AFQ.recognition.roi#
Module Contents#
Functions#
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Helper function to check that a streamline is close to a list of |
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Helper function to check that a streamline is not too close to a |
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Clean a collection of streamlines based on an endpoint ROI. |
- AFQ.recognition.roi.check_sl_with_inclusion(sl, include_rois, include_roi_tols)[source]#
Helper function to check that a streamline is close to a list of inclusion ROIS.
- AFQ.recognition.roi.check_sl_with_exclusion(sl, exclude_rois, exclude_roi_tols)[source]#
Helper function to check that a streamline is not too close to a list of exclusion ROIs.
- AFQ.recognition.roi.clean_by_endpoints(streamlines, target, target_idx, tol=0, flip_sls=None, accepted_idxs=None)[source]#
Clean a collection of streamlines based on an endpoint ROI. Filters down to only include items that have their start or end points close to the targets. Parameters ———- streamlines : sequence of N by 3 arrays
Where N is number of nodes in the array, the collection of streamlines to filter down to.
- target: Nifti1Image
Nifti1Image containing a boolean representation of the ROI.
- target_idx: int.
Index within each streamline to check if within the target region. Typically 0 for startpoint ROIs or -1 for endpoint ROIs. If using flip_sls, this becomes (len(sl) - this_idx - 1) % len(sl)
- tolint, optional
A distance tolerance (in units that the coordinates of the streamlines are represented in). Default: 0, which means that the endpoint is exactly in the coordinate of the target ROI.
- flip_sls1d array, optional
Length is len(streamlines), whether to flip the streamline.
- accepted_idxs1d array, optional
Boolean array, where entries correspond to eachs streamline, and streamlines that pass cleaning will be set to 1.
Yields#
boolean array of streamlines that survive cleaning.