From 97907e5efcfd28de307cee2aa996c04e4f820a53 Mon Sep 17 00:00:00 2001
From: Philippe Karan <philippe.karan@usherbrooke.ca>
Date: Wed, 19 Jun 2024 12:22:53 -0400
Subject: [PATCH 01/20] Adding script and module

---
 scilpy/tractanalysis/fixel_density.py |  88 +++++++++++++
 scripts/scil_bundle_fixel_analysis.py | 181 ++++++++++++++++++++++++++
 2 files changed, 269 insertions(+)
 create mode 100644 scilpy/tractanalysis/fixel_density.py
 create mode 100644 scripts/scil_bundle_fixel_analysis.py

diff --git a/scilpy/tractanalysis/fixel_density.py b/scilpy/tractanalysis/fixel_density.py
new file mode 100644
index 000000000..0a1a8877e
--- /dev/null
+++ b/scilpy/tractanalysis/fixel_density.py
@@ -0,0 +1,88 @@
+import itertools
+import multiprocessing
+import numpy as np
+
+from dipy.io.streamline import load_tractogram
+from scilpy.tractanalysis.grid_intersections import grid_intersections
+
+
+def _compute_fixel_density_parallel(args):
+    peaks = args[0]
+    max_theta = args[1]
+    bundle = args[2]
+
+    sft = load_tractogram(bundle, 'same')
+    sft.to_vox()
+    sft.to_corner()
+
+    fixel_density_maps = np.zeros((peaks.shape[:-1]) + (5,))
+
+    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)
+
+        normalized_seg = np.reshape(segments / seg_lengths[..., None], (-1, 3))
+
+        for vox_idx, seg_dir in zip(vox_indices, normalized_seg):
+            vox_idx = tuple(vox_idx)
+            peaks_at_idx = peaks[vox_idx].reshape((5, 3))
+
+            cos_theta = np.abs(np.dot(seg_dir.reshape((-1, 3)),
+                                      peaks_at_idx.T))
+
+            if (cos_theta > min_cos_theta).any():
+                lobe_idx = np.argmax(np.squeeze(cos_theta), axis=0)  # (n_segs)
+                # TODO Change that for commit weight if given
+                fixel_density_maps[vox_idx][lobe_idx] += 1
+
+    return fixel_density_maps
+
+
+def compute_fixel_density(peaks, bundles, max_theta=45, nbr_processes=None):
+    """Compute the fixel density per bundle. Can use parallel processing.
+
+    Parameters
+    ----------
+    peaks: np.ndarray (x, y, z, 15)
+        Five principal fiber orientations for each voxel.
+    bundles : list or np.array (N)
+        List of (N) paths to bundles.
+    max_theta : int, optional
+        Maximum angle between streamline and peak to be associated.
+    nbr_processes : int, optional
+        The number of subprocesses to use.
+        Default: multiprocessing.cpu_count()
+
+    Returns
+    -------
+    fixel_density : np.ndarray (x, y, z, 5, N)
+        Density per fixel per bundle.
+    """
+    nbr_processes = multiprocessing.cpu_count() \
+        if nbr_processes is None or nbr_processes <= 0 \
+        else nbr_processes
+
+    pool = multiprocessing.Pool(nbr_processes)
+    results = pool.map(_compute_fixel_density_parallel,
+                       zip(itertools.repeat(peaks),
+                           itertools.repeat(max_theta),
+                           bundles))
+    pool.close()
+    pool.join()
+
+    fixel_density = np.moveaxis(np.asarray(results), 0, -1)
+
+    return fixel_density
diff --git a/scripts/scil_bundle_fixel_analysis.py b/scripts/scil_bundle_fixel_analysis.py
new file mode 100644
index 000000000..8580724b2
--- /dev/null
+++ b/scripts/scil_bundle_fixel_analysis.py
@@ -0,0 +1,181 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Analyze bundles at the fixel level, producing various results:
+
+-
+-
+-
+
+"""
+
+import argparse
+import nibabel as nib
+import numpy as np
+from pathlib import Path
+
+from scilpy.io.utils import (add_overwrite_arg, add_processes_arg,
+                             add_reference_arg)
+from scilpy.tractanalysis.fixel_density import compute_fixel_density
+
+
+def _build_arg_parser():
+    p = argparse.ArgumentParser(
+        description=__doc__, formatter_class=argparse.RawTextHelpFormatter)
+    p.add_argument('in_peaks',
+                   help='Path of the fODF peaks. The peaks are expected to be '
+                        'given as unit directions.')
+    p.add_argument('out_folder',
+                   help='Path of the output folder for txt, png, masks and '
+                        'measures.')
+
+    p.add_argument('--in_bundles', nargs='+', default=[],
+                   action='append', required=True,
+                   help='Path to the bundle trk for where to analyze.')
+
+    p.add_argument('--abs_thr', default=1, type=int,
+                   help='Value of density maps threshold to obtain density '
+                        'masks, in number of streamlines. Any number of '
+                        'streamlines above or equal to this value will pass '
+                        'the absolute threshold test [%(default)s].')
+
+    p.add_argument('--rel_thr', default=0.01, type=float,
+                   help='Value of density maps threshold to obtain density '
+                        'masks, as a ratio of the normalized density. Any '
+                        'normalized density above or equal to this value will '
+                        'pass the relative threshold test [%(default)s].')
+
+    p.add_argument('--max_theta', default=45,
+                   help='Maximum angle between streamline and peak to be '
+                        'associated [%(default)s].')
+
+    p.add_argument('--separate_bundles', action='store_true',
+                   help='If set, save the density maps for each bundle '
+                        'separately instead of all in one file.')
+
+    p.add_argument('--save_masks', action='store_true',
+                   help='If set, save the density masks for each bundle.')
+
+    p.add_argument('--select_single_bundle', action='store_true',
+                   help='If set, select the voxels where only one bundle is '
+                        'present and save the corresponding masks '
+                        '(if save_masks), separated by bundles.')
+
+    p.add_argument('--norm', default="voxel", choices=["fixel", "voxel"],
+                   help='Way of normalizing the density maps. If fixel, '
+                        'will normalize the maps per fixel, in each voxel. '
+                        'If voxel, will normalize the maps per voxel. '
+                        '[%(default)s].')
+
+    add_overwrite_arg(p)
+    add_processes_arg(p)
+    add_reference_arg(p)
+    return p
+
+
+def main():
+    parser = _build_arg_parser()
+    args = parser.parse_args()
+
+    out_folder = Path(args.out_folder)
+
+    # Load the data
+    peaks_img = nib.load(args.in_peaks)
+    peaks = peaks_img.get_fdata()
+    affine = peaks_img.affine
+
+    # Compute NuFo SF from peaks
+    if args.select_single_bundle:
+        is_first_peak = np.sum(peaks[..., 0:3], axis=-1) != 0
+        is_second_peak = np.sum(peaks[..., 3:6], axis=-1) == 0
+        nufo_sf = np.logical_and(is_first_peak, is_second_peak)
+
+    bundles = []
+    bundles_names = []
+    for bundle in args.in_bundles[0]:
+        bundles.append(bundle)
+        bundles_names.append(Path(bundle).name.split(".")[0])
+
+    fixel_density_maps = compute_fixel_density(peaks, bundles, args.max_theta,
+                                               nbr_processes=args.nbr_processes)
+
+    # This applies a threshold on the number of streamlines.
+    fixel_density_masks_abs = fixel_density_maps >= args.abs_thr
+
+    # Normalizing the density maps
+    fixel_sum = np.sum(fixel_density_maps, axis=-1)
+    voxel_sum = np.sum(fixel_sum, axis=-1)
+
+    for i, (bundle, bundle_name) in enumerate(zip(bundles, bundles_names)):
+
+        if args.norm == "voxel":
+            fixel_density_maps[..., 0, i] /= voxel_sum
+            fixel_density_maps[..., 1, i] /= voxel_sum
+            fixel_density_maps[..., 2, i] /= voxel_sum
+            fixel_density_maps[..., 3, i] /= voxel_sum
+            fixel_density_maps[..., 4, i] /= voxel_sum
+
+        elif args.norm == "fixel":
+            fixel_density_maps[..., i] /= fixel_sum
+
+        if args.separate_bundles:
+            nib.save(nib.Nifti1Image(fixel_density_maps[..., i], affine),
+                     out_folder / "fixel_density_map_{}.nii.gz".format(bundle_name))
+
+    if not args.separate_bundles:
+        nib.save(nib.Nifti1Image(fixel_density_maps, affine),
+                 out_folder / "fixel_density_maps.nii.gz")
+        bundles_idx = np.arange(0, len(bundles_names), 1)
+        lookup_table = np.array([bundles_names, bundles_idx])
+        np.savetxt(out_folder / "bundles_lookup_table.txt",
+                   lookup_table, fmt='%s')
+
+    # This applies a threshold on the normalized density (percentage)
+    fixel_density_masks_rel = fixel_density_maps >= args.rel_thr
+
+    # Compute the fixel density masks from the rel and abs versions
+    fixel_density_masks = fixel_density_masks_rel * fixel_density_masks_abs
+
+    # Compute number of bundles per fixel
+    nb_bundles_per_fixel = np.sum(fixel_density_masks, axis=-1)
+    # Compute a mask of the present of each bundle
+    nb_unique_bundles_per_fixel = np.where(np.sum(fixel_density_masks,
+                                                  axis=-2) > 0, 1, 0)
+    # Compute number of bundles per fixel by taking the sum of the mask
+    nb_bundles_per_voxel = np.sum(nb_unique_bundles_per_fixel, axis=-1)
+
+    if args.save_masks:
+        for i, (bundle, bundle_name) in enumerate(zip(bundles, bundles_names)):
+
+            if args.separate_bundles:
+                nib.save(nib.Nifti1Image(fixel_density_masks[..., i].astype(np.uint8), affine),
+                         out_folder / "fixel_density_mask_{}.nii.gz".format(bundle_name))
+
+            if args.select_single_bundle:
+                # Single-fiber single-bundle voxels
+                single_bundle_per_voxel = nb_bundles_per_voxel == 1
+                # Making sure we also have single-fiber voxels only
+                single_bundle_per_voxel *= nufo_sf
+
+                nib.save(nib.Nifti1Image(single_bundle_per_voxel.astype(np.uint8),
+                                         affine),
+                         out_folder / "bundle_mask_only_WM.nii.gz")
+
+                bundle_mask = fixel_density_masks[..., 0, i] * single_bundle_per_voxel
+                nib.save(nib.Nifti1Image(bundle_mask.astype(np.uint8), affine),
+                         out_folder / "bundle_mask_only_{}.nii.gz".format(bundle_name))
+
+        if not args.separate_bundles:
+            nib.save(nib.Nifti1Image(fixel_density_masks.astype(np.uint8),
+                                     affine),
+                     out_folder / "fixel_density_masks.nii.gz")
+
+    nib.save(nib.Nifti1Image(nb_bundles_per_fixel.astype(np.uint8),
+             affine), out_folder / "nb_bundles_per_fixel.nii.gz")
+
+    nib.save(nib.Nifti1Image(nb_bundles_per_voxel.astype(np.uint8),
+             affine), out_folder / "nb_bundles_per_voxel.nii.gz")
+
+
+if __name__ == "__main__":
+    main()

