Continuing the discussion from Dataset_description.json missing from project root, file exists in project root:
Summary of what happened:
I am trying to run qsiprep on a BIDS validated dataset (with a few warnings but they don’t seem relevant to the issue I am having here).
I checked and /opt/conda directory does not exist on my laptop. It may be in the container?
On my end, I use VSCode Version: 1.95.2 (Universal)
I created a /.conda virtual environment with Python 3.9.20
And my laptop is Apple M3 Pro with Mac OS Sonoma 14.7.1
Command used (and if a helper script was used, a link to the helper script or the command generated):
import os
import os.path as op
#
# qsiprep (preprocessing)
version = "latest"
bids_dir = op.join(op.expanduser('~'), 'Documents/research/ampb_mt_tractometry_analysis/ampb')
output_dir = op.join(op.expanduser('~'), 'Documents/research/ampb_mt_tractometry_analysis/ampb/derivatives')
participants = [f for f in os.listdir(bids_dir) if f not in {".DS_Store", "dataset_description.json", "code","derivatives"}]
participants_cleaned = [f.replace("sub-", "") for f in participants]
print(participants_cleaned)
for participant in participants_cleaned:
cmd = f"docker run --rm " \
f"--volume {bids_dir} " \
f"--volume {output_dir} " \
f"--volume $FREESURFER_HOME/license.txt " \
f"pennlinc/qsiprep:{version} " \
f"--skip-bids-validation " \
f"{bids_dir} {output_dir} " \
f"participant --participant-label {participant} " \
f"--ignore fieldmaps " \
f"--output-resolution 1.5 " \
f"--fs-license-file $FREESURFER_HOME/license.txt "
os.system(cmd)
Version:
1.0.0rc1
Environment (Docker, Singularity / Apptainer, custom installation):
I am using Docker, I installed Docker desktop from the website
Docker version 27.3.1, build ce12230
I then pulled pennlinc/qsiprep:latest from DockerHub.
Data formatted according to a validatable standard? Please provide the output of the validator:
deno run -A jsr:@bids/validator /Users/ldaumail3/Documents/Research/AMPB_MT_tractometry_analysis/AMPB
[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.
DatasetType
/dataset_description.json
GeneratedBy
/dataset_description.json
SourceDatasets
/dataset_description.json
Please visit https://neurostars.org/search?q=JSON_KEY_RECOMMENDED for existing conversations about this issue.
[WARNING] SIDECAR_KEY_RECOMMENDED A data file's JSON sidecar is missing a key listed as recommended.
GradientSetType
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-PA_epi.nii.gz
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-AP_epi.nii.gz
961 more files with the same issue
MRTransmitCoilSequence
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-PA_epi.nii.gz
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-AP_epi.nii.gz
961 more files with the same issue
MatrixCoilMode
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-PA_epi.nii.gz
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-AP_epi.nii.gz
961 more files with the same issue
CoilCombinationMethod
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-PA_epi.nii.gz
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-AP_epi.nii.gz
961 more files with the same issue
PulseSequenceType
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-PA_epi.nii.gz
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-AP_epi.nii.gz
961 more files with the same issue
MTState
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-PA_epi.nii.gz
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-AP_epi.nii.gz
961 more files with the same issue
SpoilingState
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-PA_epi.nii.gz
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-AP_epi.nii.gz
961 more files with the same issue
NumberShots
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-PA_epi.nii.gz
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-AP_epi.nii.gz
961 more files with the same issue
ParallelReductionFactorInPlane
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-PA_epi.nii.gz
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-AP_epi.nii.gz
810 more files with the same issue
ParallelReductionFactorOutOfPlane
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-PA_epi.nii.gz
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-AP_epi.nii.gz
961 more files with the same issue
ParallelAcquisitionTechnique
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-PA_epi.nii.gz
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-AP_epi.nii.gz
961 more files with the same issue
PartialFourierDirection
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-PA_epi.nii.gz
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-AP_epi.nii.gz
961 more files with the same issue
MixingTime
