qsiprep.utils.grouping module

Utilities to group scans based on their acquisition parameters

Download many variations of fieldmaps and dwi data

Examples

Set up tests >>> import os >>> from qsiprep.utils.testing import get_grouping_test_data >>> data_root = get_grouping_test_data() >>> os.chdir(data_root)

qsiprep.utils.grouping.find_fieldmaps_from_other_dwis(dwi_files, dwi_file_metadatas)[source]

Find a list of files in the dwi/ directory that can be used for distortion correction.

It is common to acquire DWI scans with opposite phase encoding directions so they can be used to correct each other’s EPI distortion. There is currently no mechanism in BIDS to specify whether b=0 scans in dwi/ can be used as fieldmaps for one another.

Parameters:

dwi_files (list of str) – A list of full paths to dwi nifti files in a BIDS tree.
dwi_file_metadatas (list of dict) – A list of dictionaries containing metadata for each dwi file. Each dictionary should have a PhaseEncodingDirection key.

Returns:

dwi_series_fieldmaps – A dictionary where the keys are the full paths to dwi files and the values are dictionaries describing the fieldmap. If no fieldmap is found, the dictionary will be empty.

Return type:

dict

Examples

A single scan with no opportunities to SDC with a DWI scan >>> from qsiprep.utils.grouping import find_fieldmaps_from_other_dwis >>> single_dwi_file = [“/data/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz”] >>> single_dwi_file_metadatas = [{“PhaseEncodingDirection”: “j”}] >>> find_fieldmaps_from_other_dwis(single_dwi_file, single_dwi_file_metadatas) {‘/data/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’: {}}

Two scans with the same PE direction: again no opportunities to SDC >>> repeat_dwi_files = [“/data/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz”, … “/data/sub-1/dwi/sub-1_dir-AP_run-2_dwi.nii.gz”] >>> repeat_dwi_file_metadatas = [{“PhaseEncodingDirection”: “j”}, … {“PhaseEncodingDirection”: “j”}] >>> find_fieldmaps_from_other_dwis(repeat_dwi_files, … repeat_dwi_file_metadatas) # doctest: +NORMALIZE_WHITESPACE {‘/data/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’: {},

‘/data/sub-1/dwi/sub-1_dir-AP_run-2_dwi.nii.gz’: {}}

Paired scans, each in opposite PE directions >>> paired_dwi_files = [ … “/data/sub-1/dwi/sub-1_dir-AP_dwi.nii.gz”, … “/data/sub-1/dwi/sub-1_dir-PA_dwi.nii.gz”] >>> paired_dwi_file_metadatas = [ … {“PhaseEncodingDirection”: “j”}, … {“PhaseEncodingDirection”: “j-“}] >>> find_fieldmaps_from_other_dwis(paired_dwi_files, … paired_dwi_file_metadatas) # doctest: +NORMALIZE_WHITESPACE {‘/data/sub-1/dwi/sub-1_dir-AP_dwi.nii.gz’: {‘suffix’: ‘dwi’,

‘dwi’: [‘/data/sub-1/dwi/sub-1_dir-PA_dwi.nii.gz’]},

‘/data/sub-1/dwi/sub-1_dir-PA_dwi.nii.gz’: {‘suffix’: ‘dwi’,
‘dwi’: [‘/data/sub-1/dwi/sub-1_dir-AP_dwi.nii.gz’]}}

Multiple scans in multiple PE directions >>> multi_dwi_files = [ … “/data/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz”, … “/data/sub-1/dwi/sub-1_dir-AP_run-2_dwi.nii.gz”, … “/data/sub-1/dwi/sub-1_dir-AP_run-3_dwi.nii.gz”, … “/data/sub-1/dwi/sub-1_dir-PA_run-1_dwi.nii.gz”, … “/data/sub-1/dwi/sub-1_dir-PA_run-2_dwi.nii.gz”] >>> multi_dwi_file_metadatas = [ … {“PhaseEncodingDirection”: “j”}, … {“PhaseEncodingDirection”: “j”}, … {“PhaseEncodingDirection”: “j”}, … {“PhaseEncodingDirection”: “j-“}, … {“PhaseEncodingDirection”: “j-“}] >>> find_fieldmaps_from_other_dwis(multi_dwi_files, … multi_dwi_file_metadatas) # doctest: +NORMALIZE_WHITESPACE {‘/data/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’: {‘suffix’: ‘dwi’,

‘dwi’: [‘/data/sub-1/dwi/sub-1_dir-PA_run-1_dwi.nii.gz’,
‘/data/sub-1/dwi/sub-1_dir-PA_run-2_dwi.nii.gz’]},

‘/data/sub-1/dwi/sub-1_dir-AP_run-2_dwi.nii.gz’: {‘suffix’: ‘dwi’,

‘dwi’: [‘/data/sub-1/dwi/sub-1_dir-PA_run-1_dwi.nii.gz’,
‘/data/sub-1/dwi/sub-1_dir-PA_run-2_dwi.nii.gz’]},

‘/data/sub-1/dwi/sub-1_dir-AP_run-3_dwi.nii.gz’: {‘suffix’: ‘dwi’,

‘dwi’: [‘/data/sub-1/dwi/sub-1_dir-PA_run-1_dwi.nii.gz’,
‘/data/sub-1/dwi/sub-1_dir-PA_run-2_dwi.nii.gz’]},

‘/data/sub-1/dwi/sub-1_dir-PA_run-1_dwi.nii.gz’: {‘suffix’: ‘dwi’,

‘dwi’: [‘/data/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’,
‘/data/sub-1/dwi/sub-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-1/dwi/sub-1_dir-AP_run-3_dwi.nii.gz’]},

‘/data/sub-1/dwi/sub-1_dir-PA_run-2_dwi.nii.gz’: {‘suffix’: ‘dwi’,

‘dwi’: [‘/data/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’,
‘/data/sub-1/dwi/sub-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-1/dwi/sub-1_dir-AP_run-3_dwi.nii.gz’]}}

No information available >>> empty_dwi_files = [ … “/data/sub-1/dwi/sub-1_run-1_dwi.nii.gz”, … “/data/sub-1/dwi/sub-1_run-2_dwi.nii.gz”] >>> empty_dwi_file_metadatas = [ … {}, … {}] >>> find_fieldmaps_from_other_dwis(empty_dwi_files, … empty_dwi_file_metadatas) # doctest: +NORMALIZE_WHITESPACE {‘/data/sub-1/dwi/sub-1_run-1_dwi.nii.gz’: {},

‘/data/sub-1/dwi/sub-1_run-2_dwi.nii.gz’: {}}

qsiprep.utils.grouping.get_concatenated_bids_name(dwi_group)[source]

Derive the output file name for a group of dwi files.

