fMRIprep BIDS Validation

Alberto_Benelli · December 11, 2024, 3:16pm

Summary of what happened

Dear fMRIPrep,

I’m trying to run a fMRIPrep to preprocess subject data, using this command:

The data_description.json file is:
{"Name":"MS Fatigue study","BIDSVersion":"1.8.0","License":"PDDL","Authors":["Benelli A.","Cortese R.","Tatti E.","Massucco E.","Luchetti L.","Battaglini M.","Cudeiro J.","de Mauro A.","Plantone D.","Pasqualetti P.","Righi D.","Neri F.","Stromillo M.L.","Cinti A.","Giannotta A.","Lomi F.","Scoccia A.","Lai G.","De Stefano N.","Ulivelli M.","Rossi S."],"HowToAcknowledge":"When using this data, please cite Benelli et al.","Funding":"to be defined","ReferencesAndLinks":["to be defined"]}

the task-rest_bold.json file is:

{
	"Modality": "MR",
	"MagneticFieldStrength": 3,
	"ImagingFrequency": 127.738237,
	"Manufacturer": "Philips",
	"ManufacturersModelName": "Achieva dStream",
	"InstitutionName": "Ospedale Pediatrico Meyer",
	"InstitutionalDepartmentName": "Risonanza Magnetica",
	"InstitutionAddress": "Viale Pieraccini 24, Firenze",
	"DeviceSerialNumber": "17260",
	"StationName": "PHILIPS-P9BMSKQ",
	"BodyPart": "BRAIN",
	"PatientPosition": "HFS",
	"ProcedureStepDescription": "RM ENCEFALO",
	"SoftwareVersions": "5.3.1/5.3.1.4",
	"MRAcquisitionType": "2D",
	"StudyDescription": "RM ENCEFALO",
	"SeriesDescription": "FE_EPI SENSE",
	"ProtocolName": "FE_EPI SENSE",
	"ScanningSequence": "GR",
	"SequenceVariant": "SK",
	"ScanOptions": "FS",
	"PulseSequenceName": "EPI",
	"ImageType": ["ORIGINAL", "PRIMARY", "T2", "NONE", "MAGNITUDE"],
	"SeriesNumber": 701,
	"AcquisitionTime": "15:30:53.300000",
	"AcquisitionNumber": 7,
	"PhilipsRescaleSlope": 0.951893,
	"PhilipsRescaleIntercept": 0,
	"PhilipsScaleSlope": 0.0288861,
	"UsePhilipsFloatNotDisplayScaling": 1,
	"SliceThickness": 4,
	"SpacingBetweenSlices": 4,
	"TablePosition": [
		0,
		0,
		0.3	],
	"EchoTime": 0.035,
	"RepetitionTime": 3,
	"MTState": false,
	"FlipAngle": 90,
	"CoilString": "MULTI COIL",
	"PercentPhaseFOV": 100,
	"PercentSampling": 98.4375,
	"EchoTrainLength": 71,
	"PhaseEncodingSteps": 126,
	"FrequencyEncodingSteps": 128,
	"PhaseEncodingStepsOutOfPlane": 1,
	"AcquisitionMatrixPE": 126,
	"ReconMatrixPE": 128,
	"ParallelReductionFactorInPlane": 1.8,
	"ParallelAcquisitionTechnique": "SENSE",
	"WaterFatShift": 22.1019,
	"EstimatedEffectiveEchoSpacing": 0.00039514,
	"EstimatedTotalReadoutTime": 0.0501828,
	"AcquisitionDuration": 611.938,
	"PixelBandwidth": 2330.35,
	"PhaseEncodingAxis": "j",
	"ImageOrientationPatientDICOM": [
		0.998752,
		0.0473536,
		0.0158947,
		-0.0470147,
		0.998672,
		-0.0210601	],
	"InPlanePhaseEncodingDirectionDICOM": "COL",
	"BidsGuess": ["func","_acq-SKGRFEEPIp18_run-701_bold"],
	"ConversionSoftware": "dcm2niix",
	"ConversionSoftwareVersion": "v1.0.20241208"
}

Within the study folder I’ve these subfolders: derivatives (empty), work (empty), sub-01 (with both anat and func subsubfolders); I’ve license.txt also.

Inside both anat and fund subsubfolders there the .gz file and the descriptive .json file, following the correct names for BIDS format.

I don’t know how to fix it.

Is there anyone who can help me woth that?

