIR: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/fsl/6.0.7.7
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: While running '/project/6001995/coopapap/scripts/HCPpipelines-master/ICAFIX/hcp_fix_multi_run --fmri-names=/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK1_AP/tfMRI_TASK1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK2_AP/tfMRI_TASK2_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK3_AP/tfMRI_TASK3_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK4_AP/tfMRI_TASK4_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/rfMRI_REST1_AP/rfMRI_REST1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE1_AP/tfMRI_MOVIE1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE2_AP/tfMRI_MOVIE2_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE3_AP/tfMRI_MOVIE3_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE4_AP/tfMRI_MOVIE4_AP --high-pass=0 --concat-fmri-name=/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/all_fMRI_data/all_fMRI_data --motion-regression=FALSE --training-file=HCP_Style_Single_Multirun_Dedrift.RData --fix-threshold=10 --delete-intermediates=FALSE --config= --processing-mode=HCPStyleData':
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: While running '/project/6001995/coopapap/scripts/HCPpipelines-master/ICAFIX/hcp_fix_multi_run --fmri-names=/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK1_AP/tfMRI_TASK1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK2_AP/tfMRI_TASK2_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK3_AP/tfMRI_TASK3_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK4_AP/tfMRI_TASK4_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/rfMRI_REST1_AP/rfMRI_REST1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE1_AP/tfMRI_MOVIE1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE2_AP/tfMRI_MOVIE2_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE3_AP/tfMRI_MOVIE3_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE4_AP/tfMRI_MOVIE4_AP --high-pass=0 --concat-fmri-name=/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/all_fMRI_data/all_fMRI_data --motion-regression=FALSE --training-file=HCP_Style_Single_Multirun_Dedrift.RData --fix-threshold=10 --delete-intermediates=FALSE --config= --processing-mode=HCPStyleData':
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: ERROR: FSL_FIXDIR environment variable must be set
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: ERROR: FSL_FIXDIR environment variable must be set
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: ABORTING
FREESURFER_HOME /home/coopapap/.local/easybuild/software/2023/x86-64-v3/Core/freesurfer/6.0.1
FSFAST_HOME /home/coopapap/.local/easybuild/software/2023/x86-64-v3/Core/freesurfer/6.0.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /home/coopapap/.local/easybuild/software/2023/x86-64-v3/Core/freesurfer/6.0.1/subjects
MNI_DIR /home/coopapap/.local/easybuild/software/2023/x86-64-v3/Core/freesurfer/6.0.1/mni
FSL_DIR /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/fsl/6.0.7.7
the subject being processed is 17
##############################################################
##############################################################
##############################################################
############## running IcaFixProcessingBatch.sh ##############
##############################################################
##############################################################
##############################################################
-- IcaFixProcessingBatch.sh: Specified Command-Line Options: -- Start --
StudyFolder: /scratch/coopapap/data/MGH/HCPNaming/glaucoma
Subjlist: 17
EnvironmentScript: /project/6001995/coopapap/scripts/HCPpipelines-master/Examples/glaucoma_scripts/SetUpHCPPipeline.sh
FixDir: /project/6001995/coopapap/scripts/HCPpipelines-master/fix
RunLocal: FALSE
-- IcaFixProcessingBatch.sh: Specified Command-Line Options: -- End --
17
InputFile: /scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK1_AP/tfMRI_TASK1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK2_AP/tfMRI_TASK2_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK3_AP/tfMRI_TASK3_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK4_AP/tfMRI_TASK4_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/rfMRI_REST1_AP/rfMRI_REST1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE1_AP/tfMRI_MOVIE1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE2_AP/tfMRI_MOVIE2_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE3_AP/tfMRI_MOVIE3_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE4_AP/tfMRI_MOVIE4_AP
About to run: /project/6001995/coopapap/scripts/HCPpipelines-master/ICAFIX/hcp_fix_multi_run --fmri-names=/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK1_AP/tfMRI_TASK1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK2_AP/tfMRI_TASK2_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK3_AP/tfMRI_TASK3_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK4_AP/tfMRI_TASK4_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/rfMRI_REST1_AP/rfMRI_REST1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE1_AP/tfMRI_MOVIE1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE2_AP/tfMRI_MOVIE2_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE3_AP/tfMRI_MOVIE3_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE4_AP/tfMRI_MOVIE4_AP --high-pass=0 --concat-fmri-name=/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/all_fMRI_data/all_fMRI_data --motion-regression=FALSE --training-file=HCP_Style_Single_Multirun_Dedrift.RData --fix-threshold=10 --delete-intermediates=FALSE --config= --processing-mode=HCPStyleData