Strip away non-shared key/values from the input list of files. This function assumes you have already split the dwi group into something meaningful and really want to combine all the inputs.

Parameters:: dwi_group (list of str) – A list of full paths to dwi nifti files in a BIDS tree.
Returns:: fname – The BIDS name of the concatenated dwi series.
Return type:: str

Examples

>>> get_concatenated_bids_name([
...    '/data/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz',
...    '/data/sub-1/dwi/sub-1_dir-AP_run-2_dwi.nii.gz',
...    '/data/sub-1/dwi/sub-1_dir-AP_run-3_dwi.nii.gz',
...    '/data/sub-1/dwi/sub-1_dir-AP_run-4_dwi.nii.gz'
... ])
'sub-1_dir-AP'

>>> get_concatenated_bids_name([
...    '/data/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz',
...    '/data/sub-1/dwi/sub-1_dir-AP_run-2_dwi.nii.gz',
...    '/data/sub-1/dwi/sub-1_dir-PA_run-1_dwi.nii.gz',
...    '/data/sub-1/dwi/sub-1_dir-PA_run-2_dwi.nii.gz'
... ])
'sub-1'

>>> get_concatenated_bids_name([
...    '/data/sub-1/dwi/sub-1_acq-HCP-dir-AP_run-1_dwi.nii.gz',
...    '/data/sub-1/dwi/sub-1_acq-HCP_dir-AP_run-2_dwi.nii.gz',
...    '/data/sub-1/dwi/sub-1_acq-HCP_dir-PA_run-1_dwi.nii.gz',
...    '/data/sub-1/dwi/sub-1_acq-HCP_dir-PA_run-2_dwi.nii.gz'
... ])
'sub-1_acq-HCP'

qsiprep.utils.grouping.get_highest_priority_fieldmap(fmap_infos)[source]

Return a dictionary describing the highest priority fieldmap.

Parameters:: fmap_infos (list of dict) – A list of dictionaries describing fieldmaps. Each dictionary must have a suffix key and may have an epi key.
Returns:: selected_fmap_info – The dictionary describing the highest priority fieldmap. This will be the entry from fmap_infos with the highest priority value. If no fieldmaps are found, the dictionary will have a suffix key with a value of None.
Return type:: dict

Examples

Invent some potential fieldmaps >>> epi_fmap1 = {“epi”: “/data/sub-1/fmap/sub-1_dir-AP_run-1_epi.nii.gz”, “suffix”: “epi”} >>> epi_fmap2 = {“epi”: “/data/sub-1/fmap/sub-1_dir-AP_run-2_epi.nii.gz”, “suffix”: “epi”} >>> epi_fmap3 = {“epi”: “/data/sub-1/fmap/sub-1_dir-PA_epi.nii.gz”, “suffix”: “epi”} >>> >>> phasediff_fmap = {“phasediff”: “/data/sub-1/fmap/sub-1_phasediff.nii.gz”, … “suffix”: “phasediff”} >>> phases_fmap = {“phase1”: “/data/sub-1/fmap/sub-1_phase1.nii.gz”, … “suffix”: “phase1”} >>> >>> dwi_fmap1 = {“dwi”: “/data/sub-1/dwi/sub-1_dir-AP_dwi.nii.gz”, “suffix”: “dwi”} >>> dwi_fmap2 = {‘suffix’: ‘dwi’, … ‘dwi’: [‘/data/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’, … ‘/data/sub-1/dwi/sub-1_dir-AP_run-2_dwi.nii.gz’, … ‘/data/sub-1/dwi/sub-1_dir-AP_run-3_dwi.nii.gz’]}

When there are no fieldmaps in fmaps/, but a reverse PE DWI series >>> get_highest_priority_fieldmap([dwi_fmap1]) {‘dwi’: ‘/data/sub-1/dwi/sub-1_dir-AP_dwi.nii.gz’, ‘suffix’: ‘dwi’}

There is both an epi fieldmap and a phase1/phase2 GRE fieldmap >>> get_highest_priority_fieldmap([epi_fmap1, phases_fmap]) {‘suffix’: ‘epi’, ‘epi’: [‘/data/sub-1/fmap/sub-1_dir-AP_run-1_epi.nii.gz’]}

Multiple EPI fieldmaps >>> get_highest_priority_fieldmap( … [epi_fmap1, epi_fmap2, epi_fmap3]) # doctest: +NORMALIZE_WHITESPACE {‘suffix’: ‘epi’,

‘epi’: [‘/data/sub-1/fmap/sub-1_dir-AP_run-1_epi.nii.gz’,
‘/data/sub-1/fmap/sub-1_dir-AP_run-2_epi.nii.gz’, ‘/data/sub-1/fmap/sub-1_dir-PA_epi.nii.gz’]}

An EPI fieldmap from fmap/ should be chosen over a reverse PE DWI series >>> get_highest_priority_fieldmap([epi_fmap1, dwi_fmap2]) {‘suffix’: ‘epi’, ‘epi’: [‘/data/sub-1/fmap/sub-1_dir-AP_run-1_epi.nii.gz’]}

qsiprep.utils.grouping.get_session_groups(layout, subject_data, combine_all_dwis)[source]

Handle the grouping of multiple dwi files within a session.

Parameters:

layout (pybids.BIDSLayout) – A PyBIDS layout
subject_data (dict) – A dictionary of BIDS data for a single subject
combine_all_dwis (bool) – If True, combine all dwi files within a session into a single group

Returns:

dwi_session_groups – A list of lists of dwi files. Each list of dwi files is a group of scans that can be concatenated together.

