ERROR: Embedding failed: 'odict_values' object does not support indexing & BIDS validator

Dear Heudiconv's experts,

I have run heudiconv docker image on FDG PET data with the following command line et execution message:

docker run --rm -it -v /Users/mattvan83/fMRIprep/COMAJ:/data:ro -v /Users/mattvan83/fMRIprep/BIDS:/output nipy/heudiconv:latest -d /data/{subject}/*/* -s s001 -f /data/IMAP_AGEWELL_bids.py -b -o /output
/src/heudiconv/heudiconv/dicoms.py:7: UserWarning: The DICOM readers are highly experimental, unstable, and only work for Siemens time-series at the moment
Please use with caution.  We would be grateful for your help in improving them
  from nibabel.nicom import csareader
INFO: Running heudiconv version 0.5.2-dev
INFO: Need to process 1 study sessions
INFO: PROCESSING STARTS: {'subject': 's001', 'outdir': '/output/', 'session': None}
INFO: Processing 47 dicoms
INFO: Analyzing 47 dicoms
INFO: Generated sequence info with 1 entries
INFO: Doing conversion using dcm2niix
INFO: Converting /output/sub-s001/pet/sub-s001_task-rest_acq-FDG_rec-AC_run-01_pet (47 DICOMs) -> /output/sub-s001/pet . Converter: dcm2niix . Output types: ('nii.gz',)
181230-10:03:23,191 nipype.workflow INFO:
     [Node] Setting-up "convert" in "/tmp/dcm2niixadifah8v/convert".
INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixadifah8v/convert".
181230-10:03:23,603 nipype.workflow INFO:
     [Node] Running "convert" ("nipype.interfaces.dcm2nii.Dcm2niix"), a CommandLine Interface with command:
dcm2niix -b y -z y -x n -t n -m n -f pet -o . -s n -v n /tmp/dcm2niixadifah8v/convert
INFO: [Node] Running "convert" ("nipype.interfaces.dcm2nii.Dcm2niix"), a CommandLine Interface with command:
dcm2niix -b y -z y -x n -t n -m n -f pet -o . -s n -v n /tmp/dcm2niixadifah8v/convert
181230-10:03:24,486 nipype.interface INFO:
     stdout 2018-12-30T10:03:24.485856:Chris Rorden's dcm2niiX version v1.0.20180622 GCC6.3.0 (64-bit Linux)
INFO: stdout 2018-12-30T10:03:24.485856:Chris Rorden's dcm2niiX version v1.0.20180622 GCC6.3.0 (64-bit Linux)
181230-10:03:24,486 nipype.interface INFO:
     stdout 2018-12-30T10:03:24.485856:Found 47 DICOM file(s)
INFO: stdout 2018-12-30T10:03:24.485856:Found 47 DICOM file(s)
181230-10:03:24,486 nipype.interface INFO:
     stdout 2018-12-30T10:03:24.485856:Convert 47 DICOM as ./pet (256x256x47x1)
INFO: stdout 2018-12-30T10:03:24.485856:Convert 47 DICOM as ./pet (256x256x47x1)
181230-10:03:24,832 nipype.interface INFO:
     stdout 2018-12-30T10:03:24.832191:compress: "/usr/bin/pigz" -n -f -6 "./pet.nii"
INFO: stdout 2018-12-30T10:03:24.832191:compress: "/usr/bin/pigz" -n -f -6 "./pet.nii"
181230-10:03:24,832 nipype.interface INFO:
     stdout 2018-12-30T10:03:24.832191:Conversion required 1.112542 seconds (0.126743 for core code).
INFO: stdout 2018-12-30T10:03:24.832191:Conversion required 1.112542 seconds (0.126743 for core code).
181230-10:03:24,898 nipype.workflow INFO:
     [Node] Finished "convert".
INFO: [Node] Finished "convert".
181230-10:03:25,70 nipype.workflow INFO:
     [Node] Setting-up "embedder" in "/tmp/embedmetaf18vnj85/embedder".
INFO: [Node] Setting-up "embedder" in "/tmp/embedmetaf18vnj85/embedder".
181230-10:03:25,227 nipype.workflow INFO:
     [Node] Running "embedder" ("nipype.interfaces.utility.wrappers.Function")
INFO: [Node] Running "embedder" ("nipype.interfaces.utility.wrappers.Function")
181230-10:03:26,887 nipype.workflow WARNING:
     [Node] Error on "embedder" (/tmp/embedmetaf18vnj85/embedder)
WARNING: [Node] Error on "embedder" (/tmp/embedmetaf18vnj85/embedder)
ERROR: Embedding failed: 'odict_values' object does not support indexing
INFO: Post-treating /output/sub-s001/pet/sub-s001_task-rest_acq-FDG_rec-AC_run-01_pet.json file
INFO: Populating template files under /output/
INFO: PROCESSING DONE: {'subject': 's001', 'outdir': '/output/', 'session': None}

It seems that there is an error of embedder following the message above:

181230-10:03:26,887 nipype.workflow WARNING:
     [Node] Error on "embedder" (/tmp/embedmetaf18vnj85/embedder)
WARNING: [Node] Error on "embedder" (/tmp/embedmetaf18vnj85/embedder)
ERROR: Embedding failed: 'odict_values' object does not support indexing

What is the impact of this error ?

Moreover, it seems that my BIDS PET data are in wrong format according BIDS validator:

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.

I have used 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

Thanks in advance for any help.

Best, Matt

nipy / heudiconv

ERROR: Embedding failed: 'odict_values' object does not support indexing & BIDS validator #291