[RESOLVED] Trouble running hcp_icafix in v0.99.2

Issues
1

Hi, I am trying to run hcp_icafix on all the resting data in a study (2 pairs of reverse PE encoded scans), and my main goal is the concatenated output file (fMRI_CONCAT_ALL). The only functional scans in the study are resting scans, so I let the command run with the default settings (i.e., without specifying which bolds to use). Everything seems to run as expected for the first ~2hrs and then errors out. I combed through the error messages in the log files but it’s not clear what the exact problem is – any advice is appreciated, as always! Thanks so much.

Call:

DIR=/gpfs/gibbs/pi/n3/Studies/
my_study=ExTx3
my_study_folder=$DIR/$my_study
batch_file=$my_study_folder/processing/batch2024.txt

 qunex hcp_icafix \
	--batchfile="$my_study_folder/processing/batch2024.txt" \
	--overwrite="yes" \
	--logfolder="$my_study_folder/processing/logs/icafix/" \
	--hcp_matlab_mode="interpreted" \
	--sessionsfolder="$my_study_folder/sessions"  \
	--scheduler="SLURM,time=1-00:00:00,ntasks=1,cpus-per-task=2,mem-per-cpu=64000,partition=day,jobname=icafix"

Logs:

log files are here:

/gpfs/gibbs/pi/n3/Studies//ExTx3/processing/logs/icafix/

And the last few lines (with error messages) of a sample log file are pasted here:

> (qunex) [login1 comlogs]$ cat error_hcp_icafix_fMRI_CONCAT_ALL_pb10215_2024-04-22_13.41.05.341654.log
> # Generated by QuNex 0.99.2 on 2024-04-22_13.41.05.341654#
> ------------------------------------------------------------
> Running external command via QuNex:
> 
> /gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/ICAFIX/hcp_fix_multi_run                 --fmri-names="/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb10215/hcp/pb10215/MNINonLinear/Results/1/1@/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb10215/hcp/pb10215/MNINonLinear/Results/2/2@/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb10215/hcp/pb10215/MNINonLinear/Results/3/3@/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb10215/hcp/pb10215/MNINonLinear/Results/4/4"                 --high-pass=0                 --concat-fmri-name="/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb10215/hcp/pb10215/MNINonLinear/Results/fMRI_CONCAT_ALL/fMRI_CONCAT_ALL"
> 

.....

