[RESOLVED] Issue for dwi parcellate

Issues
1

Description:

Hi!

I am having problems getting dwi_parcellate to parcellate the lengths matrix. Even though I use --lengths=‘yes’ the logs show “NOTE --lengths not specified. Assuming default [no]” and the length matrix is not parcellated.

Call:

qunex_container dwi_parcellate   --lengths='yes'   --matrixversion='3'   --parcellationfile='/gpfs01/home/mszspp/Atlases/Tian2020MSA/3T/Cortex-Subcortex/Schaefer2018_200Parcels_7Networks_order_Tian_Subcortex_S1.dlabel.nii'   --outname='Schaefer2018_200Parcels_7Networks_order_Tian_Subcortex_S1'   --waytotal='standard'   --batchfile='/gpfs01/imgshare/BRIGHTMIND//HCP_format/processing/batch.txt'   --overwrite='yes'   --action='copy'   --parsessions='1'   --bash_pre="module load qunex-img/0.100.0"   --bash_post="export STUDY_FOLDER=/gpfs01/imgshare/BRIGHTMIND//HCP_format"   --studyfolder="/gpfs01/imgshare/BRIGHTMIND//HCP_format"   --bind=/gpfs01/imgshare/BRIGHTMIND/:/gpfs01/imgshare/BRIGHTMIND/   --sessions="SN10000107022019SM_MR1"   --parallel_sessions   --container="/gpfs01/software/imaging/QuNex/0.100.0/qunex_suite-0.100.0.sif"   --scheduler="SLURM,time=48:00:00,ntasks=1,cpus-per-task=1,mem-per-cpu=10000,partition=imgcomputeq,qos=img"

Logs:

slurm log: qunex_container_2025-10-22_14.51.19.579254.txt (7.5 KB)

runlog: Log-dwi_parcellate_SN10000107022019SM_MR1_2025-10-22_14.52.55.033358.log (532 Bytes)

comlog: done_dwi_parcellate_SN10000107022019SM_MR1_2025-10-22_14.52.55.033358.log (2.3 KB)

** For an example of how to report an issue, please refer to this post.

2

Hi Daniel,

Yes, this is indeed a bug. The lengths parameter is not passed properly to the command script. I already fixed this. I expect a QuNex version release with this early in November.

If this timeline does not work for you, I prepared a workaround. To apply it, do the following:

1/ Download the dwi_parcellat.sh script below. Say to `/home/oliver/dwi_parcellate.sh`. I patched DWI parcellate so the default in there for lengths is yes.

dwi_parcellate.sh (12.0 KB)

2/ Run QuNex, but bind the patched script over the one in the container:

qunex_container dwi_parcellate \
  ... other params ... \
  --bind="/home/oliver/dwi_parcellate.sh:/opt/qunex/bash/qx_utilities/dwi_parcellate.sh" \
  ... other params ... \

Since you already have a bind above, you need to have both, list them comma separated. Let me know how it goes.

Best, Jure