Return type:

list of list

qsiprep.utils.grouping.group_by_warpspace(dwi_files, layout, ignore_fieldmaps)[source]

Groups a session’s DWI files by their acquisition parameters.

DWIs are grouped by their warped space. Two DWI series that are listed in the IntendedFor field of a fieldmap are assumed to have the same susceptibility distortions and therefore be in the same warped space. The goal of this function is to combine DWI series into groups of acquisitions that are in the same warped space into a list of scans that can be combined after unwarping.

Parameters:

dwi_files (list of str) – A list of full paths to dwi nifti files in a BIDS tree
layout (pybids.BIDSLayout) – A representation of the BIDS tree
ignore_fieldmaps (bool) – If True, ignore any fieldmaps in the fmap/ directory. Images in dwi/ will still be considered for SDC.

Returns:

dwi_groups – A list of dictionaries describing each group of dwi files. Each dictionary has the following keys:

dwi_series: A list of full paths to dwi nifti files in a BIDS tree.
fieldmap_info: A dictionary describing the fieldmap.
If no fieldmap is found, the dictionary will be empty.
dwi_series_pedir: The phase encoding direction of the dwi series.
If no information is available, the value will be an empty string.
concatenated_bids_name: The BIDS name of the concatenated dwi series.
If no information is available, the value will be an empty string.

Return type:

list of dict

Examples

Set up tests >>> from qsiprep.utils.bids import collect_data >>> SUBJECT_ID = “1”

No fieldmap data, a single DWI series >>> subject_data, layout = collect_data(“easy”, SUBJECT_ID) >>> group_by_warpspace( … subject_data[‘dwi’], layout, False) # doctest: +NORMALIZE_WHITESPACE +ELLIPSIS [{‘dwi_series’: [’…sub-1_dwi.nii.gz’],

‘fieldmap_info’: {‘suffix’: None}, ‘dwi_series_pedir’: ‘j’, ‘concatenated_bids_name’: ‘sub-1’}]

Two DWIs with the same PE direction, to be concatenated >>> subject_data, layout = collect_data(“concat1”, SUBJECT_ID) >>> group_by_warpspace( … subject_data[‘dwi’], layout, False) # doctest: +NORMALIZE_WHITESPACE +ELLIPSIS [{‘dwi_series’: [’…/concat1/sub-1/dwi/sub-1_run-01_dwi.nii.gz’,

‘…/concat1/sub-1/dwi/sub-1_run-02_dwi.nii.gz’],

‘fieldmap_info’: {‘suffix’: None}, ‘dwi_series_pedir’: ‘j’, ‘concatenated_bids_name’: ‘sub-1’}]

Two DWI series intended to SDC each other >>> subject_data, layout = collect_data(“opposite”, SUBJECT_ID) >>> group_by_warpspace( … subject_data[‘dwi’], layout, False) # doctest: +NORMALIZE_WHITESPACE +ELLIPSIS [{‘dwi_series’: [’…/opposite/sub-1/dwi/sub-1_dir-AP_dwi.nii.gz’],

‘fieldmap_info’: {‘suffix’: ‘dwi’,
‘dwi’: [’…/opposite/sub-1/dwi/sub-1_dir-PA_dwi.nii.gz’]},

‘dwi_series_pedir’: ‘j’, ‘concatenated_bids_name’: ‘sub-1_dir-AP’},

{‘dwi_series’: [’…/opposite/sub-1/dwi/sub-1_dir-PA_dwi.nii.gz’],

‘fieldmap_info’: {‘suffix’: ‘dwi’,
‘dwi’: [’…/opposite/sub-1/dwi/sub-1_dir-AP_dwi.nii.gz’]},

‘dwi_series_pedir’: ‘j-‘, ‘concatenated_bids_name’: ‘sub-1_dir-PA’}]

Multiple DWI series in two different PE directions >>> subject_data, layout = collect_data(“opposite_concat”, SUBJECT_ID) >>> group_by_warpspace( … subject_data[‘dwi’], layout, False) # doctest: +NORMALIZE_WHITESPACE +ELLIPSIS [{‘dwi_series’: [’…/opposite_concat/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’,

‘…/opposite_concat/sub-1/dwi/sub-1_dir-AP_run-2_dwi.nii.gz’],

‘fieldmap_info’: {‘suffix’: ‘dwi’,

‘dwi’: [’…/opposite_concat/sub-1/dwi/sub-1_dir-PA_run-1_dwi.nii.gz’,
‘…/opposite_concat/sub-1/dwi/sub-1_dir-PA_run-2_dwi.nii.gz’]},

‘dwi_series_pedir’: ‘j’, ‘concatenated_bids_name’: ‘sub-1_dir-AP’},

{‘dwi_series’: [’…/opposite_concat/sub-1/dwi/sub-1_dir-PA_run-1_dwi.nii.gz’,

‘…/opposite_concat/sub-1/dwi/sub-1_dir-PA_run-2_dwi.nii.gz’],

‘fieldmap_info’: {‘suffix’: ‘dwi’,

‘dwi’: [’…/opposite_concat/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’,
‘…/opposite_concat/sub-1/dwi/sub-1_dir-AP_run-2_dwi.nii.gz’]},

‘dwi_series_pedir’: ‘j-‘, ‘concatenated_bids_name’: ‘sub-1_dir-PA’}]

A phasediff fieldmap defines the warped group >>> subject_data, layout = collect_data(“phasediff”, SUBJECT_ID) >>> group_by_warpspace( … subject_data[‘dwi’], layout, False) # doctest: +NORMALIZE_WHITESPACE +ELLIPSIS [{‘dwi_series’: [’…/phasediff/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’,

‘…/phasediff/sub-1/dwi/sub-1_dir-AP_run-2_dwi.nii.gz’],

‘fieldmap_info’: {‘phasediff’: ‘…/phasediff/sub-1/fmap/sub-1_phasediff.nii.gz’,
‘magnitude1’: ‘…/magnitude1/sub-1/fmap/sub-1_magnitude1.nii.gz’, ‘suffix’: ‘phasediff’},