> >> Mon Apr 22 14:45:07 EDT 2024:hcp_fix_multi_run: Dim: 221
> Mon Apr 22 14:45:07 EDT 2024:hcp_fix_multi_run: Running MELODIC located at: /gpfs/gibbs/pi/n3/software/fsl/fsl/share/fsl/bin/melodic
> Mon Apr 22 14:45:07 EDT 2024:hcp_fix_multi_run: melodic_cmd: /gpfs/gibbs/pi/n3/software/fsl/fsl/share/fsl/bin/melodic -i fMRI_CONCAT_ALL_hp0_vnts -o fMRI_CONCAT_ALL_hp0.ica/filtered_func_data.ica --nobet --report --Oall --tr=0.800000 --vn --dim=221 -m fMRI_CONCAT_ALL_brain_mask
> Mon Apr 22 15:31:57 EDT 2024:hcp_fix_multi_run: melodic has been run: return_code = 0
> Mon Apr 22 15:32:11 EDT 2024:hcp_fix_multi_run: Running FIX
> Mon Apr 22 15:32:11 EDT 2024:hcp_fix_multi_run: training data file not specified
> Mon Apr 22 15:32:11 EDT 2024:hcp_fix_multi_run: using training data file: /gpfs/gibbs/pi/n3/software/fsl/fix/training_files/HCP_Style_Single_Multirun_Dedrift.RData
> Mon Apr 22 15:32:11 EDT 2024:hcp_fix_multi_run: fix_cmd: /gpfs/gibbs/pi/n3/software/fsl/fix/fix fMRI_CONCAT_ALL_hp0.ica /gpfs/gibbs/pi/n3/software/fsl/fix/training_files/HCP_Style_Single_Multirun_Dedrift.RData 10
> Mon Apr 22 15:32:11 EDT 2024:hcp_fix_multi_run: Check fMRI_CONCAT_ALL_hp0.ica/fix/logMatlab.txt for log output from feature extraction
> Mon Apr 22 15:32:11 EDT 2024:hcp_fix_multi_run: Check fMRI_CONCAT_ALL_hp0.ica/.fix_2b_predict.log for log output from component classification
> Mon Apr 22 15:32:11 EDT 2024:hcp_fix_multi_run: Check fMRI_CONCAT_ALL_hp0.ica/.fix.log for log output from cleanup stage
> FIX Feature extraction for Melodic output directory: fMRI_CONCAT_ALL_hp0.ica
>  create edge masks
>  run FAST
>  registration of standard space masks
>  extract features
> FIX Classifying components in Melodic directory: fMRI_CONCAT_ALL_hp0.ica using training file: /gpfs/gibbs/pi/n3/software/fsl/fix/training_files/HCP_Style_Single_Multirun_Dedrift.RData and threshold 10
> /gpfs/gibbs/pi/n3/software/fsl/fix/fix: line 250: CMD: command not found
> No valid labelling file specified
> Mon Apr 22 16:11:15 EDT 2024:hcp_fix_multi_run: Done running FIX
> Could not find a supported file with prefix "fMRI_CONCAT_ALL_hp0.ica/filtered_func_data_clean"
> Mon Apr 22 16:11:22 EDT 2024:hcp_fix_multi_run: While running '/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/ICAFIX/hcp_fix_multi_run --fmri-names=/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb10215/hcp/pb10215/MNINonLinear/Results/1/1@/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb10215/hcp/pb10215/MNINonLinear/Results/2/2@/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb10215/hcp/pb10215/MNINonLinear/Results/3/3@/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb10215/hcp/pb10215/MNINonLinear/Results/4/4 --high-pass=0 --concat-fmri-name=/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb10215/hcp/pb10215/MNINonLinear/Results/fMRI_CONCAT_ALL/fMRI_CONCAT_ALL':
> Mon Apr 22 16:11:22 EDT 2024:hcp_fix_multi_run: While running '/gpfs/gibbs/pi/n3/software/HCP/HCPpipelines/ICAFIX/hcp_fix_multi_run --fmri-names=/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb10215/hcp/pb10215/MNINonLinear/Results/1/1@/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb10215/hcp/pb10215/MNINonLinear/Results/2/2@/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb10215/hcp/pb10215/MNINonLinear/Results/3/3@/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb10215/hcp/pb10215/MNINonLinear/Results/4/4 --high-pass=0 --concat-fmri-name=/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb10215/hcp/pb10215/MNINonLinear/Results/fMRI_CONCAT_ALL/fMRI_CONCAT_ALL':
> Mon Apr 22 16:11:22 EDT 2024:hcp_fix_multi_run: ERROR: '/gpfs/gibbs/pi/n3/software/fsl/fsl/bin/immv' command failed with return code: 1
> Mon Apr 22 16:11:22 EDT 2024:hcp_fix_multi_run: ERROR: '/gpfs/gibbs/pi/n3/software/fsl/fsl/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: /gpfs/gibbs/pi/n3/software/fsl/fsl/bin/immv fMRI_CONCAT_ALL_hp0.ica/filtered_func_data_clean fMRI_CONCAT_ALL_hp0_clean
>        hostname: r815u03n05.grace.ycrc.yale.edu
>       exit code: 1
> ---------------------------------------------------
> 
> ===> Aborting execution!
2

Hi Rachael,

You should be running QuNex through the container as the system on Grace cannot be reliably setup to work with QuNex. Try this:

