Summary of what happened:
Hi all, first-time xcp-d user here and I feel like I’m losing my mind, or possibly doing something very, very basic wrong, so apologies if this turns out to be a stupid question. I’m trying to run xcp-d via docker on a M2 Max Mac Studio (I know M-series processors are not recommended, but… it’s what I’ve got) after processing with fmriprep (version 24.1.1). Fmriprep seems to run fine on my data and gives the expected outputs.
Problem is: xcp-d doesn’t seem to recognise my file paths. I get this error:
xcp_d: error: Path does not exist: </Users/Shared/MRIData/MW_fmriprep_test/bids/derivatives/fmriprep>.
I’ve tried running the command in the correct working directory, and with relative file paths (i.e. ./) and then I get a different error, saying that it can’t find the ‘dataset_description.json’ file, but the file is definitely there! I’ve also tried moving the directory around a bit (shorter file paths) but still get the same issue.
Command used (and if a helper script was used, a link to the helper script or the command generated):
docker run pennlinc/xcp_d /Users/Shared/MRIData/MW_fmriprep_test/bids/derivatives/fmriprep /Users/Shared/MRIData/MW_fmriprep_test/bids/derivatives/xcp-d participant --participant-label 001 --mode none --input-type fmriprep --despike y --motion-filter-type none --fd-thresh 0 --output-type censored --nuisance-regressors acompcor --smoothing 6 --combine-runs n --disable-bandpass-filter --abcc-qc n --file-format nifti --linc-qc n --min-coverage 0.5 --warp-surfaces-native2std n
#I've also tried running a 'minimal' version for test purposes:
docker run pennlinc/xcp_d /Users/Shared/MRIData/MW_fmriprep_test/bids/derivatives/fmriprep /Users/Shared/MRIData/MW_fmriprep_test/bids/derivatives/xcp-d participant --mode linc --smoothing 6
Version:
XCP-D v0.10.0
Environment (Docker, Singularity / Apptainer, custom installation):
Docker.
Data formatted according to a validatable standard? Please provide the output of the validator:
Running a bids validator on the directory does identify some issues, but since this directory was created with fmriprep, I’m guessing this is probably OK?
[WARNING] SIDECAR_KEY_RECOMMENDED A data file's JSON sidecar is missing a key listed as recommended.
Description
/sub-001.html
/dataset_description.json
69 more files with the same issue
TaskName
/sub-001/figures/sub-001_ses-1_task-rest_desc-coreg_bold.svg
/sub-001/figures/sub-001_ses-1_task-rest_desc-compcorvar_bold.svg
16 more files with the same issue
SpatialReference
/sub-001/figures/sub-001_ses-1_space-MNI152NLin6Asym_T1w.svg
/sub-001/ses-1/anat/sub-001_ses-1_space-MNI152NLin6Asym_label-WM_probseg.nii.gz
9 more files with the same issue
Manufacturer
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
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ManufacturersModelName
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
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DeviceSerialNumber
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
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StationName
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
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SoftwareVersions
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
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MagneticFieldStrength
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
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ReceiveCoilName
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
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ReceiveCoilActiveElements
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
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GradientSetType
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
16 more files with the same issue
MRTransmitCoilSequence
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
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MatrixCoilMode
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
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CoilCombinationMethod
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
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PulseSequenceType
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
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ScanningSequence
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
16 more files with the same issue
SequenceVariant
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
16 more files with the same issue
ScanOptions
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
16 more files with the same issue
SequenceName
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
16 more files with the same issue
PulseSequenceDetails
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
16 more files with the same issue
MTState
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
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SpoilingState
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
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NumberShots
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
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ParallelReductionFactorInPlane
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
16 more files with the same issue
ParallelReductionFactorOutOfPlane
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
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ParallelAcquisitionTechnique