‘dwi_series_pedir’: ‘j’, ‘concatenated_bids_name’: ‘sub-1_dir-AP’}]

Two DWI series, each with its own fieldmap/warped space >>> subject_data, layout = collect_data(“separate_fmaps”, SUBJECT_ID) >>> group_by_warpspace( … subject_data[‘dwi’], layout, False) # doctest: +NORMALIZE_WHITESPACE +ELLIPSIS [{‘dwi_series’: [’…/separate_fmaps/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’],

‘fieldmap_info’: {‘suffix’: ‘epi’,
‘epi’: [’…/separate_fmaps/sub-1/fmap/sub-1_dir-PA_run-1_epi.nii.gz’]},

‘dwi_series_pedir’: ‘j’, ‘concatenated_bids_name’: ‘sub-1_dir-AP_run-1’},

{‘dwi_series’: [’…/separate_fmaps/sub-1/dwi/sub-1_dir-AP_run-2_dwi.nii.gz’],

‘fieldmap_info’: {‘suffix’: ‘epi’,
‘epi’: [’…/separate_fmaps/sub-1/fmap/sub-1_dir-PA_run-2_epi.nii.gz’]},

‘dwi_series_pedir’: ‘j’, ‘concatenated_bids_name’: ‘sub-1_dir-AP_run-2’}]

Same as above but ignoring fieldmaps. Data gets concatenated >>> subject_data, layout = collect_data(“separate_fmaps”, SUBJECT_ID) >>> group_by_warpspace( … subject_data[‘dwi’], layout, True) # doctest: +NORMALIZE_WHITESPACE +ELLIPSIS [{‘dwi_series’: [’…/separate_fmaps/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’,

‘…/separate_fmaps/sub-1/dwi/sub-1_dir-AP_run-2_dwi.nii.gz’],

‘fieldmap_info’: {‘suffix’: None}, ‘dwi_series_pedir’: ‘j’, ‘concatenated_bids_name’: ‘sub-1_dir-AP’}]

Two DWI series, opposite PE directions, dedicated EPI fieldmap for each >>> subject_data, layout = collect_data(“mixed_fmaps”, SUBJECT_ID) >>> group_by_warpspace( … subject_data[‘dwi’], layout, False) # doctest: +NORMALIZE_WHITESPACE +ELLIPSIS [{‘dwi_series’: [’…/mixed_fmaps/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’],

‘fieldmap_info’: {‘suffix’: ‘epi’,
‘epi’: [’…/mixed_fmaps/sub-1/fmap/sub-1_dir-PA_run-1_epi.nii.gz’]},

‘dwi_series_pedir’: ‘j’, ‘concatenated_bids_name’: ‘sub-1_dir-AP_run-1’},

{‘dwi_series’: [’…/mixed_fmaps/sub-1/dwi/sub-1_dir-PA_run-2_dwi.nii.gz’],

‘fieldmap_info’: {‘suffix’: ‘epi’,
‘epi’: [’…/mixed_fmaps/sub-1/fmap/sub-1_dir-AP_run-2_epi.nii.gz’]}, ‘dwi_series_pedir’: ‘j-‘, ‘concatenated_bids_name’: ‘sub-1_dir-PA_run-2’}]

Same as last one, but ignore fieldmaps. The DWI series will be used for SDC instead >>> subject_data, layout = collect_data(“mixed_fmaps”, SUBJECT_ID) >>> group_by_warpspace( … subject_data[‘dwi’], layout, True) # doctest: +NORMALIZE_WHITESPACE +ELLIPSIS [{‘dwi_series’: [’…/mixed_fmaps/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’],

‘fieldmap_info’: {‘suffix’: ‘dwi’,
‘dwi’: [’…/mixed_fmaps/sub-1/dwi/sub-1_dir-PA_run-2_dwi.nii.gz’]},

‘dwi_series_pedir’: ‘j’, ‘concatenated_bids_name’: ‘sub-1_dir-AP_run-1’},

{‘dwi_series’: [’…/mixed_fmaps/sub-1/dwi/sub-1_dir-PA_run-2_dwi.nii.gz’],

‘fieldmap_info’: {‘suffix’: ‘dwi’,
‘dwi’: [’…/mixed_fmaps/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’]},

‘dwi_series_pedir’: ‘j-‘, ‘concatenated_bids_name’: ‘sub-1_dir-PA_run-2’}]

There is no metadata related to epi distortion: don’t concatenate anything >>> subject_data, layout = collect_data(“missing_info”, SUBJECT_ID) >>> group_by_warpspace( … subject_data[‘dwi’], layout, False) # doctest: +NORMALIZE_WHITESPACE +ELLIPSIS [{‘dwi_series’: [’…/missing_info/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’],

‘fieldmap_info’: {‘suffix’: None}, ‘dwi_series_pedir’: ‘’, ‘concatenated_bids_name’: ‘sub-1_dir-AP_run-1’},

{‘dwi_series’: [’…/missing_info/sub-1/dwi/sub-1_dir-PA_run-2_dwi.nii.gz’],
‘fieldmap_info’: {‘suffix’: None}, ‘dwi_series_pedir’: ‘’, ‘concatenated_bids_name’: ‘sub-1_dir-PA_run-2’}]

A bizarre mix of PE directions and some missing data >>> subject_data, layout = collect_data(“wtf”, SUBJECT_ID) >>> group_by_warpspace( … subject_data[‘dwi’], layout, False) # doctest: +NORMALIZE_WHITESPACE +ELLIPSIS [{‘dwi_series’: [’…/wtf/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’,

‘…/wtf/sub-1/dwi/sub-1_dir-AP_run-2_dwi.nii.gz’],

‘fieldmap_info’: {‘suffix’: ‘dwi’,

‘dwi’: [’…/wtf/sub-1/dwi/sub-1_dir-PA_run-1_dwi.nii.gz’,
‘…/wtf/sub-1/dwi/sub-1_dir-PA_run-2_dwi.nii.gz’]},