DIR=/gpfs/gibbs/pi/n3/Studies/
my_study=ExTx3
my_study_folder=$DIR/$my_study
batch_file=$my_study_folder/processing/batch2024.txt

qunex_container hcp_icafix \
  --batchfile="$my_study_folder/processing/batch2024.txt" \
  --overwrite="yes" \
  --logfolder="$my_study_folder/processing/logs/icafix/" \
  --sessionsfolder="$my_study_folder/sessions"  \
  --container="/gpfs/gibbs/pi/n3/software/Singularity/qunex_suite-0.99.2d.sif" \
  --scheduler="SLURM,time=12:00:00,cpus-per-task=2,mem-per-cpu=32G,partition=day,jobname=icafix"

Let me know how it goes.

Best, Jure

3

Hi Jure, appreciate the quick reply! Thanks for bringing me up to speed, I will use the container on Grace from here on. I tried what you suggested (as written) and it errors out after a few minutes:

> (qunex) [login2 comlogs]$ cat error_hcp_icafix_fMRI_CONCAT_ALL_pb8993_2024-04-23_11.40.08.123007.log
> # Generated by QuNex 0.99.2 on 2024-04-23_11.40.08.123007#
> ------------------------------------------------------------
> Running external command via QuNex:
> 
> /opt/HCP/HCPpipelines/ICAFIX/hcp_fix_multi_run                 --fmri-names="/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb8993/hcp/pb8993/MNINonLinear/Results/1/1@/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb8993/hcp/pb8993/MNINonLinear/Results/2/2@/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb8993/hcp/pb8993/MNINonLinear/Results/3/3@/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb8993/hcp/pb8993/MNINonLinear/Results/4/4"                 --high-pass=0                 --concat-fmri-name="/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb8993/hcp/pb8993/MNINonLinear/Results/fMRI_CONCAT_ALL/fMRI_CONCAT_ALL"
> 
> Test file: 
> /gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb8993/hcp/pb8993/MNINonLinear/Results/fMRI_CONCAT_ALL/fMRI_CONCAT_ALL_hp0_clean.nii.gz
> ------------------------------------------------------------
> 
> Tue Apr 23 11:40:08 EDT 2024:hcp_fix_multi_run: arguments: --fmri-names=/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb8993/hcp/pb8993/MNINonLinear/Results/1/1@/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb8993/hcp/pb8993/MNINonLinear/Results/2/2@/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb8993/hcp/pb8993/MNINonLinear/Results/3/3@/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb8993/hcp/pb8993/MNINonLinear/Results/4/4 --high-pass=0 --concat-fmri-name=/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb8993/hcp/pb8993/MNINonLinear/Results/fMRI_CONCAT_ALL/fMRI_CONCAT_ALL
> Tue Apr 23 11:40:08 EDT 2024:hcp_fix_multi_run: fmrilist: /gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb8993/hcp/pb8993/MNINonLinear/Results/1/1@/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb8993/hcp/pb8993/MNINonLinear/Results/2/2@/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb8993/hcp/pb8993/MNINonLinear/Results/3/3@/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb8993/hcp/pb8993/MNINonLinear/Results/4/4
> Tue Apr 23 11:40:08 EDT 2024:hcp_fix_multi_run: hp: 0
> Tue Apr 23 11:40:08 EDT 2024:hcp_fix_multi_run: ConcatName: /gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb8993/hcp/pb8993/MNINonLinear/Results/fMRI_CONCAT_ALL/fMRI_CONCAT_ALL
> Tue Apr 23 11:40:08 EDT 2024:hcp_fix_multi_run: doMotionRegression: FALSE
> Tue Apr 23 11:40:08 EDT 2024:hcp_fix_multi_run: TrainingData: 
> Tue Apr 23 11:40:08 EDT 2024:hcp_fix_multi_run: FixThresh: 10