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
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PartialFourier
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
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PartialFourierDirection
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
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EffectiveEchoSpacing
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
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MixingTime
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
16 more files with the same issue
PhaseEncodingDirection
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
16 more files with the same issue
TotalReadoutTime
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
16 more files with the same issue
EchoTime
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
16 more files with the same issue
InversionTime
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
16 more files with the same issue
DwellTime
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
16 more files with the same issue
FlipAngle
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
16 more files with the same issue
MultibandAccelerationFactor
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
16 more files with the same issue
InstitutionName
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
16 more files with the same issue
InstitutionAddress
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
16 more files with the same issue
InstitutionalDepartmentName
/sub-001/ses-1/anat/sub-001_ses-1_desc-preproc_T1w.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
16 more files with the same issue
Sources
/sub-001/ses-1/anat/sub-001_ses-1_desc-brain_mask.nii.gz
/sub-001/ses-1/anat/sub-001_ses-1_space-MNI152NLin6Asym_desc-brain_mask.nii.gz
NumberOfVolumesDiscardedByScanner
/sub-001/ses-1/func/sub-001_ses-1_task-rest_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
/sub-001/ses-1/func/sub-001_ses-1_task-music_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
NumberOfVolumesDiscardedByUser
/sub-001/ses-1/func/sub-001_ses-1_task-rest_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
/sub-001/ses-1/func/sub-001_ses-1_task-music_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
AcquisitionDuration
/sub-001/ses-1/func/sub-001_ses-1_task-rest_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
/sub-001/ses-1/func/sub-001_ses-1_task-music_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
DelayAfterTrigger
/sub-001/ses-1/func/sub-001_ses-1_task-rest_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
/sub-001/ses-1/func/sub-001_ses-1_task-music_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
Instructions
/sub-001/ses-1/func/sub-001_ses-1_task-rest_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
/sub-001/ses-1/func/sub-001_ses-1_task-music_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
TaskDescription
/sub-001/ses-1/func/sub-001_ses-1_task-rest_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
/sub-001/ses-1/func/sub-001_ses-1_task-music_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
CogAtlasID
/sub-001/ses-1/func/sub-001_ses-1_task-rest_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
/sub-001/ses-1/func/sub-001_ses-1_task-music_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
CogPOID
/sub-001/ses-1/func/sub-001_ses-1_task-rest_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
/sub-001/ses-1/func/sub-001_ses-1_task-music_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
Type
/sub-001/ses-1/func/sub-001_ses-1_task-music_space-MNI152NLin6Asym_desc-brain_mask.nii.gz
/sub-001/ses-1/func/sub-001_ses-1_task-music_desc-brain_mask.nii.gz
2 more files with the same issue
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[WARNING] README_FILE_MISSING The recommended file /README is missing.
See Section 03 (Modality agnostic files) of the BIDS specification.
/dataset_description.json
Please visit https://neurostars.org/search?q=README_FILE_MISSING for existing conversations about this issue.
[WARNING] TOO_FEW_AUTHORS The 'Authors' field of 'dataset_description.json' should contain an array of values -
with one author per value.
This was triggered based on the presence of only one author field.
Please ignore if all contributors are already properly listed.
/dataset_description.json
Please visit https://neurostars.org/search?q=TOO_FEW_AUTHORS for existing conversations about this issue.
[WARNING] JSON_KEY_RECOMMENDED A JSON file is missing a key listed as recommended.
License
/dataset_description.json
SourceDatasets
/dataset_description.json
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[WARNING] NO_AUTHORS The Authors field of dataset_description.json should contain an array of fields -
with one author per field. This was triggered because there are no authors, which
will make DOI registration from dataset metadata impossible.
Authors
/dataset_description.json
Please visit https://neurostars.org/search?q=NO_AUTHORS for existing conversations about this issue.
[ERROR] NOT_INCLUDED Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.
/sub-001.html
/logs/CITATION.tex
31 more files with the same issue
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[ERROR] ALL_FILENAME_RULES_HAVE_ISSUES Multiple filename rules were found as potential matches. All of them had at least one issue during filename validation.