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: arguments: --fmri-names=/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK1_AP/tfMRI_TASK1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK2_AP/tfMRI_TASK2_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK3_AP/tfMRI_TASK3_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK4_AP/tfMRI_TASK4_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/rfMRI_REST1_AP/rfMRI_REST1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE1_AP/tfMRI_MOVIE1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE2_AP/tfMRI_MOVIE2_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE3_AP/tfMRI_MOVIE3_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE4_AP/tfMRI_MOVIE4_AP --high-pass=0 --concat-fmri-name=/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/all_fMRI_data/all_fMRI_data --motion-regression=FALSE --training-file=HCP_Style_Single_Multirun_Dedrift.RData --fix-threshold=10 --delete-intermediates=FALSE --config= --processing-mode=HCPStyleData
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: fmrilist: /scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK1_AP/tfMRI_TASK1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK2_AP/tfMRI_TASK2_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK3_AP/tfMRI_TASK3_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK4_AP/tfMRI_TASK4_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/rfMRI_REST1_AP/rfMRI_REST1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE1_AP/tfMRI_MOVIE1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE2_AP/tfMRI_MOVIE2_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE3_AP/tfMRI_MOVIE3_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE4_AP/tfMRI_MOVIE4_AP
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: hp: 0
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: ConcatName: /scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/all_fMRI_data/all_fMRI_data
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: doMotionRegression: FALSE
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: TrainingData: HCP_Style_Single_Multirun_Dedrift.RData
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: FixThresh: 10
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: DeleteIntermediates: FALSE
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: RewishartThresh: 0
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: volwisharts: 2
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: ciftiwisharts: 3
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: icadimmode: default
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: ProcessingMode: HCPStyleData
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: HCPPIPEDIR: /project/6001995/coopapap/scripts/HCPpipelines-master
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: CARET7DIR: /cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v4/Compiler/gcccore/connectomeworkbench/2.0.1/bin
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: FSLDIR: /cvmfs/restricted.computecanada.ca/easybuild/software/2023/x86-64-v3/Core/fsl/6.0.7.7
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: While running '/project/6001995/coopapap/scripts/HCPpipelines-master/ICAFIX/hcp_fix_multi_run --fmri-names=/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK1_AP/tfMRI_TASK1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK2_AP/tfMRI_TASK2_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK3_AP/tfMRI_TASK3_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK4_AP/tfMRI_TASK4_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/rfMRI_REST1_AP/rfMRI_REST1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE1_AP/tfMRI_MOVIE1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE2_AP/tfMRI_MOVIE2_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE3_AP/tfMRI_MOVIE3_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE4_AP/tfMRI_MOVIE4_AP --high-pass=0 --concat-fmri-name=/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/all_fMRI_data/all_fMRI_data --motion-regression=FALSE --training-file=HCP_Style_Single_Multirun_Dedrift.RData --fix-threshold=10 --delete-intermediates=FALSE --config= --processing-mode=HCPStyleData':
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: While running '/project/6001995/coopapap/scripts/HCPpipelines-master/ICAFIX/hcp_fix_multi_run --fmri-names=/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK1_AP/tfMRI_TASK1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK2_AP/tfMRI_TASK2_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK3_AP/tfMRI_TASK3_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_TASK4_AP/tfMRI_TASK4_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/rfMRI_REST1_AP/rfMRI_REST1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE1_AP/tfMRI_MOVIE1_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE2_AP/tfMRI_MOVIE2_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE3_AP/tfMRI_MOVIE3_AP@/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/tfMRI_MOVIE4_AP/tfMRI_MOVIE4_AP --high-pass=0 --concat-fmri-name=/scratch/coopapap/data/MGH/HCPNaming/glaucoma/17_scan1/MNINonLinear/Results/all_fMRI_data/all_fMRI_data --motion-regression=FALSE --training-file=HCP_Style_Single_Multirun_Dedrift.RData --fix-threshold=10 --delete-intermediates=FALSE --config= --processing-mode=HCPStyleData':
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: ERROR: FSL_FIXDIR environment variable must be set
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: ERROR: FSL_FIXDIR environment variable must be set
Sun Dec 28 13:27:26 EST 2025:hcp_fix_multi_run: ABORTING
I wonder if there is a simple line that I can add that sets this folder to the folder that will enable this to run through?
Thanks for your help!
Glasser, Matthew
Jan 16, 2026, 1:27:35 PM (2 days ago) Jan 16
to hcp-...@humanconnectome.org, tim.c...@gmail.com, Austin Cooper
Are you using the latest version of the HCP Pipelines?
Matt.
To view this discussion visit
https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/1b53a36d-40ad-4445-ad66-9c0272644feen%40humanconnectome.org.
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Reply all
Reply to author
Forward
0 new messages