> Tue Apr 23 11:40:08 EDT 2024:hcp_fix_multi_run: DeleteIntermediates: FALSE
> Tue Apr 23 11:40:08 EDT 2024:hcp_fix_multi_run: RewishartThresh: 0
> Tue Apr 23 11:40:08 EDT 2024:hcp_fix_multi_run: volwisharts: 2
> Tue Apr 23 11:40:08 EDT 2024:hcp_fix_multi_run: ciftiwisharts: 3
> Tue Apr 23 11:40:08 EDT 2024:hcp_fix_multi_run: icadimmode: default
> Tue Apr 23 11:40:08 EDT 2024:hcp_fix_multi_run: ProcessingMode: HCPStyleData
> Tue Apr 23 11:40:08 EDT 2024:hcp_fix_multi_run: HCPPIPEDIR: /opt/HCP/HCPpipelines
> Tue Apr 23 11:40:08 EDT 2024:hcp_fix_multi_run: CARET7DIR: /opt/workbench/workbench/bin_rh_linux64
> Tue Apr 23 11:40:08 EDT 2024:hcp_fix_multi_run: FSLDIR: /opt/fsl/fsl
> Tue Apr 23 11:40:08 EDT 2024:hcp_fix_multi_run: FSL_FIXDIR: /opt/fsl/fix
> Tue Apr 23 11:40:08 EDT 2024:hcp_fix_multi_run: HCPCIFTIRWDIR: /opt/HCP/HCPpipelines/global/matlab/cifti-matlab
> Tue Apr 23 11:40:08 EDT 2024:hcp_fix_multi_run: Showing HCP Pipelines version
> Post-v4.7.0-5df95e4
> Tue Apr 23 11:40:11 EDT 2024:hcp_fix_multi_run: Showing Connectome Workbench (wb_command) version
> Connectome Workbench
> Type: Command Line Application
> Version: 1.5.0
> Qt Compiled Version: 5.7.0
> Qt Runtime Version: 5.7.0
> Commit: 76441605d20536d81034a64c9d34ec393aa528b9
> Commit Date: 2021-02-16 13:46:47 -0600
> Compiled with OpenMP: YES
> Compiler: g++ (/export/gcc-4.8.5/bin)
> Compiler Version: 4.8.5
> Compiled Debug: NO
> Operating System: Linux
> Tue Apr 23 11:40:11 EDT 2024:hcp_fix_multi_run: Showing FSL version
> Tue Apr 23 11:40:11 EDT 2024:hcp_fix_multi_run: INFO: Determined that the FSL version in use is 6.0.7.1
> Tue Apr 23 11:40:11 EDT 2024:hcp_fix_multi_run: FSL version: 6.0.7.1
> Tue Apr 23 11:40:11 EDT 2024:hcp_fix_multi_run: FIX version: 1.06.15
> Tue Apr 23 11:40:11 EDT 2024:hcp_fix_multi_run: FSL_FIX_MATLAB_MODE: 0
> Tue Apr 23 11:40:11 EDT 2024:hcp_fix_multi_run: hp=0 corresponds to a linear detrend
> Tue Apr 23 11:40:11 EDT 2024:hcp_fix_multi_run: PWD: /gpfs/gibbs/pi/n3/Studies/ExTx3
> Tue Apr 23 11:40:11 EDT 2024:hcp_fix_multi_run: Looping over files and doing highpass to each of them
> Tue Apr 23 11:40:11 EDT 2024:hcp_fix_multi_run: Top of loop through fmris: fmri: /gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb8993/hcp/pb8993/MNINonLinear/Results/1/1
> parsed 'TCS - MEAN' as 'TCS - MEAN'
> Tue Apr 23 11:44:07 EDT 2024:hcp_fix_multi_run: tr: 0.800000
> Tue Apr 23 11:44:07 EDT 2024:hcp_fix_multi_run: processing FMRI file 1 with highpass 0
> Tue Apr 23 11:44:07 EDT 2024:hcp_fix_multi_run: MATLAB_COMPILER_RUNTIME: /opt/matlab/v93
> Tue Apr 23 11:44:07 EDT 2024:hcp_fix_multi_run: Run compiled MATLAB with command...
> Tue Apr 23 11:44:07 EDT 2024:hcp_fix_multi_run: /opt/fsl/fix/call_matlab.sh -c /opt/matlab/v93 -b /opt/HCP/HCPpipelines/ICAFIX/scripts/Compiled_functionhighpassandvariancenormalize -f functionhighpassandvariancenormalize 0.800000 0 1 /opt/workbench/workbench/bin_rh_linux64/wb_command  2 3 default
> ------------------------------------------
> Setting up environment variables
> ---
> LD_LIBRARY_PATH is .:/opt/matlab/v93/runtime/glnxa64:/opt/matlab/v93/bin/glnxa64:/opt/matlab/v93/sys/os/glnxa64:/opt/matlab/v93/sys/opengl/lib/glnxa64
> Warning: functionhighpassandvariancenormalize: hp=0 will be interpreted as polynomial detrending of order 1
> > In functionhighpassandvariancenormalize (line 86)
> Elapsed time is 2.482818 seconds.
> Warning: MATLAB was unable to open a pseudo-tty: Unknown error [0,1].