‘dwi_series_pedir’: ‘j’, ‘concatenated_bids_name’: ‘sub-1_dir-AP’},

{‘dwi_series’: [’…/wtf/sub-1/dwi/sub-1_dir-IS_dwi.nii.gz’],
‘fieldmap_info’: {‘suffix’: None}, ‘dwi_series_pedir’: ‘k-‘, ‘concatenated_bids_name’: ‘sub-1_dir-IS’},

{‘dwi_series’: [’…/wtf/sub-1/dwi/sub-1_run-1_dwi.nii.gz’],
‘fieldmap_info’: {‘suffix’: None}, ‘dwi_series_pedir’: ‘’, ‘concatenated_bids_name’: ‘sub-1_run-1’},

{‘dwi_series’: [’…/wtf/sub-1/dwi/sub-1_run-2_dwi.nii.gz’],
‘fieldmap_info’: {‘suffix’: None}, ‘dwi_series_pedir’: ‘’, ‘concatenated_bids_name’: ‘sub-1_run-2’},

{‘dwi_series’: [’…/wtf/sub-1/dwi/sub-1_dir-PA_run-1_dwi.nii.gz’,

‘…/wtf/sub-1/dwi/sub-1_dir-PA_run-2_dwi.nii.gz’],

‘fieldmap_info’: {‘suffix’: ‘dwi’,

‘dwi’: [’…/wtf/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’,
‘…/wtf/sub-1/dwi/sub-1_dir-AP_run-2_dwi.nii.gz’]},

‘dwi_series_pedir’: ‘j-‘, ‘concatenated_bids_name’: ‘sub-1_dir-PA’}]

qsiprep.utils.grouping.group_dwi_scans(subject_data, using_fsl=False, combine_scans=True, ignore_fieldmaps=False, concatenate_distortion_groups=False)[source]

Determine which scans can be concatenated based on their acquisition parameters.

Parameters:

bids_layout (pybids.BIDSLayout) – A PyBIDS layout
group_for_eddy (bool) – Should a plus and minus series be grouped together for TOPUP/eddy?
combine_scans (bool) – Should scan concatention happen?
concatenate_distortion_groups (bool) – Will distortion groups get merged at the end of the pipeline?

Returns:

scan_groups – A dict where the keys are the BIDS derivatives name of the output file after concatenation. The values are lists of dwi files in that group.

Return type:

list of dict

qsiprep.utils.grouping.group_for_concatenation(all_dwi_fmap_groups)[source]

Find matched pairs of phase encoding directions that can be combined after SHORELine.

Any groups that don’t have a phase encoding direction won’t be correctable by SHORELine.

Parameters:: all_dwi_fmap_groups (list of dict) – A list of dictionaries describing each group of dwi files.
Returns:: concatenation_grouping – A dictionary mapping the concatenated BIDS name of each group to the name of the group that it should be concatenated with.
Return type:: dict

qsiprep.utils.grouping.group_for_eddy(all_dwi_fmap_groups)[source]

Find matched pairs of phase encoding directions that can be combined for TOPUP/eddy.

Any groups that don’t have a phase encoding direction won’t be correctable by eddy/TOPUP.

Parameters:

all_dwi_fmap_groups (list of dict) – A list of dictionaries describing each group of dwi files.

Returns:

eddy_groups – A list of dictionaries describing each group of dwi files. Each dictionary has the following keys:

dwi_series: A list of full paths to dwi nifti files in a BIDS tree.
fieldmap_info: A dictionary describing the fieldmap.
If no fieldmap is found, the dictionary will be empty.
dwi_series_pedir: The phase encoding direction of the dwi series.
If no information is available, the value will be an empty string.
concatenated_bids_name: The BIDS name of the concatenated dwi series.
If no information is available, the value will be an empty string.

Return type:

list of dict

Examples

Paired DWI series to correct each other: >>> dwi_groups = [ … {‘dwi_series’: [’…/mixed_fmaps/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’], … ‘fieldmap_info’: {‘suffix’: ‘dwi’, … ‘dwi’: [’…/mixed_fmaps/sub-1/dwi/sub-1_dir-PA_run-2_dwi.nii.gz’]}, … ‘dwi_series_pedir’: ‘j’, … ‘concatenated_bids_name’: ‘sub-1_dir-AP_run-1’}, … {‘dwi_series’: [’…/mixed_fmaps/sub-1/dwi/sub-1_dir-PA_run-2_dwi.nii.gz’], … ‘fieldmap_info’: {‘suffix’: ‘dwi’, … ‘dwi’: [’…/mixed_fmaps/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’]}, … ‘dwi_series_pedir’: ‘j-‘, … ‘concatenated_bids_name’: ‘sub-1_dir-PA_run-2’}] >>> group_for_eddy(dwi_groups) # doctest: +NORMALIZE_WHITESPACE [{‘dwi_series’: [’…/mixed_fmaps/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’],

‘dwi_series_pedir’: ‘j’, ‘fieldmap_info’: {‘suffix’: ‘rpe_series’,

‘rpe_series’: [’…/mixed_fmaps/sub-1/dwi/sub-1_dir-PA_run-2_dwi.nii.gz’]},

‘concatenated_bids_name’: ‘sub-1’}]

AP/PA EPI fieldmaps >>> dwi_groups = [ … {‘dwi_series’: [’…/mixed_fmaps/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’], … ‘fieldmap_info’: {‘suffix’: ‘epi’, … ‘epi’: [’…/mixed_fmaps/sub-1/fmap/sub-1_dir-PA_run-1_epi.nii.gz’]}, … ‘dwi_series_pedir’: ‘j’, … ‘concatenated_bids_name’: ‘sub-1_dir-AP_run-1’}, … {‘dwi_series’: [’…/mixed_fmaps/sub-1/dwi/sub-1_dir-PA_run-2_dwi.nii.gz’], … ‘fieldmap_info’: {‘suffix’: ‘epi’, … ‘epi’: [’…/mixed_fmaps/sub-1/fmap/sub-1_dir-AP_run-2_epi.nii.gz’]}, … ‘dwi_series_pedir’: ‘j-‘, … ‘concatenated_bids_name’: ‘sub-1_dir-PA_run-2’}] >>> group_for_eddy(dwi_groups) # doctest: +NORMALIZE_WHITESPACE [{‘dwi_series’: [’…/mixed_fmaps/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’],