From 319e7273b0292a73ee0d20f0acde8c6af356a544 Mon Sep 17 00:00:00 2001
From: Philippe Karan <philippe.karan@usherbrooke.ca>
Date: Wed, 19 Jun 2024 18:16:30 -0400
Subject: [PATCH 02/20] Cleaning the code

---
 scilpy/tractanalysis/fixel_density.py |  56 ++++++-
 scripts/scil_bundle_fixel_analysis.py | 215 +++++++++++++-------------
 2 files changed, 157 insertions(+), 114 deletions(-)

diff --git a/scilpy/tractanalysis/fixel_density.py b/scilpy/tractanalysis/fixel_density.py
index 0a1a8877e..fcbe1e0d6 100644
--- a/scilpy/tractanalysis/fixel_density.py
+++ b/scilpy/tractanalysis/fixel_density.py
@@ -6,7 +6,7 @@
 from scilpy.tractanalysis.grid_intersections import grid_intersections
 
 
-def _compute_fixel_density_parallel(args):
+def _fixel_density_parallel(args):
     peaks = args[0]
     max_theta = args[1]
     bundle = args[2]
@@ -51,8 +51,8 @@ def _compute_fixel_density_parallel(args):
     return fixel_density_maps
 
 
-def compute_fixel_density(peaks, bundles, max_theta=45, nbr_processes=None):
-    """Compute the fixel density per bundle. Can use parallel processing.
+def fixel_density(peaks, bundles, max_theta=45, nbr_processes=None):
+    """Compute the fixel density map per bundle. Can use parallel processing.
 
     Parameters
     ----------
@@ -76,7 +76,7 @@ def compute_fixel_density(peaks, bundles, max_theta=45, nbr_processes=None):
         else nbr_processes
 
     pool = multiprocessing.Pool(nbr_processes)
-    results = pool.map(_compute_fixel_density_parallel,
+    results = pool.map(_fixel_density_parallel,
                        zip(itertools.repeat(peaks),
                            itertools.repeat(max_theta),
                            bundles))
@@ -86,3 +86,51 @@ def compute_fixel_density(peaks, bundles, max_theta=45, nbr_processes=None):
     fixel_density = np.moveaxis(np.asarray(results), 0, -1)
 
     return fixel_density
+
+
+def maps_to_masks(maps, abs_thr, rel_thr, norm, nb_bundles):
+    """Compute the fixel density masks from fixel density maps.
+
+    Parameters
+    ----------
+    maps : np.ndarray (x, y, z, 5, N)
+        Density per fixel per bundle.
+    abs_thr : int
+        Value of density maps threshold to obtain density masks, in number of
+        streamlines.
+    rel_thr : float
+        Value of density maps threshold to obtain density masks, as a ratio of
+        the normalized density. Must be between 0 and 1.
+    norm : string, ["fixel", "voxel"]
+        Way of normalizing the density maps. If fixel, will normalize the maps
+        per fixel, in each voxel. If voxel, will normalize the maps per voxel.
+    nb_bundles : int (N)
+        Number of bundles (N).
+
+    Returns
+    -------
+    masks : np.ndarray (x, y, z, 5, N)
+        Density masks per fixel per bundle.
+    """
+    # Apply a threshold on the number of streamlines
+    masks_abs = maps >= abs_thr
+
+    # Normalizing the density maps per voxel or fixel
+    fixel_sum = np.sum(maps, axis=-1)
+    voxel_sum = np.sum(fixel_sum, axis=-1)
+    for i in range(nb_bundles):
+        if norm == "voxel":
+            maps[..., 0, i] /= voxel_sum
+            maps[..., 1, i] /= voxel_sum
+            maps[..., 2, i] /= voxel_sum
+            maps[..., 3, i] /= voxel_sum
+            maps[..., 4, i] /= voxel_sum
+        elif norm == "fixel":
+            maps[..., i] /= fixel_sum
+
+    # Apply a threshold on the normalized density (percentage)
+    masks_rel = maps >= rel_thr
+    # Compute the fixel density masks from the rel and abs versions
+    masks = masks_rel * masks_abs
+
+    return masks.astype(np.uint8)
diff --git a/scripts/scil_bundle_fixel_analysis.py b/scripts/scil_bundle_fixel_analysis.py
index 8580724b2..4e9d2455d 100644
--- a/scripts/scil_bundle_fixel_analysis.py
+++ b/scripts/scil_bundle_fixel_analysis.py
@@ -14,62 +14,69 @@
 import numpy as np
 from pathlib import Path
 
-from scilpy.io.utils import (add_overwrite_arg, add_processes_arg,
-                             add_reference_arg)
-from scilpy.tractanalysis.fixel_density import compute_fixel_density
+from scilpy.io.utils import (add_overwrite_arg, add_processes_arg)
+from scilpy.tractanalysis.fixel_density import (fixel_density, maps_to_masks)
 
 
 def _build_arg_parser():
     p = argparse.ArgumentParser(
         description=__doc__, formatter_class=argparse.RawTextHelpFormatter)
     p.add_argument('in_peaks',
-                   help='Path of the fODF peaks. The peaks are expected to be '
-                        'given as unit directions.')
-    p.add_argument('out_folder',
-                   help='Path of the output folder for txt, png, masks and '
-                        'measures.')
+                   help='Path of the peaks. The peaks are expected to be '
+                        'given as unit directions. \nTo get these from fODF '
+                        'or SH data, use the script scil_fodf_metrics.py '
+                        '\nwith the abs_peaks_and_values option.')
 