/sub-001/figures/sub-001_ses-1_task-rest_desc-coreg_bold.svg - Rules that matched with issues: rules.files.deriv.imaging.func_volumetric, rules.files.deriv.preprocessed_data.func_func_common, rules.files.raw.func.func
/sub-001/figures/sub-001_ses-1_task-rest_desc-compcorvar_bold.svg - Rules that matched with issues: rules.files.deriv.imaging.func_volumetric, rules.files.deriv.preprocessed_data.func_func_common, rules.files.raw.func.func
17 more files with the same issue
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[ERROR] EMPTY_FILE Empty files not allowed.
/sub-001/figures/sub-001_ses-1_task-rest_desc-validation_bold.html
/sub-001/figures/sub-001_ses-1_task-music_desc-validation_bold.html
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[ERROR] SIDECAR_KEY_REQUIRED A data file's JSON sidecar is missing a key listed as required.
SpatialReference
/sub-001/figures/sub-001_ses-1_space-MNI152NLin6Asym_T1w.svg
/sub-001/ses-1/anat/sub-001_ses-1_space-MNI152NLin6Asym_label-WM_probseg.nii.gz
9 more files with the same issue
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[ERROR] JSON_SCHEMA_VALIDATION_ERROR Invalid JSON sidecar file. The sidecar is not formatted according the schema.
TaskName
/sub-001/ses-1/func/sub-001_ses-1_task-rest_space-MNI152NLin6Asym_desc-preproc_bold.json - must be string
/sub-001/ses-1/func/sub-001_ses-1_task-music_space-MNI152NLin6Asym_desc-preproc_bold.json - must be string
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Summary: Available Tasks: Available Modalities:
81 Files, 904 MB MRI
1 - Subjects 1 - Sessions
If you have any questions, please post on https://neurostars.org/tags/bids.
Relevant log outputs (up to 20 lines):
No log files created! :o(
PASTE LOG OUTPUT HERE
Screenshots / relevant information:
Running pwd in the directory produces the following output:
/Users/Shared/MRIData/MW_fmriprep_test/bids/derivatives/fmriprep
So the directory certainly exists. Running ls -al in the directory gives the following:
drwxrwxrwx 7 Matt wheel 224 20 Dec 20:24 .
drwxr-xr-x 4 Matt wheel 128 21 Dec 06:33 ..
-rwxrwxrwx@ 1 Matt wheel 6148 20 Dec 21:57 .DS_Store
-rwxrwxrwx@ 1 Matt wheel 618 20 Dec 19:00 dataset_description.json
drwxrwxrwx 6 Matt wheel 192 20 Dec 18:19 logs
drwxrwxrwx 6 Matt wheel 192 20 Dec 18:29 sub-001
-rwxrwxrwx@ 1 Matt wheel 68669 20 Dec 19:00 sub-001.html
So the dataset_description.json file also definitely exists. Contents of that file:
{
"Name": "fMRIPrep - fMRI PREProcessing workflow",
"BIDSVersion": "1.4.0",
"DatasetType": "derivative",
"GeneratedBy": [
{
"Name": "fMRIPrep",
"Version": "24.1.1",
"CodeURL": "https://github.com/nipreps/fmriprep/archive/24.1.1.tar.gz"
}
],
"HowToAcknowledge": "Please cite our paper (https://doi.org/10.1038/s41592-018-0235-4), and include the generated citation boilerplate within the Methods section of the text.",
"DatasetLinks": {
"raw": "/data",
"templateflow": "https://github.com/templateflow/templateflow"
}
}
Full directory tree:
fmriprep
├── dataset_description.json
├── logs
│ ├── CITATION.bib