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-PA_epi.nii.gz
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-AP_epi.nii.gz
961 more files with the same issue
InversionTime
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-PA_epi.nii.gz
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-AP_epi.nii.gz
826 more files with the same issue
DwellTime
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-PA_epi.nii.gz
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-AP_epi.nii.gz
961 more files with the same issue
SliceEncodingDirection
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-PA_epi.nii.gz
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-AP_epi.nii.gz
562 more files with the same issue
B0FieldIdentifier
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-PA_epi.nii.gz
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-AP_epi.nii.gz
606 more files with the same issue
InstitutionalDepartmentName
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-PA_epi.nii.gz
/sub-NSxLxIUx1994/ses-02/fmap/sub-NSxLxIUx1994_ses-02_acq-opphase_dir-AP_epi.nii.gz
961 more files with the same issue
StimulusPresentation
/sub-NSxLxIUx1994/ses-02/func/sub-NSxLxIUx1994_ses-02_task-ampb_run-3_events.tsv
/sub-NSxLxIUx1994/ses-02/func/sub-NSxLxIUx1994_ses-02_task-ampb_run-6_events.tsv
322 more files with the same issue
NumberOfVolumesDiscardedByScanner
/sub-NSxLxIUx1994/ses-02/func/sub-NSxLxIUx1994_ses-02_task-ampb_run-4_bold.nii.gz
/sub-NSxLxIUx1994/ses-02/func/sub-NSxLxIUx1994_ses-02_task-ampb_run-1_bold.nii.gz
322 more files with the same issue
NumberOfVolumesDiscardedByUser
/sub-NSxLxIUx1994/ses-02/func/sub-NSxLxIUx1994_ses-02_task-ampb_run-4_bold.nii.gz
/sub-NSxLxIUx1994/ses-02/func/sub-NSxLxIUx1994_ses-02_task-ampb_run-1_bold.nii.gz
322 more files with the same issue
DelayTime
/sub-NSxLxIUx1994/ses-02/func/sub-NSxLxIUx1994_ses-02_task-ampb_run-4_bold.nii.gz
/sub-NSxLxIUx1994/ses-02/func/sub-NSxLxIUx1994_ses-02_task-ampb_run-1_bold.nii.gz
322 more files with the same issue
AcquisitionDuration
/sub-NSxLxIUx1994/ses-02/func/sub-NSxLxIUx1994_ses-02_task-ampb_run-4_bold.nii.gz
/sub-NSxLxIUx1994/ses-02/func/sub-NSxLxIUx1994_ses-02_task-ampb_run-1_bold.nii.gz
322 more files with the same issue
DelayAfterTrigger
/sub-NSxLxIUx1994/ses-02/func/sub-NSxLxIUx1994_ses-02_task-ampb_run-4_bold.nii.gz
/sub-NSxLxIUx1994/ses-02/func/sub-NSxLxIUx1994_ses-02_task-ampb_run-1_bold.nii.gz
322 more files with the same issue
Instructions
/sub-NSxLxIUx1994/ses-02/func/sub-NSxLxIUx1994_ses-02_task-ampb_run-4_bold.nii.gz
/sub-NSxLxIUx1994/ses-02/func/sub-NSxLxIUx1994_ses-02_task-ampb_run-1_bold.nii.gz
322 more files with the same issue
TaskDescription
/sub-NSxLxIUx1994/ses-02/func/sub-NSxLxIUx1994_ses-02_task-ampb_run-4_bold.nii.gz
/sub-NSxLxIUx1994/ses-02/func/sub-NSxLxIUx1994_ses-02_task-ampb_run-1_bold.nii.gz
322 more files with the same issue
CogAtlasID
/sub-NSxLxIUx1994/ses-02/func/sub-NSxLxIUx1994_ses-02_task-ampb_run-4_bold.nii.gz
/sub-NSxLxIUx1994/ses-02/func/sub-NSxLxIUx1994_ses-02_task-ampb_run-1_bold.nii.gz
322 more files with the same issue
CogPOID
/sub-NSxLxIUx1994/ses-02/func/sub-NSxLxIUx1994_ses-02_task-ampb_run-4_bold.nii.gz
/sub-NSxLxIUx1994/ses-02/func/sub-NSxLxIUx1994_ses-02_task-ampb_run-1_bold.nii.gz
322 more files with the same issue
EffectiveEchoSpacing
/sub-NSxLxIUx1994/ses-01/anat/sub-NSxLxIUx1994_ses-01_acq-MEMPRvNav_rec-RMS_T1w.nii.gz
/sub-NSxLxIUx1994/ses-01/anat/sub-NSxLxIUx1994_ses-01_acq-MEMPRvNav_echo-2_T1w.nii.gz
397 more files with the same issue
PhaseEncodingDirection
/sub-NSxLxIUx1994/ses-01/anat/sub-NSxLxIUx1994_ses-01_acq-MEMPRvNav_rec-RMS_T1w.nii.gz
/sub-NSxLxIUx1994/ses-01/anat/sub-NSxLxIUx1994_ses-01_acq-MEMPRvNav_echo-2_T1w.nii.gz
381 more files with the same issue
TotalReadoutTime
/sub-NSxLxIUx1994/ses-01/anat/sub-NSxLxIUx1994_ses-01_acq-MEMPRvNav_rec-RMS_T1w.nii.gz
/sub-NSxLxIUx1994/ses-01/anat/sub-NSxLxIUx1994_ses-01_acq-MEMPRvNav_echo-2_T1w.nii.gz
397 more files with the same issue
MultibandAccelerationFactor
/sub-NSxLxIUx1994/ses-01/anat/sub-NSxLxIUx1994_ses-01_acq-MEMPRvNav_rec-RMS_T1w.nii.gz
/sub-NSxLxIUx1994/ses-01/anat/sub-NSxLxIUx1994_ses-01_acq-MEMPRvNav_echo-2_T1w.nii.gz
461 more files with the same issue
Manufacturer
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-headMTw_RB1COR.nii
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-bodyMTw_RB1COR.nii
246 more files with the same issue
ManufacturersModelName
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-headMTw_RB1COR.nii
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-bodyMTw_RB1COR.nii
246 more files with the same issue
DeviceSerialNumber
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-headMTw_RB1COR.nii
