Receiving 'desc' value error when I have no desc images in my sub files

[Rubana]

Summary of what happened:

Hi guys, I’m trying to run ASLPrep through an aslprep.sh script (submitting a job through slurm) but I keep encountering this value error even though I have no desk images - someone suggested it might be an issue with the latest version of ASLPrep, was wondering if anyone has any insight?

Command used (and if a helper script was used, a link to the helper script or the command generated):

and this is my script, I even modified it to bypass the error but it hasn’t worked:

#!/bin/bash
#SBATCH --job-name=ASLprep_sub4028
#SBATCH --output=/data/raulab/aslprep/derivatives/logs/aslprep_%j.out
#SBATCH --error=/data/raulab/aslprep/derivatives/logs/aslprep_%j.err
#SBATCH --nodes=1     
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --time=07:00:00
#SBATCH --mail-user=rubana.mursh@gmail.com
#SBATCH --mail-type=FAIL

## cd /data/raulab/aslprep/derivatives/logs 
## sbatch /data/raulab/aslprep/aslprep_rubana.sh

# Environment Variables
export FS_LICENSE=/data/raulab/aslprep/config/license.txt
export PYBIDS_INVALID_FILTERS=allow     #added to bypass desc error 
export APPTAINERENV_PYBIDS_INVALID_FILTERS=allow  
export TEMPLATEFLOW_HOME=/data/raulab/aslprep/config/templateflow
export APPTAINERENV_FS_LICENSE=/FreeSurferLicense/license.txt
export APPTAINERENV_TEMPLATEFLOW_HOME=/templateflow

# Node-local work directory
WORKDIR=/scratch/murrub/aslprep_${SLURM_JOB_ID}
mkdir -p "${WORKDIR}"

echo "Using node-local workdir: ${WORKDIR}"

apptainer run --cleanenv \
  --env TEMPLATEFLOW_HOME=/templateflow \
  --bind /data/raulab/aslprep/preprocessed:/data:ro \
  --bind /data/raulab/aslprep/derivatives:/out \
  --bind /data/raulab/aslprep/config/license.txt:/freesurfer_license/license.txt \
  --bind /data/raulab/aslprep/config/templateflow:/templateflow \
  --bind ${WORKDIR}:/work \
  /data/raulab/aslprep/aslprep-25.1.0.sif \
  /data /out participant \
  --participant-label 4028\
  --skip_bids_validation \
  --output-spaces T1w MNI152NLin2009aSym \
  --random-seed 42 \
  --n_cpus 16 \
  --basil \
  --skull-strip-fixed-seed \
  --use-syn-sdc \
  --fs-license-file /freesurfer_license/license.txt \
  --work-dir /work \
  --clean-workdir

Version:

25.1.0

Environment (Docker, Singularity / Apptainer, custom installation):

Apptainer, submitted via Slurm on HPC

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):

this is my error log:

slurmstepd: error: Unable to create TMPDIR [/tmp/user/50084]: Permission denied
slurmstepd: error: Setting TMPDIR to /tmp
INFO:    Environment variable SINGULARITY_BINDPATH is set, but APPTAINER_BINDPATH is preferred
WARNING: While bind mounting '/data:/data': destination is already in the mount point list
Process Process-2:
Traceback (most recent call last):
  File "/opt/conda/envs/aslprep/lib/python3.11/multiprocessing/process.py", line 314, in _bootstrap
    self.run()
  File "/opt/conda/envs/aslprep/lib/python3.11/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/aslprep/cli/workflow.py", line 101, in build_workflow
    retval['workflow'] = init_aslprep_wf()
                         ^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/aslprep/workflows/base.py", line 69, in init_aslprep_wf
    single_subject_wf = init_single_subject_wf(subject_id)
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/aslprep/workflows/base.py", line 575, in init_single_subject_wf
    all_estimators, estimator_map = map_fieldmap_estimation(
                                    ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/aslprep/workflows/base.py", line 896, in map_fieldmap_estimation
    fmap_estimators = find_estimators(
                      ^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/sdcflows/utils/wrangler.py", line 525, in find_estimators
    estimator_specs = find_anatomical_estimators(
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/sdcflows/utils/wrangler.py", line 625, in find_anatomical_estimators
    intent = [Path(epi) for epi in layout.get(suffix=suffixes, **query)]
                                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/bids/layout/layout.py", line 680, in get
    raise ValueError(msg + "If you're sure you want to impose "
ValueError: 'desc' is not a recognized entity. If you're sure you want to impose this constraint, set invalid_filters='allow'.

Screenshots / relevant information:

---

[Steven]

Hi @Rubana,

In the future please use the Software Support post category and post template, and format your code with the </> button in the text editor (or surround the text in tickmarks). You can see I edited it for you this time.

Please provide the BIDS validator output, as requested by the post template, and the tree directory structure of one subject’s raw data folder.

Best,
Steven

[Rubana]

Apologies Steven, will note to do so from now onwards and thank you!

Here’s the picture for both, I see the errors from the BIDS validator but I’m confused because I had the same structure/BIDS layout when running from my home directory and it was fine. I also have the sidecarkey values in my .json files that they’re flagging

[Rubana]

[Steven]

Hi @Rubana,

The screenshots are not detailed enough to say what the exact error is. Do you have the json output from the validator?

Also are you sure you’re showing the folder structure from the right data? Looks like you’re showing me a folder in aslprep/preprocessed, not raw data. But those also don’t look like aslprep outputs, and aslprep doesn’t make any folder called raulab, so I’m not sure what you’re showing me exactly.

Best,
Steven

[Rubana]

Hey Steven, sorry for the confusing, I cleaned up my subject folder, here it is now! I’m still getting the sec error when trying to run my script

[Rubana]

here’s my current file on the bids validator, there’s only 1 error, I can still share the json if that helps!

[Steven]

Seems like you just need to change the background suppression field to be a boolean, see here: Magnetic Resonance Imaging - Brain Imaging Data Structure 1.10.1

[Rubana]

got it, thank you so much Steven