Summary of what happened:
Hi XCP_D Experts,
We are trying to use XCP_D (pennlinc/xcp_d) to further process outputs from fmriprep. I have created a few fmriprep directories on a HPC using SLURM as the scheduler for the enhanced Nathan Kline Institute-Rockland Sample (NKI-RS) (http://fcon_1000.projects.nitrc.org/indi/enhanced/neurodata.html). I am trying to process one subject on my local machine, with the intention of moving it to the HPC cluster once I have determined if it improves the scan.
Command used (and if a helper script was used, a link to the helper script or the command generated):
fmriprep
singularity run --cleanenv ${image_path} \
${bids_path} \
${out_path} \
participant --participant_label ${participant_id} \
--write-graph \
--notrack \
--nthreads 10 \
--omp-nthreads 10 \
--mem_mb 52000 \
--skip_bids_validation \
--fs-license-file ${license_path} \
--work-dir ${work_dir_path} \
--ignore=slicetiming \
--cifti-output \
--fs-subjects-dir ${fs_sub_dir} \
--use-aroma
XCP
$ docker run --rm -it -v ~/NKI/fmriprep:/fmriprep:ro -v /tmp/wkdir:/work:rw \
-v ~/NKI/xcp_d:/out:rw -v ~/NKI/fmriprep/out_sub-A00039820/sourcedata/freesurfer:/freesurfer:ro \
pennlinc/xcp_d:latest /fmriprep /out participant --participant_label sub-A00039820 \
--cifti --despike --head_radius 40 -w /work --smoothing 6
Version:
We use fmriprep version: 22.1.1 and XCP_D version: 0.3.2
Environment (Docker, Singularity, custom installation):
docker ($ docker --version - Docker version 20.10.12, build 20.10.12-0ubuntu4) on my local machine.
Data formatted according to a validatable standard? Please provide the output of the validator:
Relevant log outputs (up to 20 lines):
230109-20:51:37,268 nipype.workflow IMPORTANT:
Running xcp_d version 0.3.2+0.g665840c.dirty:
* fMRI directory path: /fmriprep.
* Participant list: ['A00039820'].
* Run identifier: 20230109-205126_5f2781d5-e1a2-48bc-b937-0b8b37fe0c40.
Process Process-2:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/usr/local/miniconda/lib/python3.8/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/usr/local/miniconda/lib/python3.8/site-packages/xcp_d/cli/run.py", line 962, in build_workflow
retval["workflow"] = init_xcpd_wf(
File "/usr/local/miniconda/lib/python3.8/site-packages/xcp_d/workflow/base.py", line 180, in init_xcpd_wf
single_subj_wf = init_subject_wf(
File "/usr/local/miniconda/lib/python3.8/site-packages/xcp_d/workflow/base.py", line 340, in init_subject_wf
layout, subj_data = collect_data(
File "/usr/local/miniconda/lib/python3.8/site-packages/xcp_d/utils/bids.py", line 247, in collect_data
bold_data = layout.get(**queries["bold"])
File "/usr/local/miniconda/lib/python3.8/site-packages/bids/layout/layout.py", line 626, 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:
I have also tried using singularity on my local machine again using the default example and have received the same error. I tried it with another ‘small’ dataset OpenNeuro generated the fmripep derivatve using fmriprep 22.1.0 because I thought there might be something wrong with the data, but when I ran it, it again produced the same error.
… so can anyone who has used the latest iteration of xpc_d provide some advice about what I could try next?
thanks!
William
