ICAfix Single-run/Multi-run Fail to Generate Cleaned Files
Bowen Qin
We met errors while running IcaFixBatchProcessing.sh using either single-run or multi-run FIX:
Tue Jun 8 23:53:21 EDT 2021:hcp_fix_multi_run: Check rfMRI_REST1_RL_TEST_hp2000.ica/.fix.log for log output from cleanup stage
FIX Feature extraction for Melodic output directory: rfMRI_REST1_RL_TEST_hp2000.ica
create edge masks
run FAST
registration of standard space masks
extract features
FIX Classifying components in Melodic directory: rfMRI_REST1_RL_TEST_hp2000.ica using training file: /share/pkg.7/fix/1.06.15/install/training_files/HCP_hp2000.RData and threshold 10
No valid labelling file specified
Wed Jun 9 00:07:08 EDT 2021:hcp_fix_multi_run: Done running FIX
Could not find a supported file with prefix "rfMRI_REST1_RL_TEST_hp2000.ica/filtered_func_data_clean"
Wed Jun 9 00:07:10 EDT 2021:hcp_fix_multi_run: ERROR: '/share/pkg.7/fsl/6.0.4/install/bin/immv' command failed with return code: 1
===> ERROR: Command returned with nonzero exit code
---------------------------------------------------
script: hcp_fix_multi_run
stopped at line: 793
call: $FSLDIR/bin/immv ${concatfmrihp}.ica/filtered_func_data_clean ${concatfmrihp}_clean
expanded call: /share/pkg.7/fsl/6.0.4/install/bin/immv rfMRI_REST1_RL_TEST_hp2000.ica/filtered_func_data_clean rfMRI_REST1_RL_TEST_hp2000_clean
exit code: 1
---------------------------------------------------
===> Aborting execution!
wb_command -cifti-dilate ${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas${ProcString}.dtseries.nii COLUMN 0 5 ${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas${ProcString}.dtseries.nii -left-surface ${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR${LowResMesh}k/${Subject}.R.midthickness.${LowResMesh}k_fs_LR.surf.gii -right-surface ${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR${LowResMesh}k/${Subject}.R.midthickness.${LowResMesh}k_fs_LR.surf.gii -nearest -merged-volume
Harms, Michael
Based on a quick look, I can’t tell if the problem is the customizations that you’ve added to the Batch script have broken something, or if there is some version incompatibility with your R setup.
I’d first try running using the Batch file template in the 4.3.0 release. You’ll need to set the variables in that correctly, but please don’t make other customizations.
Cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: Bowen Qin <bw...@bu.edu>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Wednesday, June 9, 2021 at 1:44 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: "Cheng, Chia Hsin" <chia...@bu.edu>
Subject: [hcp-users] ICAfix Single-run/Multi-run Fail to Generate Cleaned Files
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Glasser, Matthew
Also as described in the FSL FIX website you need to check the R and matlab logfiles for any errors related to “No valid labelling file specified.”
Matt.
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