BIDS validator on PET images

1

Dear experts,

I have used heudiconv to convert PET data to BIDS format using the following heuristics:

import os

def create_key(template, outtype=('nii.gz'), annotation_classes=None):
    if template is None or not template:
        raise ValueError('Template must be a valid format string')
    return (template, outtype, annotation_classes)


def infotodict(seqinfo):
    """Heuristic evaluator for determining which runs belong where

    allowed template fields - follow python string module:

    item: index within category
    subject: participant id
    seqitem: run number during scanning
    subindex: sub index within group
    """
    pet = create_key('sub-{subject}/pet/sub-{subject}_task-rest_acq-{acq}_rec-{rec}_run-{item:02d}_pet')

    info = {pet:[]}

    for idx, s in enumerate(seqinfo):
        if (s.dim3 == 47) and (s.TR == -1) and ('CERVEAU 3D SALENGRO' in s.protocol_name):
            rectype = s.series_description.split('_')[-1]
            info[pet].append({'item': s.series_id, 'acq': 'FDG', 'rec': rectype}) # append if multiple series meet criteria


    # You can even put checks in place for your protocol
    msg = []
    if len(info[pet]) != 1: msg.append('Missing correct number of pet runs')
    if msg:
        raise ValueError('\n'.join(msg))
    return info

However, it seems that BIDS validator didn’ t recognize the output format:

Error 1: [Code 61] QUICK_VALIDATION_FAILED
Quick validation failed - the general folder structure does not resemble a BIDS dataset. Have you chosen the right folder (with "sub-*/" subfolders)? Check for structural/naming issues and presence of at least one subject.

Have I done anything wrong ?

Thanks in advance.

Best,
Matt

2

PET extension to BIDS is still in the draft stage and thus it is not yet supported by the validator.

1 Like