‘dwi_series_pedir’: ‘j’, ‘fieldmap_info’: {‘suffix’: ‘rpe_series’,

‘rpe_series’: [’…/mixed_fmaps/sub-1/dwi/sub-1_dir-PA_run-2_dwi.nii.gz’], ‘epi’: [’…/mixed_fmaps/sub-1/fmap/sub-1_dir-AP_run-2_epi.nii.gz’,

‘…/mixed_fmaps/sub-1/fmap/sub-1_dir-PA_run-1_epi.nii.gz’]},

‘concatenated_bids_name’: ‘sub-1’}]

Repeated scans per PE direction >>> dwi_groups = [ … {‘dwi_series’: [’…/opposite_concat/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’, … ‘…/opposite_concat/sub-1/dwi/sub-1_dir-AP_run-2_dwi.nii.gz’], … ‘fieldmap_info’: {‘suffix’: ‘dwi’, … ‘dwi’: [’…/opposite_concat/sub-1/dwi/sub-1_dir-PA_run-1_dwi.nii.gz’, … ‘…/opposite_concat/sub-1/dwi/sub-1_dir-PA_run-2_dwi.nii.gz’]}, … ‘dwi_series_pedir’: ‘j’, … ‘concatenated_bids_name’: ‘sub-1_dir-AP’}, … {‘dwi_series’: [’…/opposite_concat/sub-1/dwi/sub-1_dir-PA_run-1_dwi.nii.gz’, … ‘…/opposite_concat/sub-1/dwi/sub-1_dir-PA_run-2_dwi.nii.gz’], … ‘fieldmap_info’: {‘suffix’: ‘dwi’, … ‘dwi’: [’…/opposite_concat/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’, … ‘…/opposite_concat/sub-1/dwi/sub-1_dir-AP_run-2_dwi.nii.gz’]}, … ‘dwi_series_pedir’: ‘j-‘, … ‘concatenated_bids_name’: ‘sub-1_dir-PA’}] >>> group_for_eddy(dwi_groups) # doctest: +NORMALIZE_WHITESPACE [{‘dwi_series’: [’…/opposite_concat/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’,

‘…/opposite_concat/sub-1/dwi/sub-1_dir-AP_run-2_dwi.nii.gz’],

‘dwi_series_pedir’: ‘j’, ‘fieldmap_info’: {‘suffix’: ‘rpe_series’,

‘rpe_series’: [’…/opposite_concat/sub-1/dwi/sub-1_dir-PA_run-1_dwi.nii.gz’,
‘…/opposite_concat/sub-1/dwi/sub-1_dir-PA_run-2_dwi.nii.gz’]},

‘concatenated_bids_name’: ‘sub-1’}]

A phasediff fieldmap (Not used by eddy) >>> dwi_groups = [ … {‘dwi_series’: [’…/phasediff/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’, … ‘…/phasediff/sub-1/dwi/sub-1_dir-AP_run-2_dwi.nii.gz’], … ‘fieldmap_info’: {‘phasediff’: ‘…/phasediff/sub-1/fmap/sub-1_phasediff.nii.gz’, … ‘magnitude1’: ‘…/magnitude1/sub-1/fmap/sub-1_magnitude1.nii.gz’, … ‘suffix’: ‘phasediff’}, … ‘dwi_series_pedir’: ‘j’, … ‘concatenated_bids_name’: ‘sub-1_dir-AP’}] >>> group_for_eddy(dwi_groups) # doctest: +NORMALIZE_WHITESPACE [{‘dwi_series’: [’…/phasediff/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’,

‘…/phasediff/sub-1/dwi/sub-1_dir-AP_run-2_dwi.nii.gz’],

‘fieldmap_info’: {‘phasediff’: ‘…/phasediff/sub-1/fmap/sub-1_phasediff.nii.gz’,
‘magnitude1’: ‘…/magnitude1/sub-1/fmap/sub-1_magnitude1.nii.gz’, ‘suffix’: ‘phasediff’},

‘dwi_series_pedir’: ‘j’, ‘concatenated_bids_name’: ‘sub-1_dir-AP’}]

qsiprep.utils.grouping.merge_dwi_groups(dwi_groups_plus, dwi_groups_minus)[source]

Convert two dwi groups into a single group that will be concatenated for FSL.

Parameters:

dwi_groups_plus (list of dict) – A list of dictionaries describing each group of dwi files. Each dictionary has the following keys:
- dwi_series: A list of full paths to dwi nifti files in a BIDS tree.
- fieldmap_info: A dictionary describing the fieldmap.
  If no fieldmap is found, the dictionary will be empty.
- dwi_series_pedir: The phase encoding direction of the dwi series.
  If no information is available, the value will be an empty string.
- concatenated_bids_name: The BIDS name of the concatenated dwi series.
  If no information is available, the value will be an empty string.
dwi_groups_minus (list of dict) – A list of dictionaries describing each group of dwi files. Each dictionary has the same keys as dwi_groups_plus.

Returns:

merged_group – A dictionary describing the merged group of dwi files. The dictionary has the same keys as dwi_groups_plus.

Return type:

dict

Examples

Set up tests >>> SUBJECT_ID = “1”

AP/PA fieldmaps and paired DWI series >>> plus_groups = [ … {‘dwi_series’: [’…/mixed_fmaps/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’], … ‘fieldmap_info’: {‘suffix’: ‘epi’, … ‘epi’: [’…/mixed_fmaps/sub-1/fmap/sub-1_dir-PA_run-1_epi.nii.gz’]}, … ‘dwi_series_pedir’: ‘j’, … ‘concatenated_bids_name’: ‘sub-1_dir-AP_run-1’}] >>> minus_groups = [ … {‘dwi_series’: [’…/mixed_fmaps/sub-1/dwi/sub-1_dir-PA_run-2_dwi.nii.gz’], … ‘fieldmap_info’: {‘suffix’: ‘epi’, … ‘epi’: [’…/mixed_fmaps/sub-1/fmap/sub-1_dir-AP_run-2_epi.nii.gz’]}, … ‘dwi_series_pedir’: ‘j-‘, … ‘concatenated_bids_name’: ‘sub-1_dir-PA_run-2’}] >>> merge_dwi_groups(plus_groups, minus_groups) # doctest: +NORMALIZE_WHITESPACE {‘dwi_series’: [’…/mixed_fmaps/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’],

