AFQ.api.participant

Classes

ParticipantAFQ

Module Contents

class AFQ.api.participant.ParticipantAFQ(dwi_data_file, bval_file, bvec_file, t1_file, output_dir, logging_level=logging.INFO, **kwargs)

Bases: object

logger

og_kwargs

kwargs

make_workflow()

export(attr_name='help')

Export a specific output. To print a list of available outputs, call export without arguments.

Parameters:

attr_namestr

Name of the output to export. Default: “help”

Returns:

outputany

The specific output, or None if called without arguments.

export_up_to(attr_name='help')

export_all(viz=True, xforms=True, indiv=True)

participant_montage(images_per_row=3, anatomy=True, bundle_names=None)

Generate montage of all bundles for a given subject.

Parameters:

images_per_rowint

Number of bundle images per row in output file. Default: 3

anatomybool

Whether to include anatomical images in the montage. Default: True

bundle_nameslist of str or None

List of bundle names to include in the montage. Default: None (includes all bundles)

Returns:

filename of montage images

cmd_outputs(cmd='rm', dependent_on=None, up_to=None, exceptions=None, suffix='')

Perform some command some or all outputs of pyafq. This is useful if you change a parameter and need to recalculate derivatives that depend on it. Some examples: cp, mv, rm . -r will be automatically added when necessary.

Parameters:

cmdstr

Command to run on outputs. Default: ‘rm’

dependent_onstr or None

Which derivatives to perform command on . If None, perform on all. If “track”, perform on all derivatives that depend on the tractography. If “recog”, perform on all derivatives that depend on the bundle recognition. If “prof”, perform on all derivatives that depend on the bundle profiling. Default: None

up_tostr or None

If None, will perform on all derivatives. If “track”, will perform on all derivatives up to (but not including) tractography. If “recog”, will perform on all derivatives up to (but not including) bundle recognition. If “prof”, will perform on all derivatives up to (but not including) bundle profiling. Default: None

exceptionslist of str

Name outputs that the command should not be applied to. Default: []

suffixstr

Parts of command that are used after the filename. Default: “”

clobber