JSONDecodeError

1

Dear experts,

I’m getting the following error on fMRIPrep ver 20.2.1:

/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/validation.py:46: UserWarning: The ability to pass arguments to BIDSLayout that control indexing is likely to be removed in future; possibly as early as PyBIDS 0.14. This includes the `config_filename`, `ignore`, `force_index`, and `index_metadata` arguments. The recommended usage pattern is to initialize a new BIDSLayoutIndexer with these arguments, and pass it to the BIDSLayout via the `indexer` argument.
  warnings.warn("The ability to pass arguments to BIDSLayout that control "
Traceback (most recent call last):
  File "/usr/local/miniconda/bin/fmriprep", line 10, in <module>
sys.exit(main())
  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py", line 17, in main
parse_args()
  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/parser.py", line 602, in parse_args
config.from_dict(vars(opts))
  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py", line 617, in from_dict
execution.load(settings)
  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py", line 218, in load
cls.init()
  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py", line 453, in init
re.compile(r"^\."),
  File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 136, in __init__
root, description = validate_root(root, validate)
  File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/validation.py", line 83, in validate_root
description = json.load(desc_fd)
  File "/usr/local/miniconda/lib/python3.7/json/__init__.py", line 296, in load
parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)
  File "/usr/local/miniconda/lib/python3.7/json/__init__.py", line 348, in loads
return _default_decoder.decode(s)
  File "/usr/local/miniconda/lib/python3.7/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/usr/local/miniconda/lib/python3.7/json/decoder.py", line 353, in raw_decode
obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Expecting ',' delimiter: line 3 column 2 (char 20)

My .json file looks like this:

{
	"Modality": "MR",
	"MagneticFieldStrength": 3,
	"ImagingFrequency": 123.219,
	"Manufacturer": "Siemens",
	"ManufacturersModelName": "Verio",
	"InstitutionName": "REDACTED",
	"InstitutionalDepartmentName": "Department",
	"InstitutionAddress": "REDACTED",
	"DeviceSerialNumber": "REDACTED",
	"StationName": "REDACTED",
	"PatientPosition": "HFS",
	"ProcedureStepDescription": "Neuro_Brain_Research",
	"SoftwareVersions": "syngo_MR_B19",
	"MRAcquisitionType": "3D",
	"SeriesDescription": "T1_MPR_SAG_EM",
	"ProtocolName": "T1_MPR_SAG_EM",
	"ScanningSequence": "GR_IR",
	"SequenceVariant": "SP_MP",
	"ScanOptions": "IR",
	"SequenceName": "_tfl3d1_ns",
	"ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"],
	"SeriesNumber": 2,
	"AcquisitionTime": "16:29:4.455000",
	"AcquisitionNumber": 1,
	"SliceThickness": 1,
	"SAR": 0.039084,
	"EchoTime": 0.0035,
	"RepetitionTime": 2.53,
	"InversionTime": 1.1,
	"FlipAngle": 7,
	"PartialFourier": 1,
	"BaseResolution": 256,
	"ShimSetting": [
		-7175,
		4960,
		-9437,
		153,
		127,
		-555,
		800,
		-112	],
	"TxRefAmp": 516.209,
	"PhaseResolution": 1,
	"ReceiveCoilName": "HeadMatrix",
	"CoilString": "T:HEA;HEP",
	"PulseSequenceDetails": "%SiemensSeq%_tfl",
	"RefLinesPE": 32,
	"PercentPhaseFOV": 100,
	"PercentSampling": 100,
	"PhaseEncodingSteps": 255,
	"AcquisitionMatrixPE": 256,
	"ReconMatrixPE": 256,
	"ParallelReductionFactorInPlane": 2,
	"PixelBandwidth": 190,
	"DwellTime": 1.03e-05,
	"ImageOrientationPatientDICOM": [
		0,
		0.999998,
		-0.00174528,
		0,
		-0.00174528,
		-0.999998	],
	"InPlanePhaseEncodingDirectionDICOM": "ROW",
	"ConversionSoftware": "dcm2niix",
	"ConversionSoftwareVersion": "v1.0.20200331"
}

Everything passes BIDS Validation, and I’ve gotten other data sets to run with identical-looking JSON files, so I’m a little stumped. Has anyone encountered this error?