│ ├── CITATION.html
│ ├── CITATION.md
│ └── CITATION.tex
├── sub-001
│ ├── figures
│ │ ├── sub-001_ses-1_desc-about_T1w.html
│ │ ├── sub-001_ses-1_desc-conform_T1w.html
│ │ ├── sub-001_ses-1_desc-summary_T1w.html
│ │ ├── sub-001_ses-1_dseg.svg
│ │ ├── sub-001_ses-1_space-MNI152NLin6Asym_T1w.svg
│ │ ├── sub-001_ses-1_task-music_desc-carpetplot_bold.svg
│ │ ├── sub-001_ses-1_task-music_desc-compcorvar_bold.svg
│ │ ├── sub-001_ses-1_task-music_desc-confoundcorr_bold.svg
│ │ ├── sub-001_ses-1_task-music_desc-coreg_bold.svg
│ │ ├── sub-001_ses-1_task-music_desc-rois_bold.svg
│ │ ├── sub-001_ses-1_task-music_desc-summary_bold.html
│ │ ├── sub-001_ses-1_task-music_desc-validation_bold.html
│ │ ├── sub-001_ses-1_task-rest_desc-carpetplot_bold.svg
│ │ ├── sub-001_ses-1_task-rest_desc-compcorvar_bold.svg
│ │ ├── sub-001_ses-1_task-rest_desc-confoundcorr_bold.svg
│ │ ├── sub-001_ses-1_task-rest_desc-coreg_bold.svg
│ │ ├── sub-001_ses-1_task-rest_desc-rois_bold.svg
│ │ ├── sub-001_ses-1_task-rest_desc-summary_bold.html
│ │ └── sub-001_ses-1_task-rest_desc-validation_bold.html
│ ├── log
│ │ └── 20241220-181924_caa78584-7bf8-4a3a-86d1-59e3983938fe
│ │ └── fmriprep.toml
│ └── ses-1
│ ├── anat
│ │ ├── sub-001_ses-1_desc-brain_mask.json
│ │ ├── sub-001_ses-1_desc-brain_mask.nii.gz
│ │ ├── sub-001_ses-1_desc-preproc_T1w.json
│ │ ├── sub-001_ses-1_desc-preproc_T1w.nii.gz
│ │ ├── sub-001_ses-1_dseg.nii.gz
│ │ ├── sub-001_ses-1_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
│ │ ├── sub-001_ses-1_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5
│ │ ├── sub-001_ses-1_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
│ │ ├── sub-001_ses-1_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
│ │ ├── sub-001_ses-1_label-CSF_probseg.nii.gz
│ │ ├── sub-001_ses-1_label-GM_probseg.nii.gz
│ │ ├── sub-001_ses-1_label-WM_probseg.nii.gz
│ │ ├── sub-001_ses-1_space-MNI152NLin6Asym_desc-brain_mask.json
│ │ ├── sub-001_ses-1_space-MNI152NLin6Asym_desc-brain_mask.nii.gz
│ │ ├── sub-001_ses-1_space-MNI152NLin6Asym_desc-preproc_T1w.json
│ │ ├── sub-001_ses-1_space-MNI152NLin6Asym_desc-preproc_T1w.nii.gz
│ │ ├── sub-001_ses-1_space-MNI152NLin6Asym_dseg.nii.gz
│ │ ├── sub-001_ses-1_space-MNI152NLin6Asym_label-CSF_probseg.nii.gz
│ │ ├── sub-001_ses-1_space-MNI152NLin6Asym_label-GM_probseg.nii.gz
│ │ └── sub-001_ses-1_space-MNI152NLin6Asym_label-WM_probseg.nii.gz
│ └── func
│ ├── sub-001_ses-1_task-music_desc-brain_mask.json
│ ├── sub-001_ses-1_task-music_desc-brain_mask.nii.gz
│ ├── sub-001_ses-1_task-music_desc-confounds_timeseries.json
│ ├── sub-001_ses-1_task-music_desc-confounds_timeseries.tsv
│ ├── sub-001_ses-1_task-music_desc-coreg_boldref.json
│ ├── sub-001_ses-1_task-music_desc-coreg_boldref.nii.gz
│ ├── sub-001_ses-1_task-music_desc-hmc_boldref.json
│ ├── sub-001_ses-1_task-music_desc-hmc_boldref.nii.gz
│ ├── sub-001_ses-1_task-music_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
│ ├── sub-001_ses-1_task-music_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
│ ├── sub-001_ses-1_task-music_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
