XCP_D error: 'resolution' is not a recognized entity

Software Support
1

Hi experts,

I ran the following code in XCP_D:

disk="/home/jiayi/Desktop"
project_dir=$disk/“Control_EXCI_MRI”
data_dir=$project_dir/“data_fmriprep_fMRI_1”
output_dir=$project_dir/“data_XCPD”
scratch=$output_dir/“scratch”
plugin_file="/home/jiayi/Desktop/Intervention_EXCI_MRI/Codes/plugin.yml"

sudo docker run -it
-v /$data_dir:/fmriprep:ro
-v /$output_dir:/out
-v $data_dir/sourcedata/freesurfer:/freesurfer:ro
-v /$scratch:/scratch
-v /$project_dir/XCPD_filter.json:/filter_file:ro
pennlinc/xcp_d:0.3.0
/fmriprep /out participant -t rest --smoothing 6
-w /scratch
–despike
–head_radius 50
–input fmriprep
–nuissance-regressors acompcor
–lower-bpf 0.01 --upper-bpf 0.08
–dummytime 7.5
–omp-nthreads 4
–mem_gb 80
–verbose
–resource-monitor

and got the following message and error:

Argument ‘–nuissance-regressors’ is deprecated and will be removed in version 0.3.0. Please use ‘–nuisance-regressors’ or ‘-p’.
221204-03:17:32,450 nipype.workflow IMPORTANT:
Running xcp_d version 0.3.0+0.g5a726e9.dirty:
* fMRI directory path: /fmriprep.
* Participant list: [‘EXCI0134’].
* Run identifier: 20221204-031730_1295ce7f-2d32-4ed6-b051-768761741a32.

221204-03:17:32,536 nipype.workflow INFO:
Beginning the xcpd_wf workflow
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 929, in build_workflow
retval[“workflow”] = init_xcpd_wf(
File “/usr/local/miniconda/lib/python3.8/site-packages/xcp_d/workflow/base.py”, line 164, 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 313, in init_subject_wf
layout, subj_data = collect_data(
File “/usr/local/miniconda/lib/python3.8/site-packages/xcp_d/utils/bids.py”, line 251, in collect_data
subj_data = {
File “/usr/local/miniconda/lib/python3.8/site-packages/xcp_d/utils/bids.py”, line 253, in
layout.get(
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: ‘resolution’ is not a recognized entity. Did you mean [‘reconstruction’, ‘direction’]? If you’re sure you want to impose this constraint, set invalid_filters=‘allow’.

Does anyone know what I did wrong? does this have to do with the recent updates with the --bids-filter-file option?

I tried using the --bids-filter-file option and I got :

xcp_d: error: unrecognized arguments: --bids-filter-file

This is the code I ran:

sudo docker run -it
-v /$data_dir:/fmriprep:ro
-v /$output_dir:/out
-v $data_dir/sourcedata/freesurfer:/freesurfer:ro
-v /$scratch:/scratch
-v /$project_dir/XCPD_filter.json:/filter_file:ro
pennlinc/xcp_d:0.3.0
/fmriprep /out participant -t rest --smoothing 6
-w /scratch
–despike
–bids-filter-file /filter_file
–head_radius 50
–input fmriprep
–nuissance-regressors acompcor
–lower-bpf 0.01 --upper-bpf 0.08
–dummytime 7.5
–omp-nthreads 4
–mem_gb 80
–verbose
–resource-monitor

Can anyone spot my mistakes?

Thank you!

regards,
Vae

2

I tried pennlinc/xcp_d:0.2.0 and it is running at the moment

3

Hi Vae,

Can you describe your fMRIprep outputs? That is, the version of fmriprep and flags you used when running it? Did fmriprep finish with errors?

Best,
Steven

4

Hi Steven,

Thanks for your reply!

I ran fmriprep 22.0.0 and it finished in the terminal with some error for about the reports. However, when I checked the reports and the files they were fine. I am currently running another subject through fmriprep, and when it finish I will be able to update more details on this error.

Here is the code that I ran:

disk="/home/jiayi/Desktop"
project_dir=“Control_EXCI_MRI”
bids_dir=“MRI_raw/NIFTI_renamed”
preprocessed_dir=“data_fmriprep_fMRI”
freesurfer_licence="/home/jiayi/Desktop/Intervention_EXCI_MRI/Codes/license.txt"
plugin_file="/home/jiayi/Desktop/Intervention_EXCI_MRI/Codes/plugin.yml"
##############################

#version 22.0.0
sudo docker run -ti \
-v $disk/$project_dir/$bids_dir:/data:ro \
-v $disk/$project_dir/$preprocessed_dir:/fMRI \
-v $freesurfer_licence:/opt/freesurfer/license.txt \
-v $plugin_file:/plugin.yml \
nipreps/fmriprep:22.0.0 \
/data /fMRI participant \
--error-on-aroma-warnings --use-aroma \
--output-spaces MNI152NLin6Asym:res-2 MNI152NLin6Asym:res-1 MNI152NLin2009cAsym:res-2 MNI152NLin2009cAsym:res-1 \
--fd-spike-threshold 0.5 \
--dvars-spike-threshold 20 \
--use-plugin /plugin.yml \
--dummy-scans 5 \
--write-graph \
--n_cpus '12' \
--omp-nthreads 4 \
--mem 40GB \
--verbose \
--resource-monitor

Thank you for your help!
I will update on the fmriprep error when the current analysis is done!
5

I would guess the problem is stemming from you having two output resolutions for the same space. What do you think @tsalo?

6

The current unstable version should work fine with multiple resolutions.

--bids-filter-file is available in pennlinc:xcp_d:unstable, but it should’t be around in 0.3.0… However, if you are using 0.3.1, then I think the problem is that you need to use res instead of resolution.