[ENH] Add mrds scripts part 3

scilpy/tractanalysis/mrds_along_streamlines.py

@@ -0,0 +1,130 @@
+# -*- coding: utf-8 -*-
+
+import numpy as np
+
+from scilpy.tractanalysis.grid_intersections import grid_intersections
+
+
+def mrds_metrics_along_streamlines(sft, mrds_pdds,
+                                   metrics, max_theta,
+                                   length_weighting):
+    """
+    Compute mean map for a given fixel-specific metric along streamlines.
+
+    Parameters
+    ----------
+    sft : StatefulTractogram
+        StatefulTractogram containing the streamlines needed.
+    mrds_pdds : ndarray (X, Y, Z, 3*N_TENSORS)
+        MRDS principal diffusion directions of the tensors
+    metrics : list of ndarray
+        Array of shape (X, Y, Z, N_TENSORS) containing the fixel-specific
+        metric of interest.
+    max_theta : float
+        Maximum angle in degrees between the fiber direction and the
+        MRDS principal diffusion direction.
+    length_weighting : bool
+        If True, will weigh the metric values according to segment lengths.
+    """
+
+    mrds_sum, weights = \
+        mrds_metric_sums_along_streamlines(sft, mrds_pdds,
+                                           metrics, max_theta,
+                                           length_weighting)
+
+    all_metric = mrds_sum[0]
+    for curr_metric in mrds_sum[1:]:
+        all_metric += np.abs(curr_metric)
+
+    non_zeros = np.nonzero(all_metric)
+    weights_nz = weights[non_zeros]
+    for metric_idx in range(len(metrics)):
+        mrds_sum[metric_idx][non_zeros] /= weights_nz
+
+    return mrds_sum
+
+
+def mrds_metric_sums_along_streamlines(sft, mrds_pdds, metrics,
+                                       max_theta, length_weighting):
+    """
+    Compute a sum map along a bundle for a given fixel-specific metric.
+
+    Parameters
+    ----------
+    sft : StatefulTractogram
+        StatefulTractogram containing the streamlines needed.
+    mrds_pdds : ndarray (X, Y, Z, 3*N_TENSORS)
+        MRDS principal diffusion directions (PDDs) of the tensors
+    metrics : list of ndarray (X, Y, Z, N_TENSORS)
+        Fixel-specific metrics.
+    max_theta : float
+        Maximum angle in degrees between the fiber direction and the
+        MRDS principal diffusion direction.
+    length_weighting : bool
+        If True, will weight the metric values according to segment lengths.
+
+    Returns
+    -------
+    metric_sum_map : np.array
+        fixel-specific metrics sum map.
+    weight_map : np.array
+        Segment lengths.
+    """
+
+    sft.to_vox()
+    sft.to_corner()
+
+    X, Y, Z = metrics[0].shape[0:3]
+    metrics_sum_map = np.zeros((len(metrics), X, Y, Z))
+    weight_map = np.zeros(metrics[0].shape[:-1])
+    min_cos_theta = np.cos(np.radians(max_theta))
+
+    all_crossed_indices = grid_intersections(sft.streamlines)
+    for crossed_indices in all_crossed_indices:
+        segments = crossed_indices[1:] - crossed_indices[:-1]
+        seg_lengths = np.linalg.norm(segments, axis=1)
+
+        # Remove points where the segment is zero.
+        # This removes numpy warnings of division by zero.
+        non_zero_lengths = np.nonzero(seg_lengths)[0]
+        segments = segments[non_zero_lengths]
+        seg_lengths = seg_lengths[non_zero_lengths]
+
+        # Those starting points are used for the segment vox_idx computations
+        seg_start = crossed_indices[non_zero_lengths]
+        vox_indices = (seg_start + (0.5 * segments)).astype(int)
+
+        normalization_weights = np.ones_like(seg_lengths)
+        if length_weighting:
+            normalization_weights = seg_lengths
+
+        normalized_seg = np.reshape(segments / seg_lengths[..., None], (-1, 3))
+
+        # Reshape MRDS PDDs
+        mrds_pdds = mrds_pdds.reshape(mrds_pdds.shape[0],
+                                      mrds_pdds.shape[1],
+                                      mrds_pdds.shape[2], -1, 3)
+
+        for vox_idx, seg_dir, norm_weight in zip(vox_indices,
+                                                 normalized_seg,
+                                                 normalization_weights):
+            vox_idx = tuple(vox_idx)
+
+            mrds_peak_dir = mrds_pdds[vox_idx]
+
+            cos_theta = np.abs(np.dot(seg_dir.reshape((-1, 3)),
+                                      mrds_peak_dir.T))
+
+            metric_val = [0.0]*len(metrics)
+            if (cos_theta > min_cos_theta).any():
+                fixel_idx = np.argmax(np.squeeze(cos_theta),
+                                      axis=0)  # (n_segs)
+
+                for metric_idx, curr_metric in enumerate(metrics):
+                    metric_val[metric_idx] = curr_metric[vox_idx][fixel_idx]
+
+            for metric_idx, curr_metric in enumerate(metrics):
+                metrics_sum_map[metric_idx][vox_idx] += metric_val[metric_idx] * norm_weight
+                weight_map[vox_idx] += norm_weight
+
+    return metrics_sum_map, weight_map

