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_datatype='', p_suffix='', p_extension='', p_acquisition='', p_rec='', p_atlas='', p_res='', p_label='', p_desc='', p_task='')[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
- datatype
BIDS data type
- Type
Enum([“anat”, “dwi”, “func”, “eeg”])
- suffix
Filename suffix e.g.
sub-01_T1w.nii.gz
has suffixT1w
- Type
Str
- acquisition
Label used in
_acq-<label>_
- Type
Str
- task
Label used in
_task-<label>_
- Type
Str
- rec
Label used in
_rec-<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(subject, session=None, debug=False)[source]
Return the filename path with extension of the represented BIDS file.
- get_filename_path(base_dir, subject, session=None, debug=False)[source]
Return the filename path without extension of the represented BIDS file.
- 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.CustomEEGCartoolElectrodesBIDSFile[source]
Bases:
cmtklib.bids.io.CustomBIDSFile
Represent a custom BIDS-formatted electrode file produced by Cartool, in the form
sub-<label>_eeg.xyz
.
- class cmtklib.bids.io.CustomEEGCartoolInvSolBIDSFile[source]
Bases:
cmtklib.bids.io.CustomBIDSFile
Represent a custom BIDS-formatted inverse solution file produced by Cartool in the form
sub-<label>_eeg.[LAURA|LORETA].is
.
- class cmtklib.bids.io.CustomEEGCartoolMapSpiRoisBIDSFile[source]
Bases:
cmtklib.bids.io.CustomBIDSFile
Represent a custom BIDS-formatted spi / rois mapping file in the form
sub-<label>_eeg.pickle.rois
.
- class cmtklib.bids.io.CustomEEGCartoolSpiBIDSFile[source]
Bases:
cmtklib.bids.io.CustomBIDSFile
Represent a custom BIDS-formatted Source Point Irregularly spaced file produced by Cartool, in the form
sub-<label>_eeg.spi
.
- class cmtklib.bids.io.CustomEEGElectrodesBIDSFile[source]
Bases:
cmtklib.bids.io.CustomBIDSFile
Represent a custom BIDS-formatted EEG electrodes file in the form
sub-<label>_task-<label>_electrodes.tsv
.
- class cmtklib.bids.io.CustomEEGEpochsBIDSFile[source]
Bases:
cmtklib.bids.io.CustomBIDSFile
Represent a custom BIDS-formatted EEG Epochs file in .set or .fif format.
- class cmtklib.bids.io.CustomEEGEventsBIDSFile[source]
Bases:
cmtklib.bids.io.CustomBIDSFile
Represent a custom BIDS-formatted EEG task events file in the form
sub-<label>_task-<label>_events.tsv
.
- class cmtklib.bids.io.CustomEEGMNETransformBIDSFile[source]
Bases:
cmtklib.bids.io.CustomBIDSFile
Represent a custom BIDS-formatted electrode transform file in the form
sub-<label>_trans.fif
.
- class cmtklib.bids.io.CustomEEGPreprocBIDSFile[source]
Bases:
cmtklib.bids.io.CustomBIDSFile
Represent a custom BIDS-formatted preprocessed EEG file in the form
sub-<label>_task-<label>_desc-preproc_eeg.[set|fif]
.
- 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
.
- 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
.