-    p.add_argument('--in_bundles', nargs='+', default=[],
-                   action='append', required=True,
-                   help='Path to the bundle trk for where to analyze.')
+    p.add_argument('--in_bundles', nargs='+', action='append', required=True,
+                   help='List of paths of the bundles (.trk) to analyze.')
 
-    p.add_argument('--abs_thr', default=1, type=int,
+    p.add_argument('--in_bundles_names', nargs='+', action='append',
+                   help='List of the names of the bundles, in the same order '
+                        'as they were given. \nIf this argument is not used, '
+                        'the script assumes that the name of the bundle \nis '
+                        'its filename without extensions.')
+
+    g = p.add_argument_group(title='Mask parameters')
+
+    g.add_argument('--abs_thr', default=1, type=int,
                    help='Value of density maps threshold to obtain density '
-                        'masks, in number of streamlines. Any number of '
-                        'streamlines above or equal to this value will pass '
+                        'masks, in number of streamlines. \nAny number of '
+                        'streamlines above or equal this value will pass '
                         'the absolute threshold test [%(default)s].')
 
-    p.add_argument('--rel_thr', default=0.01, type=float,
+    g.add_argument('--rel_thr', default=0.01, type=float,
                    help='Value of density maps threshold to obtain density '
-                        'masks, as a ratio of the normalized density. Any '
-                        'normalized density above or equal to this value will '
-                        'pass the relative threshold test [%(default)s].')
+                        'masks, as a ratio of the normalized density '
+                        '\nAny normalized density above or equal to '
+                        'this value will pass the relative threshold test. '
+                        '\nMust be between 0 and 1 [%(default)s].')
+    
+    g.add_argument('--norm', default="voxel", choices=["fixel", "voxel"],
+                   help='Way of normalizing the density maps. If fixel, '
+                        'will normalize the maps per fixel, \nin each voxel. '
+                        'If voxel, will normalize the maps per voxel. '
+                        '[%(default)s]')
 
     p.add_argument('--max_theta', default=45,
                    help='Maximum angle between streamline and peak to be '
                         'associated [%(default)s].')
 
-    p.add_argument('--separate_bundles', action='store_true',
+    p.add_argument('--split_bundles', action='store_true',
                    help='If set, save the density maps for each bundle '
-                        'separately instead of all in one file.')
+                        'separately \ninstead of all in one file.')
 
-    p.add_argument('--save_masks', action='store_true',
-                   help='If set, save the density masks for each bundle.')
+    p.add_argument('--split_fixels', action='store_true',
+                   help='If set, save the density maps for each fixel '
+                        'separately \ninstead of all in one file.')
 
-    p.add_argument('--select_single_bundle', action='store_true',
-                   help='If set, select the voxels where only one bundle is '
-                        'present and save the corresponding masks '
-                        '(if save_masks), separated by bundles.')
-
-    p.add_argument('--norm', default="voxel", choices=["fixel", "voxel"],
-                   help='Way of normalizing the density maps. If fixel, '
-                        'will normalize the maps per fixel, in each voxel. '
-                        'If voxel, will normalize the maps per voxel. '
-                        '[%(default)s].')
+    p.add_argument('--single_bundle', action='store_true',
+                   help='If set, will save the single-fiber single-bundle '
+                        'masks as well. \nThese are obtained by '
+                        'selecting the voxels where only one bundle is '
+                        'present \n(and one fiber/fixel).')
 
     add_overwrite_arg(p)
     add_processes_arg(p)
-    add_reference_arg(p)
     return p
 
 
@@ -77,8 +84,6 @@ def main():
     parser = _build_arg_parser()
     args = parser.parse_args()
 
-    out_folder = Path(args.out_folder)
-
     # Load the data
     peaks_img = nib.load(args.in_peaks)
     peaks = peaks_img.get_fdata()
@@ -90,91 +95,81 @@ def main():
         is_second_peak = np.sum(peaks[..., 3:6], axis=-1) == 0
         nufo_sf = np.logical_and(is_first_peak, is_second_peak)
 
+    # Extract bundles and names
     bundles = []
     bundles_names = []
     for bundle in args.in_bundles[0]:
         bundles.append(bundle)
         bundles_names.append(Path(bundle).name.split(".")[0])
+    if args.in_bundles_names[0] != []: # If names are given
+        bundles_names = args.in_bundles_names[0]
 
-    fixel_density_maps = compute_fixel_density(peaks, bundles, args.max_theta,
-                                               nbr_processes=args.nbr_processes)
-
-    # This applies a threshold on the number of streamlines.
-    fixel_density_masks_abs = fixel_density_maps >= args.abs_thr
-
-    # Normalizing the density maps
-    fixel_sum = np.sum(fixel_density_maps, axis=-1)
-    voxel_sum = np.sum(fixel_sum, axis=-1)
-
-    for i, (bundle, bundle_name) in enumerate(zip(bundles, bundles_names)):
-
-        if args.norm == "voxel":
-            fixel_density_maps[..., 0, i] /= voxel_sum
-            fixel_density_maps[..., 1, i] /= voxel_sum
-            fixel_density_maps[..., 2, i] /= voxel_sum
-            fixel_density_maps[..., 3, i] /= voxel_sum
-            fixel_density_maps[..., 4, i] /= voxel_sum
-
-        elif args.norm == "fixel":
-            fixel_density_maps[..., i] /= fixel_sum
-
-        if args.separate_bundles:
-            nib.save(nib.Nifti1Image(fixel_density_maps[..., i], affine),
-                     out_folder / "fixel_density_map_{}.nii.gz".format(bundle_name))
-
-    if not args.separate_bundles:
-        nib.save(nib.Nifti1Image(fixel_density_maps, affine),
-                 out_folder / "fixel_density_maps.nii.gz")
-        bundles_idx = np.arange(0, len(bundles_names), 1)
-        lookup_table = np.array([bundles_names, bundles_idx])
-        np.savetxt(out_folder / "bundles_lookup_table.txt",
-                   lookup_table, fmt='%s')
-
-    # This applies a threshold on the normalized density (percentage)
-    fixel_density_masks_rel = fixel_density_maps >= args.rel_thr
-
-    # Compute the fixel density masks from the rel and abs versions
-    fixel_density_masks = fixel_density_masks_rel * fixel_density_masks_abs
+    # Compute fixel density maps and masks
+    fixel_density_maps = fixel_density(peaks, bundles, args.max_theta,
+                                       nbr_processes=args.nbr_processes)
+    
+    fixel_density_masks = maps_to_masks(fixel_density_maps, args.abs_thr,
+                                        args.rel_thr, args.norm,
+                                        len(bundles))
 
