Summary of what happened:
I’m trying to do DICOM to Nifti conversion through Singularity container and am running into a new error with the latest version of heudiconv. I have previously successfully converted this subject before and when I run the dcm2niix on the terminal just by itself the files get converted successfully to NIFTI so its not a file issue.
Command used (and if a helper script was used, a link to the helper script or the command generated):
#!/bin/bash
#SBATCH --time=04:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=2
#SBATCH --account=PAS2302
subject=$1
session=$2
echo "Starting BIDS conversion for subject" $subject $session
singularity run --cleanenv \
/fs/ess/PAS2302/Subbi/TURBO/TERBO/heudiconv_1.1.0.sif \
-d /fs/ess/PAS2302/Subbi/TURBO/TERBO/data/*/DICOM/{subject}/SCANS/*/DICOM/* \
-o /fs/ess/PCON0341/projects/TERBO/YA/BIDS \
-f /fs/ess/PAS2302/Subbi/TURBO/TERBO/Scripts/TERBO/Heuristic/convert_TURBO_Baylor_SM_YA.py \
-s $subject \
-ss $session \
-c dcm2niix \
--minmeta \
--dbg \
-b \
--overwrite ;
echo "Finished subject" $subject $session
Please note that I have run the script about using both singularity --cleanenv and singularity --no-home. Sometimes the issue is that it does not convert and I get the error below. Other times it only converts part of the data (i.e., only converts anatomy files and func files and not dwi folder).
Version:
Running heudiconv version 1.1.0 latest 1.1.0
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity container
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
Starting BIDS conversion for subject YA-381116K 1
INFO: Running heudiconv version 1.1.0 latest 1.1.0
INFO: Need to process 1 study sessions
INFO: PROCESSING STARTS: {'subject': 'YA-381116K', 'outdir': '/fs/ess/PCON0341/projects/TERBO/YA/BIDS/', 'session': '1'}
INFO: Processing 4503 dicoms
WARNING: 'YA-381116K' label contained non-alphanumeric character(s), it was cleaned to be 'YA381116K'
INFO: Analyzing 4503 dicoms
INFO: Generated sequence info for 38 studies with 4503 entries total
WARNING: We cannot setup exception hook since not in interactive mode
Finished subject YA-381116K 1