Best regards,

Alberto

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

fmriprep \
/Volumes/BENO_ALBE/prova/MS_FATIGUE_BIDS_format \
/Volumes/BENO_ALBE/prova/MS_FATIGUE_BIDS_format/derivatives participant \
-w /Volumes/BENO_ALBE/prova/MS_FATIGUE_BIDS_format/work/

Version:

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

Data formatted according to a validatable standard? Please provide the output of the validator:

Running bids-validator I get this other error (attached)

Relevant log outputs (up to 20 lines):

When I run it from terminal I get this error:

s/BENO_ALBE/prova/MS_FATIGUE_BIDS_format/work/
241211-16:15:44,887 cli WARNING:
         Telemetry disabled because sentry_sdk is not installed.
Traceback (most recent call last):
  File "/opt/anaconda3/envs/fslpy/lib/python3.10/site-packages/bids/layout/index.py", line 331, in load_json
    return json.load(handle)
  File "/opt/anaconda3/envs/fslpy/lib/python3.10/json/__init__.py", line 293, in load
    return loads(fp.read(),
  File "/opt/anaconda3/envs/fslpy/lib/python3.10/codecs.py", line 322, in decode
    (result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb0 in position 37: invalid start byte

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/opt/anaconda3/envs/fslpy/bin/fmriprep", line 8, in <module>
    sys.exit(main())
  File "/opt/anaconda3/envs/fslpy/lib/python3.10/site-packages/fmriprep/cli/run.py", line 40, in main
    parse_args()
  File "/opt/anaconda3/envs/fslpy/lib/python3.10/site-packages/fmriprep/cli/parser.py", line 878, in parse_args
    config.from_dict({})
  File "/opt/anaconda3/envs/fslpy/lib/python3.10/site-packages/fmriprep/config.py", line 729, in from_dict
    execution.load(settings, init=initialize('execution'), ignore=ignore)
  File "/opt/anaconda3/envs/fslpy/lib/python3.10/site-packages/fmriprep/config.py", line 240, in load
    cls.init()
  File "/opt/anaconda3/envs/fslpy/lib/python3.10/site-packages/fmriprep/config.py", line 503, in init
    cls._layout = BIDSLayout(
  File "/opt/anaconda3/envs/fslpy/lib/python3.10/site-packages/bids/layout/layout.py", line 177, in __init__
    _indexer(self)
  File "/opt/anaconda3/envs/fslpy/lib/python3.10/site-packages/bids/layout/index.py", line 160, in __call__
    self._index_metadata()
  File "/opt/anaconda3/envs/fslpy/lib/python3.10/site-packages/bids/layout/index.py", line 443, in _index_metadata
    file_md.update(pl())
  File "/opt/anaconda3/envs/fslpy/lib/python3.10/site-packages/bids/layout/index.py", line 333, in load_json
    raise OSError(
OSError: Error occurred while trying to decode JSON from file <BIDSJSONFile filename='/Volumes/BENO_ALBE/prova/MS_FATIGUE_BIDS_format/._task-rest_bold.json'

Screenshots / relevant information:

Steven · December 11, 2024, 3:28pm

Hi @Alberto_Benelli, and welcome to neurostars!

In the future please use the software support post template. You can see I added it in and partially reorganized your post for you this time. Also, please format terminal output / code using the </> button (or tickmarks) in the text editor so it looks nice

like this.

Searchable text is preferable to screenshots.

There is some missing information, such as your version and how you are running fmriprep. You should use containers to run fmriprep and use the latest version, if possible.

Now with the errors:

The funding part of the dataset_description should be an array, but it is also not needed. If you don’t have it yet, you can simply delete it.
license.txt is not a valid BIDS file. This should be placed in the BIDS code directory where it won’t be indexed by the validator.
You should add a TaskName field the accompanying BOLD json files.

It looks like you are trying to use BIDS inheritance, by placing an overarching BOLD JSON file in the root directory. It shouldn’t begin with ._ however. If you want it to be used for all BOLD files, it should simply be named task-rest_bold.json.

Best,
Steven

Alberto_Benelli · December 11, 2024, 3:48pm

Hi Steven,

Thank you for your quick reply.

I’m using the fMRIPrep v24.1.1 version. The data_descriptio.json file (which seems to be mandatory) dosen’t have ._ at the beginning of the name. Every time I try to run the command the data_description.json file seems having ._ at the beginning, and I don’t know why. I’m running this command from python script.

Thank you,

Alberto

Steven · December 11, 2024, 3:54pm

Hi @Alberto_Benelli,

I recommend switching to containers (Docker/Singularity).

The error you posted seems to say that it’s the BOLD json, and not the dataset_description that has the ._ in the beginning. Is there another error you’re getting that indicates there is also a ._ for the dataset_description? It is possible those with the ._ are temporary backups from text editors. If that’s the case they can be safely deleted.

Best,
Steven

Alberto_Benelli · December 11, 2024, 4:10pm

Hi @Steven thank you,

ok, I can try to use either Docker or Singularity.
Unfortunately both the data_description.json and BOLD json push out the same error ._ but no one has ._ at the begging of their own name.

Alberto

Steven · December 11, 2024, 4:18pm

Did you delete any files that have ._? Keep in mind they may be present but not be visible because many operating systems hide items beginning with a dot.

Alberto_Benelli · December 11, 2024, 4:24pm

Ok, got it. Actually I did not delete any files like that.

I just used the .json file for BOLD signal which dcm2niix pushed out. Then, I duplicate that .json file to edit it following the data_description.json file guidelines.

Alberto