fitlins.generate_dset module

class fitlins.generate_dset.DerivFuncFileCreator(base_dir, fname_params, events_df, trial_type_weights, noise_df, n_tp, cnr, metadata)

Bases: object

FILE_PARAMS = {'desc': 'preproc', 'space': 'T1w', 'suffix': 'bold'}

PATTERN = 'sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<bold|cbv|phase|sbref|boldref|dseg>}{extension<.nii|.nii.gz|.json>|.nii.gz}'

create_fname(fname_params, meta_params)

init_data(events_df, trial_type_weights, noise_df, n_tp, cnr, metadata)

write_file()

class fitlins.generate_dset.DerivMaskFileCreator(base_dir, fname_params, func_img, metadata=None)

Bases: object

FILE_PARAMS = {'desc': 'brain', 'space': 'T1w', 'suffix': 'mask'}

PATTERN = 'sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix<mask>|mask}{extension<.nii|.nii.gz|.json>|.nii.gz}'

create_fname(fname_params, meta_params)

init_data(func_img)

write_file()

class fitlins.generate_dset.DummyDerivatives(base_dir=None, database_path=None, participant_labels=None, session_labels=None, task_labels=None, run_labels=None, trial_types=None, trial_type_weights=None, n_events=None, event_duration=None, inter_trial_interval=None, cnr=None, regr_names=None, func_metadata=None)

Bases: object

Create a minimal BIDS+Derivatives dataset for testing

BIDS_DICT = {'BIDSVersion': '1.4.1', 'Name': 'ice cream and cake'}

DERIVATIVES_DICT = {'BIDSVersion': '1.4.1', 'CodeURL': 'https://github.com/nipreps/fmriprep', 'HowToAcknowledge': 'Please cite our paper (https://doi.org/10.1038/s41592-018-0235-4)', 'License': '', 'Name': 'fMRIPrep - fMRI PREProcessing workflow', 'PipelineDescription': {'CodeURL': 'https://github.com/nipreps/fmriprep/archive/1.5.0.tar.gz', 'Name': 'fMRIPrep', 'Version': '1.5.0rc2+14.gf673eaf5'}, 'SourceDatasetsURLs': ['https://doi.org/']}

create_dataset_descriptions()

create_layout()

write_bids_derivatives_dataset()

class fitlins.generate_dset.EventsFileCreator(base_dir, fname_params, n_events, trial_types, event_duration, inter_trial_interval, metadata=None)

Bases: object

FILE_PARAMS = {'datatype': 'func', 'suffix': 'events'}

PATTERN = 'sub-{subject}[/ses-{session}]/[{datatype<func|meg|beh>|func}/]sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_recording-{recording}]_{suffix<events>}{extension<.tsv|.json>|.tsv}'

create_fname(fname_params, meta_params)

init_data(n_events, trial_types, event_duration, inter_trial_interval)

write_file()

class fitlins.generate_dset.FuncFileCreator(base_dir, fname_params, events_df, trial_type_weights, noise_df, n_tp, cnr, metadata)

Bases: object

FILE_PARAMS = {'suffix': 'bold'}

PATTERN = 'sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}]_{suffix<bold|cbv|phase|sbref>}{extension<.nii|.nii.gz|.json>|.nii.gz}'

create_fname(fname_params, meta_params)

init_data(events_df, trial_type_weights, noise_df, n_tp, cnr, metadata)

write_file()

class fitlins.generate_dset.RegressorFileCreator(base_dir, fname_params, regr_names, n_tp, metadata=None)

Bases: object

Generator for _regressors files in bids derivatives dataset

FILE_PARAMS = {'datatype': 'func', 'desc': 'confounds', 'suffix': 'regressors'}

PATTERN = 'sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<timeseries|regressors>|timeseries}{extension<.json|.tsv>|.tsv}'

create_fname(fname_params, meta_params)

create the bids derivatives regressor file path and path names

init_data(regr_names, n_tp)

create the regressor data

write_file()

write the data to files

fitlins.generate_dset.write_metadata(filepath, metadata)