Adding SF amplitude thresholding as a way of create masks

pyproject.toml

@@ -206,6 +206,7 @@ scil_sh_fusion  = "scilpy.cli.scil_sh_fusion:main"
 scil_sh_to_aodf  = "scilpy.cli.scil_sh_to_aodf:main"
 scil_sh_to_rish  = "scilpy.cli.scil_sh_to_rish:main"
 scil_sh_to_sf  = "scilpy.cli.scil_sh_to_sf:main"
+scil_fodf_global_sf_threshold = "scilpy.cli.scil_fodf_global_sf_threshold:main"
 scil_stats_group_comparison  = "scilpy.cli.scil_stats_group_comparison:main"
 scil_surface_assign_custom_color  = "scilpy.cli.scil_surface_assign_custom_color:main"
 scil_surface_assign_uniform_color  = "scilpy.cli.scil_surface_assign_uniform_color:main"

src/scilpy/cli/scil_fodf_global_sf_threshold.py

@@ -0,0 +1,91 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+Compute a binary mask based on a global SF threshold.
+The script masks voxels where the maximum SF amplitude is below
+either a relative factor or an absolute threshold.
+
+When fODFs are evaluated on a sphere (SF), the amplitude of the lobes
+corresponds to the strength of the diffusion signal in those directions.
+Thresholding these amplitudes is a common practice to filter out spurious
+peaks arising from noise or the deconvolution process (e.g., ringing effects).
+
+The absolute threshold can be estimated from the mean/median maximum fODF in the
+ventricles, computed with scil_fodf_max_in_ventricles.
+"""
+
+import argparse
+import logging
+
+import nibabel as nib
+import numpy as np
+
+from scilpy.io.utils import (add_sh_basis_args, add_sphere_arg,
+                             add_verbose_arg, add_overwrite_arg,
+                             assert_inputs_exist, assert_outputs_exist,
+                             parse_sh_basis_arg)
+from scilpy.reconst.utils import compute_sf_threshold_mask
+from scilpy.version import version_string
+
+
+def _build_arg_parser():
+    p = argparse.ArgumentParser(description=__doc__,
+                                formatter_class=argparse.RawTextHelpFormatter,
+                                epilog=version_string)
+
+    p.add_argument('in_odf',
+                   help='Input ODF file (SH or Peaks) (.nii.gz).')
+    p.add_argument('out_mask',
+                   help='Output binary mask (.nii.gz).')
+
+    thr_g = p.add_mutually_exclusive_group(required=True)
+    thr_g.add_argument('--relative', type=float,
+                       help='Global SF threshold relative factor (0-1).')
+    thr_g.add_argument('--absolute', type=float,
+                       help='Global SF absolute threshold.')
+    add_sh_basis_args(p)
+    add_sphere_arg(p)
+    add_overwrite_arg(p)
+    add_verbose_arg(p)
+
+    return p
+
+
+def main():
+    parser = _build_arg_parser()
+    args = parser.parse_args()
+    logging.getLogger().setLevel(logging.getLevelName(args.verbose))
+
+    assert_inputs_exist(parser, args.in_odf)
+    assert_outputs_exist(parser, args, args.out_mask)
+
+    sh_basis, is_legacy = parse_sh_basis_arg(args)
+
+    logging.info("Loading ODF data.")
+    img = nib.load(args.in_odf)
+    data = img.get_fdata(dtype=np.float32)
+
+    logging.info("Computing global SF threshold mask.")
+    mask, global_max, threshold = compute_sf_threshold_mask(
+        data, sphere_name=args.sphere, relative_factor=args.relative,
+        absolute_threshold=args.absolute, sh_basis=sh_basis,
+        is_legacy=is_legacy)
+
+    logging.info("Global max SF amplitude: {:.4f}".format(global_max))
+    if args.relative is not None:
+        logging.info("Relative threshold: {:.4f} (Factor: {})"
+                     .format(threshold, args.relative))
+    else:
+        logging.info("Absolute threshold used: {:.4f}".format(args.absolute))
+
+    logging.info("Number of voxels in mask: {}".format(np.sum(mask)))
+
+    # Save mask
+    mask_img = nib.Nifti1Image(mask.astype(np.uint8), img.affine,
+                               img.header)
+    nib.save(mask_img, args.out_mask)
+
+
+if __name__ == "__main__":
+    main()

src/scilpy/cli/scil_tracking_local.py

@@ -5,7 +5,7 @@
 The tracking direction is chosen in the aperture cone defined by the
 previous tracking direction and the angular constraint.
 
-WARNING: This script DOES NOT support asymetric FODF input (aFODF).
+WARNING: This script DOES NOT support asymmetric FODF input (aFODF).
 
 Algo 'eudx': select the peak from the spherical function (SF) most closely
 aligned to the previous direction, and follow an average of it and the previous
@@ -41,9 +41,10 @@
     * Forward tracking: For GPU tracking, the `--forward_only` flag can be used
         to disable backward tracking. This option isn't available for CPU
         tracking.
-    * Random number generator seed (RNG): CPU and GPU use different RNG implementations,<
-        so the same `--seed` is reproducible within a backend but does not guarantee
-        identical streamlines across CPU vs GPU tracking.
+    * Random number generator seed (RNG): CPU and GPU use different RNG
+        implementations, so the same `--seed` is reproducible within a
+        backend but does not guarantee identical streamlines across CPU vs
+        GPU tracking.
 
