cmtklib.bids.io module

This module provides classes to handle custom BIDS derivatives file input.

class cmtklib.bids.io.CustomAparcAsegBIDSFile[source]

Bases: cmtklib.bids.io.CustomBIDSFile

Represent a custom BIDS-formatted Freesurfer aparc+aseg file in the form sub-<label>_desc-aparcaseg_dseg.nii.gz.

class cmtklib.bids.io.CustomBIDSFile(p_toolbox_derivatives_dir='', p_suffix='', p_extension='', p_acquisition='', p_atlas='', p_res='', p_label='', p_desc='')[source]

Bases: traits.has_traits.HasTraits

Base class used to represent a BIDS-formatted file inside a custom BIDS derivatives directory.

toolbox_derivatives_dir

Toolbox folder name in the derivatives/ of the BIDS dataset

Type: Str

suffix

Filename suffix e.g. sub-01_T1w.nii.gz has suffix T1w

Type: Str

acquisition

Label used in _acq-<label>_

Type: Str

res

Label used in _res-<label>_

Type: Str

extension

File extension

Type: Str

atlas

Label used in _atlas-<label>_

Type: Str

label

Label used in _label-<label>_

Type: Str

desc

Label used in _desc-<label>_

Type: Str

get_filename_path(base_dir, subject, session=None, debug=True)[source]

Return the number of regions by reading its associated TSV side car file describing the nodes.

Parameters

base_dir (str) – BIDS root directory or derivatives/ directory in BIDS root directory
subject (str) – Subject filename entity e.g. “sub-01”
session (str) – Session filename entity e.g. “ses-01” if applicable (Default: None)
debug (bool) – Debug mode (Extra outputed messages) if True

get_query_dict()[source]: Return the dictionary to be passed to BIDSDataGrabber to query a list of files.

get_toolbox_derivatives_dir()[source]: Return the value of custom_derivatives_dir attribute.

class cmtklib.bids.io.CustomBrainMaskBIDSFile[source]

Bases: cmtklib.bids.io.CustomBIDSFile

Represent a custom brain mask in the form sub-<label>_desc-brain_mask.nii.gz.

class cmtklib.bids.io.CustomCSFMaskBIDSFile[source]

Bases: cmtklib.bids.io.CustomBIDSFile

Represent a custom CSF mask in the form sub-<label>_label-CSF_dseg.nii.gz.

class cmtklib.bids.io.CustomGMMaskBIDSFile[source]

Bases: cmtklib.bids.io.CustomBIDSFile

Represent a custom gray-matter mask in the form sub-<label>_label-GM_dseg.nii.gz.

class cmtklib.bids.io.CustomParcellationBIDSFile[source]

Bases: cmtklib.bids.io.CustomBIDSFile

Represent a custom parcellation files in the form sub-<label>_atlas-<label>[_res-<label>]_dseg.nii.gz.

get_nb_of_regions(bids_dir, subject, session=None, debug=True)[source]

Return the number of regions by reading its associated TSV side car file describing the nodes.

Parameters

bids_dir (str) – BIDS root directory
subject (str) – Subject filename entity e.g. “sub-01”
session (str) – Session filename entity e.g. “ses-01” if applicable (Default: None)
debug (bool) – Debug mode (Extra outputed messages) if True

class cmtklib.bids.io.CustomWMMaskBIDSFile[source]

Bases: cmtklib.bids.io.CustomBIDSFile

Represent a custom white-matter mask in the form sub-<label>_label-WM_dseg.nii.gz.