> The unix() and ! commands will not work in this MATLAB session.  Other commands which depend upon unix() and ! will also fail.  Your system may be running low on resources.  If the problem persists after a reboot, check with your system administrator and confirm that your pty subsystem is properly configured.
> > In dos (line 66)
>   In save_avw_hdr (line 28)
>   In save_avw (line 26)
>   In functionhighpassandvariancenormalize (line 121)
> Error using matlab.system.internal.executeCommand
> The unix() and ! commands are disabled.
> 
> Error in dos (line 66)
> 
> 
> Error in save_avw_hdr (line 28)
> 
> 
> Error in save_avw (line 26)
> 
> 
> Error in functionhighpassandvariancenormalize (line 121)
> 
> MATLAB:bang:CommandsDisabled
> Tue Apr 23 11:44:19 EDT 2024:hcp_fix_multi_run: While running '/opt/HCP/HCPpipelines/ICAFIX/hcp_fix_multi_run --fmri-names=/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb8993/hcp/pb8993/MNINonLinear/Results/1/1@/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb8993/hcp/pb8993/MNINonLinear/Results/2/2@/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb8993/hcp/pb8993/MNINonLinear/Results/3/3@/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb8993/hcp/pb8993/MNINonLinear/Results/4/4 --high-pass=0 --concat-fmri-name=/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb8993/hcp/pb8993/MNINonLinear/Results/fMRI_CONCAT_ALL/fMRI_CONCAT_ALL':
> Tue Apr 23 11:44:19 EDT 2024:hcp_fix_multi_run: While running '/opt/HCP/HCPpipelines/ICAFIX/hcp_fix_multi_run --fmri-names=/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb8993/hcp/pb8993/MNINonLinear/Results/1/1@/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb8993/hcp/pb8993/MNINonLinear/Results/2/2@/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb8993/hcp/pb8993/MNINonLinear/Results/3/3@/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb8993/hcp/pb8993/MNINonLinear/Results/4/4 --high-pass=0 --concat-fmri-name=/gpfs/gibbs/pi/n3/Studies/ExTx3/sessions/pb8993/hcp/pb8993/MNINonLinear/Results/fMRI_CONCAT_ALL/fMRI_CONCAT_ALL':
> Tue Apr 23 11:44:19 EDT 2024:hcp_fix_multi_run: ERROR: '/opt/fsl/fix/call_matlab.sh -c /opt/matlab/v93 -b /opt/HCP/HCPpipelines/ICAFIX/scripts/Compiled_functionhighpassandvariancenormalize -f functionhighpassandvariancenormalize 0.800000 0 1 /opt/workbench/workbench/bin_rh_linux64/wb_command  2 3 default' command failed with return code: 255
> Tue Apr 23 11:44:19 EDT 2024:hcp_fix_multi_run: ERROR: '/opt/fsl/fix/call_matlab.sh -c /opt/matlab/v93 -b /opt/HCP/HCPpipelines/ICAFIX/scripts/Compiled_functionhighpassandvariancenormalize -f functionhighpassandvariancenormalize 0.800000 0 1 /opt/workbench/workbench/bin_rh_linux64/wb_command  2 3 default' command failed with return code: 255
> 
> ===> ERROR: Command returned with nonzero exit code
> ---------------------------------------------------
>          script: hcp_fix_multi_run
> stopped at line: 478
>            call: "${matlab_cmd[@]}"
>   expanded call: /opt/fsl/fix/call_matlab.sh -c /opt/matlab/v93 -b /opt/HCP/HCPpipelines/ICAFIX/scripts/Compiled_functionhighpassandvariancenormalize -f functionhighpassandvariancenormalize 0.800000 0 1 /opt/workbench/workbench/bin_rh_linux64/wb_command  2 3 default
>        hostname: r805u25n01.grace.ycrc.yale.edu
>       exit code: 255
> ---------------------------------------------------
> 
> ===> Aborting execution!
4