 All the input nifti files must be in isotropic resolution.
 
@@ -61,20 +62,20 @@
 import logging
 from time import perf_counter
 
-import nibabel as nib
-import numpy as np
-from nibabel.streamlines import TrkFile, detect_format
-
 from dipy.data import get_sphere
 from dipy.tracking import utils as track_utils
 from dipy.tracking.local_tracking import LocalTracking
 from dipy.tracking.stopping_criterion import BinaryStoppingCriterion
 from dipy.tracking.tracker import eudx_tracking
+import nibabel as nib
+from nibabel.streamlines import TrkFile, detect_format
+import numpy as np
+
 from scilpy.io.image import get_data_as_mask
 from scilpy.io.utils import (add_sphere_arg, add_verbose_arg,
                              assert_headers_compatible, assert_inputs_exist,
-                             assert_outputs_exist, parse_sh_basis_arg,
-                             verify_compression_th, load_matrix_in_any_format)
+                             assert_outputs_exist, load_matrix_in_any_format,
+                             parse_sh_basis_arg, verify_compression_th)
 from scilpy.tracking.tracker import GPUTracker
 from scilpy.tracking.utils import (add_mandatory_options_tracking,
                                    add_out_options, add_seeding_options,
@@ -104,7 +105,7 @@ def _build_arg_parser():
 
     # Other options, only available in this script:
     track_g.add_argument('--sh_to_pmf', action='store_true',
-                         help='If set, map sherical harmonics to spherical '
+                         help='If set, map spherical harmonics to spherical '
                               'function (pmf) before \ntracking (faster, '
                               'requires more memory)')
     track_g.add_argument('--algo', default='prob',
@@ -200,6 +201,18 @@ def main():
     logging.debug("Loading masks and finding seeds.")
     mask_data = get_data_as_mask(nib.load(args.in_mask), dtype=bool)
 
+    # ODF data for thresholding
+    odf_sh_data = odf_sh_img.get_fdata(dtype=np.float32)
+
+    sh_basis, is_legacy = parse_sh_basis_arg(args)
+
+    sf_mask = None
+    if args.global_sf_rel_thr is not None or \
+            args.global_sf_abs_thr is not None:
+        from scilpy.tracking.utils import get_global_sf_threshold_mask
+        sf_mask = get_global_sf_threshold_mask(
+            odf_sh_data, args, sh_basis, is_legacy)
+
     if args.npv:
         nb_seeds = args.npv
         seed_per_vox = True
@@ -235,11 +248,16 @@ def main():
             random_seed=args.seed)
     total_nb_seeds = len(seeds)
 
+    combined_mask = mask_data
+    if sf_mask is not None:
+        combined_mask = np.logical_and(mask_data, sf_mask)
+
     if not args.use_gpu:
         # LocalTracking.maxlen is actually the maximum length
         # per direction, we need to filter post-tracking.
         max_steps_per_direction = int(args.max_length / args.step_size)
-        stopping_criterion = BinaryStoppingCriterion(mask_data)
+
+        stopping_criterion = BinaryStoppingCriterion(combined_mask)
 
         logging.info("Starting CPU local tracking.")
         if args.algo == 'eudx':
@@ -248,7 +266,7 @@ def main():
                 stopping_criterion,
                 np.eye(4),
                 pam=get_direction_getter(
-                    args.in_odf, args.algo, args.sphere,
+                    odf_sh_data, args.algo, args.sphere,
                     args.sub_sphere, args.theta, sh_basis,
                     voxel_size, args.sf_threshold, args.sh_to_pmf,
                     args.probe_length, args.probe_radius,
@@ -264,7 +282,7 @@ def main():
         else:
             streamlines_generator = LocalTracking(
                 get_direction_getter(
-                    args.in_odf, args.algo, args.sphere,
+                    odf_sh_data, args.algo, args.sphere,
                     args.sub_sphere, args.theta, sh_basis,
                     voxel_size, args.sf_threshold, args.sh_to_pmf,
                     args.probe_length, args.probe_radius,
@@ -284,14 +302,13 @@ def main():
         max_strl_len = int(2.0 * args.max_length / args.step_size) + 1
 
         # data volume
-        odf_sh = odf_sh_img.get_fdata(dtype=np.float32)
 
         # GPU tracking needs the full sphere
         sphere = get_sphere(name=args.sphere).subdivide(n=args.sub_sphere)
 
         logging.info("Starting GPU local tracking.")
         streamlines_generator = GPUTracker(
-            odf_sh, mask_data, seeds,
+            odf_sh_data, combined_mask, seeds,
             vox_step_size, max_strl_len,
             theta=get_theta(args.theta, args.algo),
             sf_threshold=args.sf_threshold,