2

File “/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/validation.py”, line 83, in validate_root

The traceback seems to indicate that the error is coming from loading the top-level dataset_description.json, rather than the imaging sidecar files. Can you share that one?

3

Thank you! That was where the error was (d’oh).

I’m now getting the following error:

dim[0] is out-of-range, we'll simply try continuing to read the file, but this will most likely fail horribly.
dim[0] is out-of-range, we'll simply try continuing to read the file, but this will most likely fail horribly.
dim[0] is out-of-range, we'll simply try continuing to read the file, but this will most likely fail horribly.
dim[0] is out-of-range, we'll simply try continuing to read the file, but this will most likely fail horribly.
/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/validation.py:46: UserWarning: The ability to pass arguments to BIDSLayout that control indexing is likely to be removed in future; possibly as early as PyBIDS 0.14. This includes the `config_filename`, `ignore`, `force_index`, and `index_metadata` arguments. The recommended usage pattern is to initialize a new BIDSLayoutIndexer with these arguments, and pass it to the BIDSLayout via the `indexer` argument.
  warnings.warn("The ability to pass arguments to BIDSLayout that control "
Traceback (most recent call last):
  File "/usr/local/miniconda/bin/fmriprep", line 10, in <module>
    sys.exit(main())
  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py", line 17, in main
    parse_args()
  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/parser.py", line 703, in parse_args
    config.environment.exec_env, opts.bids_dir, opts.participant_label
  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/utils/bids.py", line 155, in validate_input_dir
    subprocess.check_call(['bids-validator', bids_dir, '-c', temp.name])
  File "/usr/local/miniconda/lib/python3.7/subprocess.py", line 341, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['bids-validator', PosixPath('PATH REDACTED'), '-c', '/scratch/local/66071616/tmppf9cdmwj']' returned non-zero exit status 1.

Can anyone shed insight on this one? The validator still indicates everything looks good.

4

That indicates that you probably have malformed NIfTI files. Might try running fslhd or mri_info on all of your NIfTIs to see if you can narrow it down. Not sure why the validator isn’t telling you which ones it is.

5

Thank you so much for your help with this.

Here’s my mri_info. Everything looks pretty similar to scans from another study that run through fMRIPrep OK, so I’m not sure what the issue might be.

Volume information for sub-5658_ses-01_task-nback_run-01_bold.nii
      type: SHORT (4)
       fov: 224.000
       dof: 1
    xstart: -112.0, xend: 112.0
    ystart: -112.0, yend: 112.0
    zstart: -63.0, zend: 63.0
        TR: 2000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 deg                                 rees
   nframes: 277
   PhEncDir: UNKNOWN
   FieldStrength: 0.000000
ras xform present
xform info: x_r =  -1.0000, y_r =   0.0000, z_r =  -0.0000, c_r =     0.0000
          : x_a =  -0.0000, y_a =   0.9219, z_a =  -0.3875, c_a =   -17.6305
          : x_s =   0.0000, y_s =   0.3875, z_s =   0.9219, c_s =    10.7645
Orientation   : LAS
Primary Slice Direction: axial

voxel to ras transform:
           -3.5000   0.0000  -0.0000   112.0000
           -0.0000   3.2265  -1.3563   -96.4657
            0.0000   1.3563   3.2265   -90.7147
            0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant -42.875

ras to voxel transform:
           -0.2857  -0.0000  -0.0000    32.0000
           -0.0000   0.2634   0.1107    35.4519
           -0.0000  -0.1107   0.2634    13.2127
           -0.0000  -0.0000  -0.0000     1.0000

Thanks again!

6

Doesn’t look like mri_info shows the dim field. fslhd should, although it may do some fixing up prior to display. Again, I think you need to run on all NIfTI files to determine which ones are causing the error.

If you have Python and nibabel installed, you could do something like:

from glob import glob
import nibabel as nb

for fname in glob("/path/to/dataset/**/*.nii*", recursive=True):
    try:
        img = nb.load(fname)
    except:
        print(f"Failed to load: {fname}")
    else:
        print(f"{fname}: {img.header['dim']}")