     # Compute number of bundles per fixel
     nb_bundles_per_fixel = np.sum(fixel_density_masks, axis=-1)
-    # Compute a mask of the present of each bundle
-    nb_unique_bundles_per_fixel = np.where(np.sum(fixel_density_masks,
-                                                  axis=-2) > 0, 1, 0)
-    # Compute number of bundles per fixel by taking the sum of the mask
-    nb_bundles_per_voxel = np.sum(nb_unique_bundles_per_fixel, axis=-1)
-
-    if args.save_masks:
-        for i, (bundle, bundle_name) in enumerate(zip(bundles, bundles_names)):
-
-            if args.separate_bundles:
-                nib.save(nib.Nifti1Image(fixel_density_masks[..., i].astype(np.uint8), affine),
-                         out_folder / "fixel_density_mask_{}.nii.gz".format(bundle_name))
-
-            if args.select_single_bundle:
-                # Single-fiber single-bundle voxels
-                single_bundle_per_voxel = nb_bundles_per_voxel == 1
-                # Making sure we also have single-fiber voxels only
-                single_bundle_per_voxel *= nufo_sf
-
-                nib.save(nib.Nifti1Image(single_bundle_per_voxel.astype(np.uint8),
-                                         affine),
-                         out_folder / "bundle_mask_only_WM.nii.gz")
-
-                bundle_mask = fixel_density_masks[..., 0, i] * single_bundle_per_voxel
-                nib.save(nib.Nifti1Image(bundle_mask.astype(np.uint8), affine),
-                         out_folder / "bundle_mask_only_{}.nii.gz".format(bundle_name))
-
-        if not args.separate_bundles:
-            nib.save(nib.Nifti1Image(fixel_density_masks.astype(np.uint8),
+    # Compute a mask of the presence of each bundle per voxel
+    # Since a bundle can be present twice in a single voxel by being associated
+    # with more than one fixel, we count the presence of a bundle if > 0.
+    presence_of_bundles_per_voxel = np.where(np.sum(fixel_density_masks,
+                                                    axis=-2) > 0, 1, 0)
+    # Compute number of bundles per voxel by taking the sum of the mask
+    nb_bundles_per_voxel = np.sum(presence_of_bundles_per_voxel, axis=-1)
+
+    # Save all results
+    for i, bundle_name in enumerate(bundles_names):
+        if args.split_bundles: # Save the maps and masks for each bundle
+            nib.save(nib.Nifti1Image(fixel_density_maps[..., i], affine),
+                     "fixel_density_map_{}.nii.gz".format(bundle_name))
+            nib.save(nib.Nifti1Image(fixel_density_masks[..., i], affine),
+                     "fixel_density_mask_{}.nii.gz".format(bundle_name))
+
+        if args.single_bundle:
+            # Single-fiber single-bundle voxels
+            one_bundle_per_voxel = nb_bundles_per_voxel == 1
+            # Making sure we also have single-fiber voxels only
+            one_bundle_per_voxel *= nufo_sf
+            # Save a single-fiber single-bundle mask for the whole WM
+            nib.save(nib.Nifti1Image(one_bundle_per_voxel.astype(np.uint8),
                                      affine),
-                     out_folder / "fixel_density_masks.nii.gz")
-
-    nib.save(nib.Nifti1Image(nb_bundles_per_fixel.astype(np.uint8),
-             affine), out_folder / "nb_bundles_per_fixel.nii.gz")
-
-    nib.save(nib.Nifti1Image(nb_bundles_per_voxel.astype(np.uint8),
-             affine), out_folder / "nb_bundles_per_voxel.nii.gz")
+                     "single_bundle_mask_WM.nii.gz")
+            # Save a single-fiber single-bundle mask for each bundle
+            bundle_mask = fixel_density_masks[..., 0, i] * one_bundle_per_voxel
+            nib.save(nib.Nifti1Image(bundle_mask.astype(np.uint8), affine),
+                     "single_bundle_mask_{}.nii.gz".format(bundle_name))
+    
+    if args.split_fixels: # Save the maps and masks for each fixel
+        for i in range(5):
+            nib.save(nib.Nifti1Image(fixel_density_maps[..., i, :], affine),
+                     "fixel_density_map_f{}.nii.gz".format(i))
+            nib.save(nib.Nifti1Image(fixel_density_masks[..., i, :], affine),
+                     "fixel_density_mask_f{}.nii.gz".format(i))
+
+    # Save bundles lookup table to know the order of the bundles
+    bundles_idx = np.arange(0, len(bundles_names), 1)
+    lookup_table = np.array([bundles_names, bundles_idx])
+    np.savetxt("bundles_lookup_table.txt",
+                lookup_table, fmt='%s')
+
+    # Save full fixel density maps, all fixels and bundles combined
+    nib.save(nib.Nifti1Image(fixel_density_maps, affine),
+             "fixel_density_maps.nii.gz")
+
+    # Save full fixel density masks, all fixels and bundles combined
+    nib.save(nib.Nifti1Image(fixel_density_masks, affine),
+             "fixel_density_masks.nii.gz")
+
+    # Save number of bundles per fixel and per voxel
+    nib.save(nib.Nifti1Image(nb_bundles_per_fixel, affine),
+             "nb_bundles_per_fixel.nii.gz")
+    nib.save(nib.Nifti1Image(nb_bundles_per_voxel, affine),
+             "nb_bundles_per_voxel.nii.gz")
 
 
 if __name__ == "__main__":

From f74f815f48bba253f021c1bacb6fd41075f47f90 Mon Sep 17 00:00:00 2001
From: Philippe Karan <philippe.karan@usherbrooke.ca>
Date: Wed, 19 Jun 2024 18:51:08 -0400
Subject: [PATCH 03/20] Adding bundle names

---
 scripts/scil_bundle_fixel_analysis.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/scripts/scil_bundle_fixel_analysis.py b/scripts/scil_bundle_fixel_analysis.py
index 4e9d2455d..7b8bffce6 100644
--- a/scripts/scil_bundle_fixel_analysis.py
+++ b/scripts/scil_bundle_fixel_analysis.py
@@ -89,8 +89,8 @@ def main():
     peaks = peaks_img.get_fdata()
     affine = peaks_img.affine
 
-    # Compute NuFo SF from peaks
-    if args.select_single_bundle:
+    # Compute NuFo single-fiber from peaks
+    if args.single_bundle:
         is_first_peak = np.sum(peaks[..., 0:3], axis=-1) != 0
         is_second_peak = np.sum(peaks[..., 3:6], axis=-1) == 0
         nufo_sf = np.logical_and(is_first_peak, is_second_peak)
@@ -101,7 +101,7 @@ def main():
     for bundle in args.in_bundles[0]:
         bundles.append(bundle)
         bundles_names.append(Path(bundle).name.split(".")[0])
-    if args.in_bundles_names[0] != []: # If names are given
+    if args.in_bundles_names: # If names are given
         bundles_names = args.in_bundles_names[0]
 
     # Compute fixel density maps and masks

From a56883b325d2882a414b4cdd7ed535af493af0f9 Mon Sep 17 00:00:00 2001
From: Philippe Karan <philippe.karan@usherbrooke.ca>
Date: Wed, 19 Jun 2024 19:38:46 -0400
Subject: [PATCH 04/20] Adding tests for input/output, rel_thr check

---
 scilpy/tractanalysis/fixel_density.py |  2 +-
 scripts/scil_bundle_fixel_analysis.py | 21 ++++++++++++++++++---
 2 files changed, 19 insertions(+), 4 deletions(-)

diff --git a/scilpy/tractanalysis/fixel_density.py b/scilpy/tractanalysis/fixel_density.py
index fcbe1e0d6..3f51753af 100644
--- a/scilpy/tractanalysis/fixel_density.py
+++ b/scilpy/tractanalysis/fixel_density.py
@@ -128,7 +128,7 @@ def maps_to_masks(maps, abs_thr, rel_thr, norm, nb_bundles):
         elif norm == "fixel":
             maps[..., i] /= fixel_sum
 
-    # Apply a threshold on the normalized density (percentage)
+    # Apply a threshold on the normalized density
     masks_rel = maps >= rel_thr
     # Compute the fixel density masks from the rel and abs versions
     masks = masks_rel * masks_abs
diff --git a/scripts/scil_bundle_fixel_analysis.py b/scripts/scil_bundle_fixel_analysis.py
index 7b8bffce6..77f1e645f 100644
--- a/scripts/scil_bundle_fixel_analysis.py
+++ b/scripts/scil_bundle_fixel_analysis.py
@@ -12,9 +12,12 @@
 import argparse
 import nibabel as nib
 import numpy as np
+import logging
 from pathlib import Path
 
