fitlins.interfaces.bids module

class fitlins.interfaces.bids.BIDSDataSink(from_file=None, resource_monitor=None, ignore_exception=False, **inputs)

Bases: nipype.interfaces.io.IOBase

input_spec

alias of fitlins.interfaces.bids.BIDSDataSinkInputSpec

output_spec

alias of fitlins.interfaces.bids.BIDSDataSinkOutputSpec

class fitlins.interfaces.bids.BIDSDataSinkInputSpec(**kwargs)

Bases: nipype.interfaces.base.specs.BaseInterfaceInputSpec

class fitlins.interfaces.bids.BIDSDataSinkOutputSpec(**kwargs)

Bases: nipype.interfaces.base.specs.TraitedSpec

class fitlins.interfaces.bids.BIDSSelect(from_file=None, resource_monitor=None, **inputs)

Bases: nipype.interfaces.base.core.SimpleInterface

input_spec

alias of fitlins.interfaces.bids.BIDSSelectInputSpec

output_spec

alias of fitlins.interfaces.bids.BIDSSelectOutputSpec

class fitlins.interfaces.bids.BIDSSelectInputSpec(**kwargs)

Bases: nipype.interfaces.base.specs.BaseInterfaceInputSpec

class fitlins.interfaces.bids.BIDSSelectOutputSpec(**kwargs)

Bases: nipype.interfaces.base.specs.TraitedSpec

class fitlins.interfaces.bids.LoadBIDSModel(from_file=None, resource_monitor=None, **inputs)

Bases: nipype.interfaces.base.core.SimpleInterface

Read a BIDS dataset and model and produce configurations that may be adapted to various model-fitting packages.

design_infolist of list of dictionaries

At the first level, a dictionary per-run containing the following keys:

‘sparse’HDF5 file containing sparse representation of events

(onset, duration, amplitude)

‘dense’HDF5 file containing dense representation of events

regressors

‘repetition_time’ : float (in seconds)

all_specsdictionary of list of dictionaries

The collection of specs from each level. Each dict at individual levels contains the following keys:

‘contrasts’a list of ContrastInfo objects each unit of analysis.

A contrast specifiction is a list of contrast dictionaries. Each dict has form:

{

‘name’: str, ‘conditions’: list, ‘weights: list, test: str, ‘entities’: dict,

}

‘entities’The entities list contains a list for each level of analysis.

At each level, the list contains a dictionary of entities that apply to each unit of analysis. For example, if the level is “Run” and there are 20 runs in the dataset, the first entry will be a list of 20 dictionaries, each uniquely identifying a run.

‘level’ : The current level of the analysis [run, subject, dataset…] ‘X’ : The design matrix ‘model’ : The model part from the BIDS-StatsModels specification. ‘metadata’ (only higher-levels): a parallel DataFrame with the same number of

rows as X that contains all known metadata variabes that vary on a row-by-row basis but aren’t actually predictiors

warningslist of files

Files containing HTML snippets with any warnings produced while processing the first level.

input_spec

alias of fitlins.interfaces.bids.LoadBIDSModelInputSpec

output_spec

alias of fitlins.interfaces.bids.LoadBIDSModelOutputSpec

class fitlins.interfaces.bids.LoadBIDSModelInputSpec(**kwargs)

Bases: nipype.interfaces.base.specs.BaseInterfaceInputSpec

class fitlins.interfaces.bids.LoadBIDSModelOutputSpec(**kwargs)

Bases: nipype.interfaces.base.specs.TraitedSpec

class fitlins.interfaces.bids.ModelSpecLoader(from_file=None, resource_monitor=None, **inputs)

Bases: nipype.interfaces.base.core.SimpleInterface

Load BIDS Stats Models specifications from a BIDS directory

input_spec

alias of fitlins.interfaces.bids.ModelSpecLoaderInputSpec

output_spec

alias of fitlins.interfaces.bids.ModelSpecLoaderOutputSpec

class fitlins.interfaces.bids.ModelSpecLoaderInputSpec(**kwargs)

Bases: nipype.interfaces.base.specs.BaseInterfaceInputSpec

class fitlins.interfaces.bids.ModelSpecLoaderOutputSpec(**kwargs)

Bases: nipype.interfaces.base.specs.TraitedSpec

fitlins.interfaces.bids.bids_split_filename(fname)

Split a filename into parts: path, base filename, and extension

Respects multi-part file types used in BIDS standard and draft extensions

Largely copied from nipype.utils.filemanip.split_filename

fnamestr

file or path name

pthstr

path of fname

fnamestr

basename of filename, without extension

extstr

file extension of fname