scripts/scil_bundle_mean_fixel_mrds_metric.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+Given a bundle and MRDS metrics, compute the fixel-specific
+metrics at each voxel intersected by the bundle. Intersected voxels are
+found by computing the intersection between the voxel grid and each streamline
+in the input tractogram.
+
+This script behaves like scil_bundle_mean_fixel_afd.py for fODFs,
+but here for MRDS metrics. These latest distributions add the unique
+possibility to capture fixel-based fractional anisotropy (fixel-FA), mean
+diffusivity (fixel-MD), radial diffusivity (fixel-RD) and
+axial diffusivity (fixel-AD).
+
+Fixel-specific metrics are metrics extracted from
+Multi-Resolution Discrete-Search (MRDS) solutions.
+There are as many values per voxel as there are fixels extracted. The
+values chosen for a given voxel is the one belonging to the lobe better aligned
+with the current streamline segment.
+
+Input files come from scil_mrds_metrics.py command.
+
+Output metrics will be named: [prefix]_mrds_[metric_name].nii.gz
+
+Please use a bundle file rather than a whole tractogram.
+"""
+
+import argparse
+
+import nibabel as nib
+import numpy as np
+
+from scilpy.io.streamlines import load_tractogram_with_reference
+from scilpy.io.utils import (add_overwrite_arg,
+                             add_reference_arg,
+                             assert_headers_compatible,
+                             assert_inputs_exist, assert_outputs_exist)
+from scilpy.tractanalysis.mrds_along_streamlines \
+    import mrds_metrics_along_streamlines
+
+
+def _build_arg_parser():
+    p = argparse.ArgumentParser(description=__doc__,
+                                formatter_class=argparse.RawTextHelpFormatter)
+    p.add_argument('in_bundle',
+                   help='Path of the bundle file.')
+    p.add_argument('in_pdds',
+                   help='Path of the MRDS PDDs volume.')
+
+    g = p.add_argument_group(title='MRDS metrics input')
+    g.add_argument('--fa',
+                   help='Path of the fixel-specific metric FA volume.')
+    g.add_argument('--md',
+                   help='Path of the fixel-specific metric MD volume.')
+    g.add_argument('--rd',
+                   help='Path of the fixel-specific metric RD volume.')
+    g.add_argument('--ad',
+                   help='Path of the fixel-specific metric AD volume.')
+
+    p.add_argument('--prefix', default='result',
+                   help='Prefix of the MRDS fixel results.')
+
+    p.add_argument('--length_weighting', action='store_true',
+                   help='If set, will weight the values according to '
+                        'segment lengths. [%(default)s]')
+
+    p.add_argument('--max_theta', default=60, type=float,
+                   help='Maximum angle (in degrees) condition on fixel '
+                        'alignment. [%(default)s]')
+
+    add_reference_arg(p)
+    add_overwrite_arg(p)
+    return p
+
+
+def main():
+    parser = _build_arg_parser()
+    args = parser.parse_args()
+
+    in_metrics = []
+    out_metrics = []
+    if args.fa is not None:
+        in_metrics.append(args.fa)
+        out_metrics.append('{}_mrds_fFA.nii.gz'.format(args.prefix))
+    if args.ad is not None:
+        in_metrics.append(args.ad)
+        out_metrics.append('{}_mrds_fAD.nii.gz'.format(args.prefix))
+    if args.rd is not None:
+        in_metrics.append(args.rd)
+        out_metrics.append('{}_mrds_fRD.nii.gz'.format(args.prefix))
+    if args.md is not None:
+        in_metrics.append(args.md)
+        out_metrics.append('{}_mrds_fMD.nii.gz'.format(args.prefix))
+
+    if in_metrics == []:
+        parser.error('At least one metric is required.')
+
+    assert_inputs_exist(parser, [args.in_bundle,
+                                 args.in_pdds], in_metrics)
+    assert_headers_compatible(parser, [args.in_bundle, args.in_pdds],
+                              in_metrics)
+
+    assert_outputs_exist(parser, args, out_metrics)
+
+    sft = load_tractogram_with_reference(parser, args, args.in_bundle)
+    pdds_img = nib.load(args.in_pdds)
+    affine = pdds_img.affine
+    header = pdds_img.header
+
+    in_metrics_data = [nib.load(metric).get_fdata(dtype=np.float32) for metric in in_metrics]
+    fixel_metrics =\
+        mrds_metrics_along_streamlines(sft,
+                                       pdds_img.get_fdata(dtype=np.float32),
+                                       in_metrics_data,
+                                       args.max_theta,
+                                       args.length_weighting)
+
+    for metric_id, curr_metric in enumerate(fixel_metrics):
+        nib.Nifti1Image(curr_metric.astype(np.float32),
+                        affine=affine,
+                        header=header,
+                        dtype=np.float32).to_filename(out_metrics[metric_id])
+
+
+if __name__ == '__main__':
+    main()

scripts/tests/test_bundle_mean_fixel_mrds_metric.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+def test_help_option(script_runner):
+    ret = script_runner.run(
+        'scil_bundle_mean_fixel_mrds_metric.py', '--help')
+
+    assert ret.success