-from scilpy.io.utils import (add_overwrite_arg, add_processes_arg)
+from scilpy.io.utils import (add_overwrite_arg, add_processes_arg,
+                             assert_headers_compatible, assert_inputs_exist,
+                             assert_outputs_exist)
 from scilpy.tractanalysis.fixel_density import (fixel_density, maps_to_masks)
 
 
@@ -83,6 +86,18 @@ def _build_arg_parser():
 def main():
     parser = _build_arg_parser()
     args = parser.parse_args()
+    logging.getLogger().setLevel(logging.getLevelName(args.verbose))
+
+    assert_inputs_exist(parser, args.in_peaks + args.in_bundles[0])
+    assert_outputs_exist(parser, args, ["bundles_lookup_table.txt",
+                                        "fixel_density_maps.nii.gz",
+                                        "fixel_density_masks.nii.gz",
+                                        "nb_bundles_per_fixel.nii.gz",
+                                        "nb_bundles_per_voxel.nii.gz"])
+    assert_headers_compatible(parser, args.in_peaks + args.in_bundles[0])
+
+    if args.rel_thr < 0 or args.rel_thr > 1:
+        parser.error("Argument rel_thr must be a value between 0 and 1.")
 
     # Load the data
     peaks_img = nib.load(args.in_peaks)
@@ -166,9 +181,9 @@ def main():
              "fixel_density_masks.nii.gz")
 
     # Save number of bundles per fixel and per voxel
-    nib.save(nib.Nifti1Image(nb_bundles_per_fixel, affine),
+    nib.save(nib.Nifti1Image(nb_bundles_per_fixel.astype(np.uint16), affine),
              "nb_bundles_per_fixel.nii.gz")
-    nib.save(nib.Nifti1Image(nb_bundles_per_voxel, affine),
+    nib.save(nib.Nifti1Image(nb_bundles_per_voxel.astype(np.uint16), affine),
              "nb_bundles_per_voxel.nii.gz")
 
 

From 8c55dc37b6fff739517099d571dad1598a660410 Mon Sep 17 00:00:00 2001
From: Philippe Karan <philippe.karan@usherbrooke.ca>
Date: Wed, 19 Jun 2024 19:49:45 -0400
Subject: [PATCH 05/20] Fixing bugs

---
 scripts/scil_bundle_fixel_analysis.py | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/scripts/scil_bundle_fixel_analysis.py b/scripts/scil_bundle_fixel_analysis.py
index 77f1e645f..9be4096b6 100644
--- a/scripts/scil_bundle_fixel_analysis.py
+++ b/scripts/scil_bundle_fixel_analysis.py
@@ -17,7 +17,7 @@
 
 from scilpy.io.utils import (add_overwrite_arg, add_processes_arg,
                              assert_headers_compatible, assert_inputs_exist,
-                             assert_outputs_exist)
+                             assert_outputs_exist, add_verbose_arg)
 from scilpy.tractanalysis.fixel_density import (fixel_density, maps_to_masks)
 
 
@@ -53,7 +53,7 @@ def _build_arg_parser():
                         '\nAny normalized density above or equal to '
                         'this value will pass the relative threshold test. '
                         '\nMust be between 0 and 1 [%(default)s].')
-    
+
     g.add_argument('--norm', default="voxel", choices=["fixel", "voxel"],
                    help='Way of normalizing the density maps. If fixel, '
                         'will normalize the maps per fixel, \nin each voxel. '
@@ -80,6 +80,7 @@ def _build_arg_parser():
 
     add_overwrite_arg(p)
     add_processes_arg(p)
+    add_verbose_arg(p)
     return p
 
 
@@ -88,13 +89,13 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_peaks + args.in_bundles[0])
+    assert_inputs_exist(parser, [args.in_peaks] + args.in_bundles[0])
     assert_outputs_exist(parser, args, ["bundles_lookup_table.txt",
                                         "fixel_density_maps.nii.gz",
                                         "fixel_density_masks.nii.gz",
                                         "nb_bundles_per_fixel.nii.gz",
                                         "nb_bundles_per_voxel.nii.gz"])
-    assert_headers_compatible(parser, args.in_peaks + args.in_bundles[0])
+    assert_headers_compatible(parser, [args.in_peaks] + args.in_bundles[0])
 
     if args.rel_thr < 0 or args.rel_thr > 1:
         parser.error("Argument rel_thr must be a value between 0 and 1.")
@@ -116,13 +117,13 @@ def main():
     for bundle in args.in_bundles[0]:
         bundles.append(bundle)
         bundles_names.append(Path(bundle).name.split(".")[0])
-    if args.in_bundles_names: # If names are given
+    if args.in_bundles_names:  # If names are given
         bundles_names = args.in_bundles_names[0]
 
     # Compute fixel density maps and masks
     fixel_density_maps = fixel_density(peaks, bundles, args.max_theta,
                                        nbr_processes=args.nbr_processes)
-    
+
     fixel_density_masks = maps_to_masks(fixel_density_maps, args.abs_thr,
                                         args.rel_thr, args.norm,
                                         len(bundles))
@@ -139,7 +140,7 @@ def main():
 
     # Save all results
     for i, bundle_name in enumerate(bundles_names):
-        if args.split_bundles: # Save the maps and masks for each bundle
+        if args.split_bundles:  # Save the maps and masks for each bundle
             nib.save(nib.Nifti1Image(fixel_density_maps[..., i], affine),
                      "fixel_density_map_{}.nii.gz".format(bundle_name))
             nib.save(nib.Nifti1Image(fixel_density_masks[..., i], affine),
@@ -158,19 +159,18 @@ def main():
             bundle_mask = fixel_density_masks[..., 0, i] * one_bundle_per_voxel
             nib.save(nib.Nifti1Image(bundle_mask.astype(np.uint8), affine),
                      "single_bundle_mask_{}.nii.gz".format(bundle_name))
-    
-    if args.split_fixels: # Save the maps and masks for each fixel
+
+    if args.split_fixels:  # Save the maps and masks for each fixel
         for i in range(5):
             nib.save(nib.Nifti1Image(fixel_density_maps[..., i, :], affine),
-                     "fixel_density_map_f{}.nii.gz".format(i))
+                     "fixel_density_map_f{}.nii.gz".format(i + 1))
             nib.save(nib.Nifti1Image(fixel_density_masks[..., i, :], affine),
-                     "fixel_density_mask_f{}.nii.gz".format(i))
+                     "fixel_density_mask_f{}.nii.gz".format(i + 1))
 
     # Save bundles lookup table to know the order of the bundles
     bundles_idx = np.arange(0, len(bundles_names), 1)
     lookup_table = np.array([bundles_names, bundles_idx])
-    np.savetxt("bundles_lookup_table.txt",
-                lookup_table, fmt='%s')
+    np.savetxt("bundles_lookup_table.txt", lookup_table, fmt='%s')
 
     # Save full fixel density maps, all fixels and bundles combined
     nib.save(nib.Nifti1Image(fixel_density_maps, affine),

From a2ba9eea7b8672818dab893a47ce0abb199d3762 Mon Sep 17 00:00:00 2001
From: karp2601 <karp2601@dinf-0051-20b.DInf.fsci.usherbrooke.ca>
Date: Thu, 20 Jun 2024 14:37:35 -0400
Subject: [PATCH 06/20] Adding doc and normalized maps

