time docker run --rm 
--volume /Volumes/LCproject/LC_aging/data_mri:/base nipy/heudiconv:latest 
--dicom_dir_template /base/data_BAP/{subject}_Session*{session}_*/*/* 
--outdir /base/data_BAP_BIDS 
--heuristic /base/data_BAP_BIDS/code/heuristic_postUpdate.py 
--subjects BAP120 
--ses vis 
--converter dcm2niix 
--bids 
--overwrite

INFO: Running heudiconv version 0.10.0 latest 0.12.2
INFO: Need to process 1 study sessions
INFO: PROCESSING STARTS: {'subject': 'BAP120', 'outdir': '/base/data_BAP_BIDS/', 'session': 'vis'}
INFO: Processing 1370 dicoms
INFO: Analyzing 1370 dicoms
/opt/miniconda-latest/lib/python3.7/site-packages/nibabel/nicom/dicomwrappers.py:536: UserWarning: Derived images found and removed
  warnings.warn("Derived images found and removed")
Traceback (most recent call last):
  File "/opt/miniconda-latest/bin/heudiconv", line 8, in <module>
    sys.exit(main())
  File "/opt/miniconda-latest/lib/python3.7/site-packages/heudiconv/cli/run.py", line 24, in main
    workflow(**kwargs)
  File "/opt/miniconda-latest/lib/python3.7/site-packages/heudiconv/main.py", line 351, in workflow
    grouping=grouping,)
  File "/opt/miniconda-latest/lib/python3.7/site-packages/heudiconv/convert.py", line 177, in prep_conversion
    custom_grouping=getattr(heuristic, 'grouping', None))
  File "/opt/miniconda-latest/lib/python3.7/site-packages/heudiconv/dicoms.py", line 202, in group_dicoms_into_seqinfos
    mwinfo = validate_dicom(filename, dcmfilter)
  File "/opt/miniconda-latest/lib/python3.7/site-packages/heudiconv/dicoms.py", line 106, in validate_dicom
    del mw.series_signature[sig]
  File "/opt/miniconda-latest/lib/python3.7/site-packages/nibabel/onetime.py", line 142, in __get__
    val = self.getter(obj)
  File "/opt/miniconda-latest/lib/python3.7/site-packages/nibabel/nicom/dicomwrappers.py", line 642, in series_signature
    signature['image_shape'] = (self.image_shape, eq)
  File "/opt/miniconda-latest/lib/python3.7/site-packages/nibabel/onetime.py", line 142, in __get__
    val = self.getter(obj)
  File "/opt/miniconda-latest/lib/python3.7/site-packages/nibabel/nicom/dicomwrappers.py", line 557, in image_shape
    frame_indices = np.delete(frame_indices, stackid_dim_idx, axis=1)
  File "<__array_function__ internals>", line 6, in delete
  File "/opt/miniconda-latest/lib/python3.7/site-packages/numpy/lib/function_base.py", line 4392, in delete
    axis = normalize_axis_index(axis, ndim)
numpy.AxisError: axis 1 is out of bounds for array of dimension 1

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):
    t1w_lowres = create_key('sub-{subject}/{session}/anat/sub-{subject}_{session}_acq-lowres_T1w')
    fmri_vis = create_key('sub-{subject}/{session}/func/sub-{subject}_{session}_task-vis_run-{item:01d}_bold')
    epi_AP_vis = create_key('sub-{subject}/{session}/fmap/sub-{subject}_{session}_acq-vis_dir-AP_epi')
    epi_PA_vis = create_key('sub-{subject}/{session}/fmap/sub-{subject}_{session}_acq-vis_dir-PA_epi')
    diff_HCPish_AP = create_key('sub-{subject}/{session}/dwi/sub-{subject}_{session}_acq-hcpish_dir-AP_dwi')
    diff_HCPish_PA = create_key('sub-{subject}/{session}/fmap/sub-{subject}_{session}_acq-hcpish_dir-PA_epi')

    info = {
        t1w_lowres: [], fmri_vis: [], epi_AP_vis: [], epi_PA_vis: [], diff_HCPish_AP: [], diff_HCPish_PA: []
        }

    for s in seqinfo:
        if 't1_mprage_low_res' == s.protocol_name:
            info[t1w_lowres].append(s.series_id)
        if 'visual_fMRI' in s.protocol_name and s.series_files == 245: # 245 ensures only full runs (not restarts) are bidsified
            info[fmri_vis].append(s.series_id)
        if 'visual_SE_EPI_Encoding_AP' in s.protocol_name:
            info[epi_AP_vis].append(s.series_id)
        if 'visual_SE_EPI_Encoding_PA' in s.protocol_name:
            info[epi_PA_vis].append(s.series_id)
        if 'diff_HCPish_AP' in s.protocol_name and 'TRACEW' not in s.image_type:
            info[diff_HCPish_AP].append(s.series_id)
        if 'diff_HCPish_PA' in s.protocol_name:
            info[diff_HCPish_PA].append(s.series_id)
    return info