‘dwi_series_pedir’: ‘j’, ‘fieldmap_info’: {‘suffix’: ‘rpe_series’,

‘rpe_series’: [’…/mixed_fmaps/sub-1/dwi/sub-1_dir-PA_run-2_dwi.nii.gz’], ‘epi’: [’…/mixed_fmaps/sub-1/fmap/sub-1_dir-AP_run-2_epi.nii.gz’,

‘…/mixed_fmaps/sub-1/fmap/sub-1_dir-PA_run-1_epi.nii.gz’]},

‘concatenated_bids_name’: ‘sub-1’}

Two series SDC each other >>> plus_groups = [ … {‘dwi_series’: [’…/opposite/sub-1/dwi/sub-1_dir-AP_dwi.nii.gz’], … ‘fieldmap_info’: {‘suffix’: ‘dwi’, … ‘dwi’: [’…/opposite/sub-1/dwi/sub-1_dir-PA_dwi.nii.gz’]}, … ‘dwi_series_pedir’: ‘j’, … ‘concatenated_bids_name’: ‘sub-1_dir-AP’}] >>> minus_groups = [ … {‘dwi_series’: [’…/opposite/sub-1/dwi/sub-1_dir-PA_dwi.nii.gz’], … ‘fieldmap_info’: {‘suffix’: ‘dwi’, … ‘dwi’: [’…/opposite/sub-1/dwi/sub-1_dir-AP_dwi.nii.gz’]}, … ‘dwi_series_pedir’: ‘j-‘, … ‘concatenated_bids_name’: ‘sub-1_dir-PA’}] >>> merge_dwi_groups(plus_groups, minus_groups) # doctest: +NORMALIZE_WHITESPACE {‘dwi_series’: [’…/opposite/sub-1/dwi/sub-1_dir-AP_dwi.nii.gz’],

‘dwi_series_pedir’: ‘j’, ‘fieldmap_info’: {‘suffix’: ‘rpe_series’,

‘rpe_series’: [’…/opposite/sub-1/dwi/sub-1_dir-PA_dwi.nii.gz’]},

‘concatenated_bids_name’: ‘sub-1’}

An odd case: one has an EPI >>> plus_groups = [ … {‘dwi_series’: [’…/opposite/sub-1/dwi/sub-1_dir-AP_dwi.nii.gz’], … ‘fieldmap_info’: {‘suffix’: ‘dwi’, … ‘dwi’: [’…/opposite/sub-1/dwi/sub-1_dir-PA_dwi.nii.gz’]}, … ‘dwi_series_pedir’: ‘j’, … ‘concatenated_bids_name’: ‘sub-1_dir-AP’}] >>> minus_groups = [ … {‘dwi_series’: [’…/opposite/sub-1/dwi/sub-1_dir-PA_dwi.nii.gz’], … ‘fieldmap_info’: {‘suffix’: ‘epi’, … ‘epi’: [’…/mixed_fmaps/sub-1/fmap/sub-1_dir-AP_run-2_epi.nii.gz’]}, … ‘dwi_series_pedir’: ‘j-‘, … ‘concatenated_bids_name’: ‘sub-1_dir-PA’}] >>> merge_dwi_groups(plus_groups, minus_groups) # doctest: +NORMALIZE_WHITESPACE {‘dwi_series’: [’…/opposite/sub-1/dwi/sub-1_dir-AP_dwi.nii.gz’],

‘dwi_series_pedir’: ‘j’, ‘fieldmap_info’: {‘suffix’: ‘rpe_series’,

‘rpe_series’: [’…/opposite/sub-1/dwi/sub-1_dir-PA_dwi.nii.gz’], ‘epi’: [’…/mixed_fmaps/sub-1/fmap/sub-1_dir-AP_run-2_epi.nii.gz’]},

‘concatenated_bids_name’: ‘sub-1’}

qsiprep.utils.grouping.split_by_phase_encoding_direction(dwi_files, metadatas)[source]

If no fieldmaps have been found for a group of dwi files, split them by PE direction.

Parameters:

dwi_files (list of str) – A list of full paths to dwi nifti files in a BIDS tree.
metadatas (list of dict) – A list of dictionaries containing metadata for each dwi file. The only field that is used i “PhaseEncodingDirection”.

Returns:

dwi_groups – A list of dictionaries describing each group of dwi files. Each dictionary has the following keys:

dwi_series: A list of full paths to dwi nifti files in a BIDS tree.
fieldmap_info: A dictionary describing the fieldmap.
If no fieldmap is found, the dictionary will be empty.
dwi_series_pedir: The phase encoding direction of the dwi series.
If no information is available, the value will be an empty string.
concatenated_bids_name: The BIDS name of the concatenated dwi series.
If no information is available, the value will be an empty string.

Return type:

list of dict

Examples

One of each direction (Not likely to see in the wild) >>> dwi_files = [ … ‘/data/sub-1/dwi/sub-1_dir-AP_dwi.nii.gz’, … ‘/data/sub-1/dwi/sub-1_dir-PA_dwi.nii.gz’, … ‘/data/sub-1/dwi/sub-1_dir-RL_dwi.nii.gz’, … ‘/data/sub-1/dwi/sub-1_dir-LR_dwi.nii.gz’, … ‘/data/sub-1/dwi/sub-1_dir-IS_dwi.nii.gz’, … ‘/data/sub-1/dwi/sub-1_dir-SI_dwi.nii.gz’ … ] >>> metadatas = [ … {‘PhaseEncodingDirection’: ‘j’}, … {‘PhaseEncodingDirection’: ‘j-‘}, … {‘PhaseEncodingDirection’: ‘i’}, … {‘PhaseEncodingDirection’: ‘i-‘}, … {‘PhaseEncodingDirection’: ‘k’}, … {‘PhaseEncodingDirection’: ‘k-‘} … ] >>> split_by_phase_encoding_direction(dwi_files, metadatas) # doctest: +NORMALIZE_WHITESPACE [{‘dwi_series’: [‘/data/sub-1/dwi/sub-1_dir-RL_dwi.nii.gz’],