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-bodyMTw_RB1COR.nii
246 more files with the same issue
StationName
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-headMTw_RB1COR.nii
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-bodyMTw_RB1COR.nii
246 more files with the same issue
SoftwareVersions
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-headMTw_RB1COR.nii
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-bodyMTw_RB1COR.nii
246 more files with the same issue
MagneticFieldStrength
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-headMTw_RB1COR.nii
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-bodyMTw_RB1COR.nii
246 more files with the same issue
ReceiveCoilName
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-headMTw_RB1COR.nii
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-bodyMTw_RB1COR.nii
246 more files with the same issue
ReceiveCoilActiveElements
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-headMTw_RB1COR.nii
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-bodyMTw_RB1COR.nii
246 more files with the same issue
ScanningSequence
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-headMTw_RB1COR.nii
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-bodyMTw_RB1COR.nii
246 more files with the same issue
SequenceVariant
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-headMTw_RB1COR.nii
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-bodyMTw_RB1COR.nii
246 more files with the same issue
ScanOptions
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-headMTw_RB1COR.nii
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-bodyMTw_RB1COR.nii
246 more files with the same issue
SequenceName
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-headMTw_RB1COR.nii
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-bodyMTw_RB1COR.nii
246 more files with the same issue
PulseSequenceDetails
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-headMTw_RB1COR.nii
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-bodyMTw_RB1COR.nii
246 more files with the same issue
PartialFourier
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-headMTw_RB1COR.nii
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-bodyMTw_RB1COR.nii
246 more files with the same issue
EchoTime
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-headMTw_RB1COR.nii
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-bodyMTw_RB1COR.nii
246 more files with the same issue
FlipAngle
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-headMTw_RB1COR.nii
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-bodyMTw_RB1COR.nii
246 more files with the same issue
InstitutionName
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-headMTw_RB1COR.nii
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-bodyMTw_RB1COR.nii
246 more files with the same issue
InstitutionAddress
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-headMTw_RB1COR.nii
/sub-NSxGxBAx1970/ses-04/fmap/sub-NSxGxBAx1970_ses-04_acq-bodyMTw_RB1COR.nii
246 more files with the same issue
Please visit https://neurostars.org/search?q=SIDECAR_KEY_RECOMMENDED for existing conversations about this issue.
Summary: Available Tasks: Available Modalities:
2703 Files, 44.1 GB ampb MRI
27 - Subjects 6 - Sessions ptlocal
mtlocal
If you have any questions, please post on https://neurostars.org/tags/bids.
Relevant log outputs (up to 20 lines):
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
Traceback (most recent call last):
File "/opt/conda/envs/qsiprep/bin/qsiprep", line 8, in <module>
sys.exit(main())
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/cli/run.py", line 42, in main
parse_args()
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/cli/parser.py", line 709, in parse_args
config.from_dict({})
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/config.py", line 721, in from_dict
execution.load(settings, init=initialize("execution"), ignore=ignore)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/config.py", line 251, in load
cls.init()
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/config.py", line 496, in init
cls._layout = BIDSLayout(
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/bids/layout/layout.py", line 135, in __init__
root, description = validate_root(root, validate)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/bids/layout/validation.py", line 75, in validate_root
raise BIDSValidationError(
bids.exceptions.BIDSValidationError: 'dataset_description.json' is missing from project root. Every valid BIDS dataset must have this file.
Example contents of 'dataset_description.json':
{"Name": "Example dataset", "BIDSVersion": "1.0.2"}