│ ├── sub-001_ses-1_task-music_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
│ ├── sub-001_ses-1_task-music_space-MNI152NLin6Asym_boldref.json
│ ├── sub-001_ses-1_task-music_space-MNI152NLin6Asym_boldref.nii.gz
│ ├── sub-001_ses-1_task-music_space-MNI152NLin6Asym_desc-brain_mask.json
│ ├── sub-001_ses-1_task-music_space-MNI152NLin6Asym_desc-brain_mask.nii.gz
│ ├── sub-001_ses-1_task-music_space-MNI152NLin6Asym_desc-preproc_bold.json
│ ├── sub-001_ses-1_task-music_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
│ ├── sub-001_ses-1_task-rest_desc-brain_mask.json
│ ├── sub-001_ses-1_task-rest_desc-brain_mask.nii.gz
│ ├── sub-001_ses-1_task-rest_desc-confounds_timeseries.json
│ ├── sub-001_ses-1_task-rest_desc-confounds_timeseries.tsv
│ ├── sub-001_ses-1_task-rest_desc-coreg_boldref.json
│ ├── sub-001_ses-1_task-rest_desc-coreg_boldref.nii.gz
│ ├── sub-001_ses-1_task-rest_desc-hmc_boldref.json
│ ├── sub-001_ses-1_task-rest_desc-hmc_boldref.nii.gz
│ ├── sub-001_ses-1_task-rest_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
│ ├── sub-001_ses-1_task-rest_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
│ ├── sub-001_ses-1_task-rest_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
│ ├── sub-001_ses-1_task-rest_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
│ ├── sub-001_ses-1_task-rest_space-MNI152NLin6Asym_boldref.json
│ ├── sub-001_ses-1_task-rest_space-MNI152NLin6Asym_boldref.nii.gz
│ ├── sub-001_ses-1_task-rest_space-MNI152NLin6Asym_desc-brain_mask.json
│ ├── sub-001_ses-1_task-rest_space-MNI152NLin6Asym_desc-brain_mask.nii.gz
│ ├── sub-001_ses-1_task-rest_space-MNI152NLin6Asym_desc-preproc_bold.json
│ └── sub-001_ses-1_task-rest_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
└── sub-001.html
I’ve also re-set all the permissions on the directories/files just in case it’s a permissions issue, but that hasn’t seemed to help either.
I’ve also tried enclosing the file paths in single quotes, just in case there are any weird characters in there or something (there aren’t, but you never know…):
docker run pennlinc/xcp_d `/Users/Shared/MRIData/MW_fmriprep_test/bids/output` `/Users/Shared/MRIData/MW_fmriprep_test/bids/xcp-d` participant --participant-label 001 --mode none --input-type fmriprep --despike y --motion-filter-type none --fd-thresh 0 --output-type censored --nuisance-regressors acompcor --smoothing 6 --combine-runs n --disable-bandpass-filter --abcc-qc n --file-format nifti --linc-qc n --min-coverage 0.5 --warp-surfaces-native2std n
That seems to help somewhat, in that it seems to read the input and output paths and produces a different error:
xcp_d: error: Path does not exist: <participant>.
…but I’m stuck at that point again.
I feel like I’m doing something fundamental and hopefully quite simple very wrong here, but I’m basically at a loss. Is this perhaps a weird issue specific to M-series Macs? Or am I just doing something stupid? (Hopefully the latter…) Any help would be very much appreciated! Thank you.
Matt.