---
 scilpy/tractanalysis/fixel_density.py |  4 +-
 scripts/scil_bundle_fixel_analysis.py | 60 ++++++++++++++++++++-------
 2 files changed, 49 insertions(+), 15 deletions(-)

diff --git a/scilpy/tractanalysis/fixel_density.py b/scilpy/tractanalysis/fixel_density.py
index 3f51753af..18cfc9ebd 100644
--- a/scilpy/tractanalysis/fixel_density.py
+++ b/scilpy/tractanalysis/fixel_density.py
@@ -111,6 +111,8 @@ def maps_to_masks(maps, abs_thr, rel_thr, norm, nb_bundles):
     -------
     masks : np.ndarray (x, y, z, 5, N)
         Density masks per fixel per bundle.
+    maps : np.ndarray (x, y, z, 5, N)
+        Normalized density maps per fixel per bundle.
     """
     # Apply a threshold on the number of streamlines
     masks_abs = maps >= abs_thr
@@ -133,4 +135,4 @@ def maps_to_masks(maps, abs_thr, rel_thr, norm, nb_bundles):
     # Compute the fixel density masks from the rel and abs versions
     masks = masks_rel * masks_abs
 
-    return masks.astype(np.uint8)
+    return masks.astype(np.uint8), maps
diff --git a/scripts/scil_bundle_fixel_analysis.py b/scripts/scil_bundle_fixel_analysis.py
index 9be4096b6..8c5f33356 100644
--- a/scripts/scil_bundle_fixel_analysis.py
+++ b/scripts/scil_bundle_fixel_analysis.py
@@ -1,11 +1,31 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
-Analyze bundles at the fixel level, producing various results:
-
--
--
--
+Analyze bundles at the fixel level, producing various output:
+
+    - bundles_LUT.txt : array of (N) bundle names
+      Lookup table (LUT) to know the order of the bundles in the various
+      outputs. When an output contains results for all bundles, it is always
+      the last dimension of the np.ndarray and it follows the order of the
+      lookup table.
+
+    - fixel_density_maps.nii.gz : np.ndarray (x, y, z, 5, N)
+      For each voxel, it represents the density of bundles among the 5 fixels.
+      If the normalization is chosen as the voxel-type, then the sum of the
+      density over a voxel is 1. If the normalization is chosen as the
+      fixel-type, then the sum of the density over each fixel is 1, so the sum
+      over a voxel will be higher than 1 (except in the single-fiber case).
+      The density maps can be computed using the streamline count, or any
+      streamline weighting like COMMIT or SIF, through the data_per_streamline.
+    
+    - fixel_density_masks.nii.gz : np.ndarray (x, y, z, 5, N)
+      For each voxel, it represents whether or not each bundle is associated
+      with each of the 5 fixels. In other words, it is a masked version of
+      fixel_density_maps, using two different thresholds. First, the absolute
+      threshold (abs_thr) is applied on the maps before the normalization,
+      either on the number of streamlines or the custom weight. Second, after
+      the normalization, the relative threshold (rel_thr) is applied on the
+      maps as a minimal value of density to be counted as an association.
 
 """
 
@@ -90,9 +110,10 @@ def main():
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
     assert_inputs_exist(parser, [args.in_peaks] + args.in_bundles[0])
-    assert_outputs_exist(parser, args, ["bundles_lookup_table.txt",
+    assert_outputs_exist(parser, args, ["bundles_LUT.txt",
                                         "fixel_density_maps.nii.gz",
                                         "fixel_density_masks.nii.gz",
+                                        "voxel_density_masks.nii.gz",
                                         "nb_bundles_per_fixel.nii.gz",
                                         "nb_bundles_per_voxel.nii.gz"])
     assert_headers_compatible(parser, [args.in_peaks] + args.in_bundles[0])
@@ -124,17 +145,21 @@ def main():
     fixel_density_maps = fixel_density(peaks, bundles, args.max_theta,
                                        nbr_processes=args.nbr_processes)
 
-    fixel_density_masks = maps_to_masks(fixel_density_maps, args.abs_thr,
-                                        args.rel_thr, args.norm,
-                                        len(bundles))
+    fixel_density_masks, fixel_density_maps = maps_to_masks(fixel_density_maps,
+                                                            args.abs_thr,
+                                                            args.rel_thr,
+                                                            args.norm,
+                                                            len(bundles))
 
     # Compute number of bundles per fixel
     nb_bundles_per_fixel = np.sum(fixel_density_masks, axis=-1)
+    # Compute voxel density maps and masks
+    voxel_density_maps = np.sum(fixel_density_maps, axis=-2)
+    voxel_density_masks = np.sum(fixel_density_masks, axis=-2)
     # Compute a mask of the presence of each bundle per voxel
     # Since a bundle can be present twice in a single voxel by being associated
     # with more than one fixel, we count the presence of a bundle if > 0.
-    presence_of_bundles_per_voxel = np.where(np.sum(fixel_density_masks,
-                                                    axis=-2) > 0, 1, 0)
+    presence_of_bundles_per_voxel = np.where(voxel_density_masks > 0, 1, 0)
     # Compute number of bundles per voxel by taking the sum of the mask
     nb_bundles_per_voxel = np.sum(presence_of_bundles_per_voxel, axis=-1)
 
@@ -170,7 +195,7 @@ def main():
     # Save bundles lookup table to know the order of the bundles
     bundles_idx = np.arange(0, len(bundles_names), 1)
     lookup_table = np.array([bundles_names, bundles_idx])
-    np.savetxt("bundles_lookup_table.txt", lookup_table, fmt='%s')
+    np.savetxt("bundles_LUT.txt", lookup_table, fmt='%s')
 
     # Save full fixel density maps, all fixels and bundles combined
     nib.save(nib.Nifti1Image(fixel_density_maps, affine),
@@ -179,11 +204,18 @@ def main():
     # Save full fixel density masks, all fixels and bundles combined
     nib.save(nib.Nifti1Image(fixel_density_masks, affine),
              "fixel_density_masks.nii.gz")
+    
+    # Save full voxel density maps and masks
+    if args.norm == "voxel":  # If fixel, the voxel maps do not mean anything
+        nib.save(nib.Nifti1Image(voxel_density_maps, affine),
+                 "voxel_density_maps.nii.gz")
+    nib.save(nib.Nifti1Image(voxel_density_masks.astype(np.uint8), affine),
+             "voxel_density_masks.nii.gz")
 
     # Save number of bundles per fixel and per voxel
-    nib.save(nib.Nifti1Image(nb_bundles_per_fixel.astype(np.uint16), affine),
+    nib.save(nib.Nifti1Image(nb_bundles_per_fixel.astype(np.uint8), affine),
              "nb_bundles_per_fixel.nii.gz")
-    nib.save(nib.Nifti1Image(nb_bundles_per_voxel.astype(np.uint16), affine),
+    nib.save(nib.Nifti1Image(nb_bundles_per_voxel.astype(np.uint8), affine),
              "nb_bundles_per_voxel.nii.gz")
 
 

From 74211556fbba471abf9337786c127939978b4752 Mon Sep 17 00:00:00 2001
From: Philippe Karan <philippe.karan@usherbrooke.ca>
Date: Thu, 20 Jun 2024 17:55:32 -0400
Subject: [PATCH 07/20] Finishing docstring

---
 scripts/scil_bundle_fixel_analysis.py | 74 ++++++++++++++++++++++-----
 1 file changed, 60 insertions(+), 14 deletions(-)

diff --git a/scripts/scil_bundle_fixel_analysis.py b/scripts/scil_bundle_fixel_analysis.py
index 8c5f33356..07f7193c5 100644
--- a/scripts/scil_bundle_fixel_analysis.py
+++ b/scripts/scil_bundle_fixel_analysis.py
@@ -1,7 +1,13 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
-Analyze bundles at the fixel level, producing various output:
+Analyze bundles at the fixel level using peaks and bundles (.trk). If the
+bundles files are names as {bundle_name}.trk, simply use the --in_bundles
+argument with --in_bundles_names. If it is not the case or you want other names
+to be saved, please use --in_bundles_names to provide bundles names IN THE SAME
+ORDER as the inputed bundles.
+
+The script produces various output:
 
     - bundles_LUT.txt : array of (N) bundle names
       Lookup table (LUT) to know the order of the bundles in the various
@@ -10,16 +16,17 @@
       lookup table.
 
