AFQ.api.group
#
Module Contents#
Classes#
- class AFQ.api.group.GroupAFQ(bids_path, bids_filters={'suffix': 'dwi'}, preproc_pipeline='all', participant_labels=None, output_dir=None, parallel_params={'engine': 'serial'}, bids_layout_kwargs={}, **kwargs)[source]#
Bases:
object
- export_all(self, viz=True, afqbrowser=True, xforms=True, indiv=True)[source]#
Exports all the possible outputs
- Parameters
- vizbool
Whether to output visualizations. This includes tract profile plots, a figure containing all bundles, and, if using the AFQ segmentation algorithm, individual bundle figures. Default: True
- afqbrowserbool
Whether to output an AFQ-Browser from this AFQ instance. Default: True
- xformsbool
Whether to output the reg_template image in subject space and, depending on if it is possible based on the mapping used, to output the b0 in template space. Default: True
- indivbool
Whether to output individual bundles in their own files, in addition to the one file containing all bundles. If using the AFQ segmentation algorithm, individual ROIs are also output. Default: True
- assemble_AFQ_browser(self, output_path=None, metadata=None, page_title='AFQ Browser', page_subtitle='', page_title_link='', page_subtitle_link='')[source]#
Assembles an instance of the AFQ-Browser from this AFQ instance. First, we generate the combined tract profile if it is not already generated. This includes running the full AFQ pipeline if it has not already run. The combined tract profile is one of the outputs of export_all. Second, we generate a streamlines.json file from the bundle recognized in the first subject’s first session. Third, we call AFQ-Browser’s assemble to assemble an AFQ-Browser instance in output_path.
- Parameters
- output_pathstr
Path to location to create this instance of the browser in. Called “target” in AFQ Browser API. If None, bids_path/derivatives/afq_browser is used. Default: None
- metadatastr
Path to subject metadata csv file. If None, an metadata file containing only subject ID is created. This file requires a “subjectID” column to work. Default: None
- page_titlestr
Page title. If None, prompt is sent to command line. Default: “AFQ Browser”
- page_subtitlestr
Page subtitle. If None, prompt is sent to command line. Default: “”
- page_title_linkstr
Title hyperlink (including http(s)://). If None, prompt is sent to command line. Default: “”
- page_subtitle_linkstr
Subtitle hyperlink (including http(s)://). If None, prompt is sent to command line. Default: “”