‘fieldmap_info’: {‘suffix’: None}, ‘dwi_series_pedir’: ‘i’, ‘concatenated_bids_name’: ‘sub-1_dir-RL’},

{‘dwi_series’: [‘/data/sub-1/dwi/sub-1_dir-LR_dwi.nii.gz’],
‘fieldmap_info’: {‘suffix’: None}, ‘dwi_series_pedir’: ‘i-‘, ‘concatenated_bids_name’: ‘sub-1_dir-LR’},

{‘dwi_series’: [‘/data/sub-1/dwi/sub-1_dir-AP_dwi.nii.gz’],
‘fieldmap_info’: {‘suffix’: None}, ‘dwi_series_pedir’: ‘j’, ‘concatenated_bids_name’: ‘sub-1_dir-AP’},

{‘dwi_series’: [‘/data/sub-1/dwi/sub-1_dir-PA_dwi.nii.gz’],
‘fieldmap_info’: {‘suffix’: None}, ‘dwi_series_pedir’: ‘j-‘, ‘concatenated_bids_name’: ‘sub-1_dir-PA’},

{‘dwi_series’: [‘/data/sub-1/dwi/sub-1_dir-IS_dwi.nii.gz’],
‘fieldmap_info’: {‘suffix’: None}, ‘dwi_series_pedir’: ‘k’, ‘concatenated_bids_name’: ‘sub-1_dir-IS’},

{‘dwi_series’: [‘/data/sub-1/dwi/sub-1_dir-SI_dwi.nii.gz’],
‘fieldmap_info’: {‘suffix’: None}, ‘dwi_series_pedir’: ‘k-‘, ‘concatenated_bids_name’: ‘sub-1_dir-SI’}]

Repeats of some: >>> dwi_files = [ … ‘/data/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’, … ‘/data/sub-1/dwi/sub-1_dir-AP_run-2_dwi.nii.gz’, … ‘/data/sub-1/dwi/sub-1_dir-AP_run-3_dwi.nii.gz’, … ‘/data/sub-1/dwi/sub-1_dir-PA_dwi.nii.gz’, … ‘/data/sub-1/dwi/sub-1_dir-RL_dwi.nii.gz’ … ] >>> metadatas = [ … {‘PhaseEncodingDirection’: ‘j’}, … {‘PhaseEncodingDirection’: ‘j’}, … {‘PhaseEncodingDirection’: ‘j’}, … {‘PhaseEncodingDirection’: ‘j-‘}, … {‘PhaseEncodingDirection’: ‘i’} … ] >>> split_by_phase_encoding_direction(dwi_files, metadatas) # doctest: +NORMALIZE_WHITESPACE [{‘dwi_series’: [‘/data/sub-1/dwi/sub-1_dir-RL_dwi.nii.gz’],

‘fieldmap_info’: {‘suffix’: None}, ‘dwi_series_pedir’: ‘i’, ‘concatenated_bids_name’: ‘sub-1_dir-RL’},

{‘dwi_series’: [‘/data/sub-1/dwi/sub-1_dir-AP_run-1_dwi.nii.gz’,

‘/data/sub-1/dwi/sub-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-1/dwi/sub-1_dir-AP_run-3_dwi.nii.gz’],

‘fieldmap_info’: {‘suffix’: None}, ‘dwi_series_pedir’: ‘j’, ‘concatenated_bids_name’: ‘sub-1_dir-AP’},

{‘dwi_series’: [‘/data/sub-1/dwi/sub-1_dir-PA_dwi.nii.gz’],
‘fieldmap_info’: {‘suffix’: None}, ‘dwi_series_pedir’: ‘j-‘, ‘concatenated_bids_name’: ‘sub-1_dir-PA’}]

Some missing metadata >>> dwi_files = [ … ‘/data/sub-1/dwi/sub-1_run-1_dwi.nii.gz’, … ‘/data/sub-1/dwi/sub-1_run-2_dwi.nii.gz’, … ‘/data/sub-1/dwi/sub-1_run-3_dwi.nii.gz’, … ‘/data/sub-1/dwi/sub-1_run-4_dwi.nii.gz’, … ‘/data/sub-1/dwi/sub-1_run-5_dwi.nii.gz’ … ] >>> metadatas = [ … {‘PhaseEncodingDirection’: ‘j’}, … {‘PhaseEncodingDirection’: ‘j’}, … {‘PhaseEncodingDirection’: ‘j-‘}, … {}, … {} … ] >>> split_by_phase_encoding_direction(dwi_files, metadatas) # doctest: +NORMALIZE_WHITESPACE [{‘dwi_series’: [‘/data/sub-1/dwi/sub-1_run-1_dwi.nii.gz’,

‘/data/sub-1/dwi/sub-1_run-2_dwi.nii.gz’],

‘fieldmap_info’: {‘suffix’: None}, ‘dwi_series_pedir’: ‘j’, ‘concatenated_bids_name’: ‘sub-1’},

{‘dwi_series’: [‘/data/sub-1/dwi/sub-1_run-3_dwi.nii.gz’],
‘fieldmap_info’: {‘suffix’: None}, ‘dwi_series_pedir’: ‘j-‘, ‘concatenated_bids_name’: ‘sub-1_run-3’},

{‘dwi_series’: [‘/data/sub-1/dwi/sub-1_run-4_dwi.nii.gz’],
‘fieldmap_info’: {‘suffix’: None}, ‘dwi_series_pedir’: ‘’, ‘concatenated_bids_name’: ‘sub-1_run-4’},

{‘dwi_series’: [‘/data/sub-1/dwi/sub-1_run-5_dwi.nii.gz’],
‘fieldmap_info’: {‘suffix’: None}, ‘dwi_series_pedir’: ‘’, ‘concatenated_bids_name’: ‘sub-1_run-5’}]