     - fixel_density_maps.nii.gz : np.ndarray (x, y, z, 5, N)
-      For each voxel, it represents the density of bundles among the 5 fixels.
-      If the normalization is chosen as the voxel-type, then the sum of the
-      density over a voxel is 1. If the normalization is chosen as the
-      fixel-type, then the sum of the density over each fixel is 1, so the sum
-      over a voxel will be higher than 1 (except in the single-fiber case).
-      The density maps can be computed using the streamline count, or any
-      streamline weighting like COMMIT or SIF, through the data_per_streamline.
+      For each voxel, it gives the density of bundles associated with each
+      of the 5 fixels. If the normalization is chosen as the voxel-type, then
+      the sum of the density over a voxel is 1. If the normalization is chosen
+      as the fixel-type, then the sum of the density over each fixel is 1, so
+      the sum over a voxel will be higher than 1 (except in the single-fiber
+      case). The density maps can be computed using the streamline count, or
+      any streamline weighting like COMMIT or SIF, through the
+      data_per_streamline.
     
     - fixel_density_masks.nii.gz : np.ndarray (x, y, z, 5, N)
-      For each voxel, it represents whether or not each bundle is associated
+      For each voxel, it gives whether or not each bundle is associated
       with each of the 5 fixels. In other words, it is a masked version of
       fixel_density_maps, using two different thresholds. First, the absolute
       threshold (abs_thr) is applied on the maps before the normalization,
@@ -27,6 +34,45 @@
       the normalization, the relative threshold (rel_thr) is applied on the
       maps as a minimal value of density to be counted as an association.
 
+    - voxel_density_maps.nii.gz : np.ndarray (x, y, z, N)
+      For each voxel, it gives the density of each bundle within the voxel,
+      regardless of fixels. In other words, it gives the fraction of each
+      bundle per voxel. This is only outputed if the normalization of the maps
+      is chosen as the voxel-type, because the fixel-type does not translate to
+      meaningful results when summed into a voxel.
+
+    - voxel_density_masks.nii.gz : np.ndarray (x, y, z, N)
+      For each voxel, it gives whether or not each bundle is present. This is
+      computed from fixel_density_masks, so the same thresholds prevail.
+
+    - nb_bundles_per_fixel.nii.gz : np.ndarray (x, y, z)
+      For each voxel, it gives the number of bundles associated with each of
+      the 5 fixels.
+
+    - nb_bundles_per_voxel.nii.gz : np.ndarray (x, y, z)
+      For each voxel, it gives the number of bundles within the voxel. This
+      accounts for bundles that might be associated with more than one fixel,
+      so no bundle is counted more than once in a voxel.
+
+    If the split_bundles argument is given, the script will also save the
+    fixel_density_maps and fixel_density_masks separated by bundles, with
+    names fixel_density_map_{bundle_name}.nii.gz and
+    fixel_density_mask_{bundle_name}.nii.gz. 
+    These will have the shape (x, y, z, 5).
+
+    If the split_fixels argument is given, the script will also save the
+    fixel_density_maps and fixel_density_masks separated by fixels, with
+    names fixel_density_map_f{fixel_id}.nii.gz and
+    fixel_density_mask_f{fixel_id}.nii.gz.
+    These will have the shape (x, y, z, N).
+
+    If the single_bundle argument is given, the script will also save the
+    single-fiber single-bundle masks, which are obtained by selecting the
+    voxels where only one bundle and one fiber (fixel) are present. There will
+    be one single_bundle_mask_{bundle_name}.nii.gz per bundle, and a whole WM
+    version single_bundle_mask_WM.nii.gz.
+    These will have the shape (x, y, z).
+
 """
 
 import argparse
@@ -153,15 +199,15 @@ def main():
 
     # Compute number of bundles per fixel
     nb_bundles_per_fixel = np.sum(fixel_density_masks, axis=-1)
-    # Compute voxel density maps and masks
+    # Compute voxel density maps
     voxel_density_maps = np.sum(fixel_density_maps, axis=-2)
-    voxel_density_masks = np.sum(fixel_density_masks, axis=-2)
-    # Compute a mask of the presence of each bundle per voxel
+    # Compute voxel density masks
     # Since a bundle can be present twice in a single voxel by being associated
     # with more than one fixel, we count the presence of a bundle if > 0.
-    presence_of_bundles_per_voxel = np.where(voxel_density_masks > 0, 1, 0)
+    voxel_density_masks = np.where(np.sum(fixel_density_masks, axis=-2) > 0,
+                                   1, 0)
     # Compute number of bundles per voxel by taking the sum of the mask
-    nb_bundles_per_voxel = np.sum(presence_of_bundles_per_voxel, axis=-1)
+    nb_bundles_per_voxel = np.sum(voxel_density_masks, axis=-1)
 
     # Save all results
     for i, bundle_name in enumerate(bundles_names):

From 45f6015507b3b02fa23afbd93a7a6acb5b8bcd98 Mon Sep 17 00:00:00 2001
From: Philippe Karan <philippe.karan@usherbrooke.ca>
Date: Thu, 20 Jun 2024 18:41:19 -0400
Subject: [PATCH 08/20] Adding dps key

---
 scilpy/tractanalysis/fixel_density.py | 20 ++++++++++++++------
 scripts/scil_bundle_fixel_analysis.py | 11 ++++++++---
 2 files changed, 22 insertions(+), 9 deletions(-)

diff --git a/scilpy/tractanalysis/fixel_density.py b/scilpy/tractanalysis/fixel_density.py
index 18cfc9ebd..811287236 100644
--- a/scilpy/tractanalysis/fixel_density.py
+++ b/scilpy/tractanalysis/fixel_density.py
@@ -9,7 +9,8 @@
 def _fixel_density_parallel(args):
     peaks = args[0]
     max_theta = args[1]
-    bundle = args[2]
+    dps_key = args[2]
+    bundle = args[3]
 
     sft = load_tractogram(bundle, 'same')
     sft.to_vox()
@@ -20,7 +21,7 @@ def _fixel_density_parallel(args):
     min_cos_theta = np.cos(np.radians(max_theta))
 
     all_crossed_indices = grid_intersections(sft.streamlines)
-    for crossed_indices in all_crossed_indices:
+    for i, crossed_indices in enumerate(all_crossed_indices):
         segments = crossed_indices[1:] - crossed_indices[:-1]
         seg_lengths = np.linalg.norm(segments, axis=1)
 
@@ -36,6 +37,10 @@ def _fixel_density_parallel(args):
 
         normalized_seg = np.reshape(segments / seg_lengths[..., None], (-1, 3))
 
+        weight = 1
+        if dps_key:
+            weight = sft.data_per_streamline[dps_key][i]
+
         for vox_idx, seg_dir in zip(vox_indices, normalized_seg):
             vox_idx = tuple(vox_idx)
             peaks_at_idx = peaks[vox_idx].reshape((5, 3))
@@ -45,21 +50,23 @@ def _fixel_density_parallel(args):
 
             if (cos_theta > min_cos_theta).any():
                 lobe_idx = np.argmax(np.squeeze(cos_theta), axis=0)  # (n_segs)
-                # TODO Change that for commit weight if given
-                fixel_density_maps[vox_idx][lobe_idx] += 1
+                fixel_density_maps[vox_idx][lobe_idx] += weight
 
     return fixel_density_maps
 
 
-def fixel_density(peaks, bundles, max_theta=45, nbr_processes=None):
+def fixel_density(peaks, bundles, dps_key=None, max_theta=45, nbr_processes=None):
     """Compute the fixel density map per bundle. Can use parallel processing.
 