Hi,

This is a weird issue that we saw only when using the Grace cluster, not sure what is happening there. You could try using a different container for example qunex_suite-0.95.3a.sif.

Alternatively, you could try this:

# init folders
DIR=/gpfs/gibbs/pi/n3/Studies/
my_study=ExTx3
my_study_folder=$DIR/$my_study
batch_file=$my_study_folder/processing/batch2024.txt

# load qunex tools
source $TOOLS/gracesetup.sh
source $TOOLS/qunex/env/qunex_environment.sh

# cleanup old logs
rm -rf $my_study_folder/processing/logs/icafix

qunex hcp_icafix \
  --batchfile="$my_study_folder/processing/batch2024.txt" \
  --overwrite="yes" \
  --logfolder="$my_study_folder/processing/logs/icafix" \
  --sessionsfolder="$my_study_folder/sessions" \
  --hcp_matlab_mode="interpreted" \
  --scheduler="SLURM,time=12:00:00,cpus-per-task=2,mem-per-cpu=32G,partition=day,jobname=icafix"

I do not have access to the study on Grace, so it is hard for me to try things out hands on.

Best, Jure

5

Thanks Jure – unfortunately, I get the same error as above no matter which version of the container I use. I tried four different versions.

Thanks-- this seems to produce the same error as my original attempt (attached, since it is very long).
error_hcp_icafix_fMRI_CONCAT_ALL_pb10215_2024-04-24_10.46.55.676159.log (48.8 KB)

Any ideas for what to try next? I have a deadline to complete this preprocessing by the end of the month.

6

Is there a way for me or for some of my Yale colleagues to get access to this study? Since this is super pressing, this might be the easiest way as I can take a look directly at what is happening.

7

I got access and am doing some tests. I will let you know how it goes.

1 Like
8

Good news :slight_smile:, I managed to successfully run icafix for one of the sessions. I think it might be the easiest if I run everything for all of them now, so I will just do that. You can keep track of the progress in /gpfs/gibbs/pi/n3/Studies/ExTx3/processing/logs/icafix_jd/comlogs.

The issue you are seeing started popping up after the Grace update and should be resolved once we release the next container (0.100.0).

9

Wow, thank you for this very welcome update. I can see that it’s working!

10

hcp_icafix finished successfully for all sessions (see /gpfs/gibbs/pi/n3/Studies/ExTx3/processing/logs/icafix_jd/comlogs). Steps that follow (hcp_msmall …) should now work without any additional interventions.

Best, Jure

1 Like