     Parameters
     ----------
-    peaks: np.ndarray (x, y, z, 15)
+    peaks : np.ndarray (x, y, z, 15)
         Five principal fiber orientations for each voxel.
     bundles : list or np.array (N)
         List of (N) paths to bundles.
+    dps_key : string, optional
+        Key to the data_per_streamline to use as weight instead of the number
+        of streamlines.
     max_theta : int, optional
         Maximum angle between streamline and peak to be associated.
     nbr_processes : int, optional
@@ -79,6 +86,7 @@ def fixel_density(peaks, bundles, max_theta=45, nbr_processes=None):
     results = pool.map(_fixel_density_parallel,
                        zip(itertools.repeat(peaks),
                            itertools.repeat(max_theta),
+                           itertools.repeat(dps_key),
                            bundles))
     pool.close()
     pool.join()
diff --git a/scripts/scil_bundle_fixel_analysis.py b/scripts/scil_bundle_fixel_analysis.py
index 07f7193c5..c3b918bc5 100644
--- a/scripts/scil_bundle_fixel_analysis.py
+++ b/scripts/scil_bundle_fixel_analysis.py
@@ -23,7 +23,7 @@
       the sum over a voxel will be higher than 1 (except in the single-fiber
       case). The density maps can be computed using the streamline count, or
       any streamline weighting like COMMIT or SIF, through the
-      data_per_streamline.
+      data_per_streamline using the --dps_key argument.
     
     - fixel_density_masks.nii.gz : np.ndarray (x, y, z, 5, N)
       For each voxel, it gives whether or not each bundle is associated
@@ -72,7 +72,6 @@
     be one single_bundle_mask_{bundle_name}.nii.gz per bundle, and a whole WM
     version single_bundle_mask_WM.nii.gz.
     These will have the shape (x, y, z).
-
 """
 
 import argparse
@@ -104,6 +103,11 @@ def _build_arg_parser():
                         'as they were given. \nIf this argument is not used, '
                         'the script assumes that the name of the bundle \nis '
                         'its filename without extensions.')
+    
+    p.add_argument('--dps_key', default=None,
+                   help='Key to access the data per streamline to use as '
+                        'weight when computing the maps, \ninstead of the '
+                        'number of streamlines. [%(default)s].')
 
     g = p.add_argument_group(title='Mask parameters')
 
@@ -188,7 +192,8 @@ def main():
         bundles_names = args.in_bundles_names[0]
 
     # Compute fixel density maps and masks
-    fixel_density_maps = fixel_density(peaks, bundles, args.max_theta,
+    fixel_density_maps = fixel_density(peaks, bundles, args.dps_key,
+                                       args.max_theta,
                                        nbr_processes=args.nbr_processes)
 
     fixel_density_masks, fixel_density_maps = maps_to_masks(fixel_density_maps,

From 6ed888d48286aeded44b3bd3f85d3d4464bbad1d Mon Sep 17 00:00:00 2001
From: Philippe Karan <philippe.karan@usherbrooke.ca>
Date: Fri, 21 Jun 2024 10:08:07 -0400
Subject: [PATCH 09/20] Modify asb_thr for streamline weights, pep8

---
 scilpy/tractanalysis/fixel_density.py | 11 ++++++-----
 scripts/scil_bundle_fixel_analysis.py | 27 ++++++++++++++-------------
 2 files changed, 20 insertions(+), 18 deletions(-)

diff --git a/scilpy/tractanalysis/fixel_density.py b/scilpy/tractanalysis/fixel_density.py
index 811287236..dbb3802e8 100644
--- a/scilpy/tractanalysis/fixel_density.py
+++ b/scilpy/tractanalysis/fixel_density.py
@@ -55,7 +55,8 @@ def _fixel_density_parallel(args):
     return fixel_density_maps
 
 
-def fixel_density(peaks, bundles, dps_key=None, max_theta=45, nbr_processes=None):
+def fixel_density(peaks, bundles, dps_key=None, max_theta=45,
+                  nbr_processes=None):
     """Compute the fixel density map per bundle. Can use parallel processing.
 
     Parameters
@@ -103,9 +104,9 @@ def maps_to_masks(maps, abs_thr, rel_thr, norm, nb_bundles):
     ----------
     maps : np.ndarray (x, y, z, 5, N)
         Density per fixel per bundle.
-    abs_thr : int
+    abs_thr : float
         Value of density maps threshold to obtain density masks, in number of
-        streamlines.
+        streamlines or streamline weighting.
     rel_thr : float
         Value of density maps threshold to obtain density masks, as a ratio of
         the normalized density. Must be between 0 and 1.
@@ -123,7 +124,7 @@ def maps_to_masks(maps, abs_thr, rel_thr, norm, nb_bundles):
         Normalized density maps per fixel per bundle.
     """
     # Apply a threshold on the number of streamlines
-    masks_abs = maps >= abs_thr
+    masks_abs = maps > abs_thr
 
     # Normalizing the density maps per voxel or fixel
     fixel_sum = np.sum(maps, axis=-1)
@@ -139,7 +140,7 @@ def maps_to_masks(maps, abs_thr, rel_thr, norm, nb_bundles):
             maps[..., i] /= fixel_sum
 
     # Apply a threshold on the normalized density
-    masks_rel = maps >= rel_thr
+    masks_rel = maps > rel_thr
     # Compute the fixel density masks from the rel and abs versions
     masks = masks_rel * masks_abs
 
diff --git a/scripts/scil_bundle_fixel_analysis.py b/scripts/scil_bundle_fixel_analysis.py
index c3b918bc5..ed58e2ac6 100644
--- a/scripts/scil_bundle_fixel_analysis.py
+++ b/scripts/scil_bundle_fixel_analysis.py
@@ -24,15 +24,15 @@
       case). The density maps can be computed using the streamline count, or
       any streamline weighting like COMMIT or SIF, through the
       data_per_streamline using the --dps_key argument.
-    
+
     - fixel_density_masks.nii.gz : np.ndarray (x, y, z, 5, N)
       For each voxel, it gives whether or not each bundle is associated
       with each of the 5 fixels. In other words, it is a masked version of
       fixel_density_maps, using two different thresholds. First, the absolute
       threshold (abs_thr) is applied on the maps before the normalization,
-      either on the number of streamlines or the custom weight. Second, after
-      the normalization, the relative threshold (rel_thr) is applied on the
-      maps as a minimal value of density to be counted as an association.
+      either on the number of streamlines or the streamline weights. Second,
+      after the normalization, the relative threshold (rel_thr) is applied on
+      the maps as a minimal value of density to be counted as an association.
 
     - voxel_density_maps.nii.gz : np.ndarray (x, y, z, N)
       For each voxel, it gives the density of each bundle within the voxel,
@@ -57,7 +57,7 @@
     If the split_bundles argument is given, the script will also save the
     fixel_density_maps and fixel_density_masks separated by bundles, with
     names fixel_density_map_{bundle_name}.nii.gz and
-    fixel_density_mask_{bundle_name}.nii.gz. 
+    fixel_density_mask_{bundle_name}.nii.gz.
     These will have the shape (x, y, z, 5).
 
     If the split_fixels argument is given, the script will also save the
@@ -103,24 +103,25 @@ def _build_arg_parser():
                         'as they were given. \nIf this argument is not used, '
                         'the script assumes that the name of the bundle \nis '
                         'its filename without extensions.')
-    
-    p.add_argument('--dps_key', default=None,
+
+    p.add_argument('--dps_key', default=None, type=str,
                    help='Key to access the data per streamline to use as '
                         'weight when computing the maps, \ninstead of the '
                         'number of streamlines. [%(default)s].')
 
     g = p.add_argument_group(title='Mask parameters')
 
-    g.add_argument('--abs_thr', default=1, type=int,
+    g.add_argument('--abs_thr', default=0, type=float,
                    help='Value of density maps threshold to obtain density '
-                        'masks, in number of streamlines. \nAny number of '
-                        'streamlines above or equal this value will pass '
-                        'the absolute threshold test [%(default)s].')
+                        'masks, in number of streamlines \nor streamline '
+                        'weighting if --dps_key is given. Any number of '
+                        'streamlines \nor weight above this value will '
+                        'pass the absolute threshold test [%(default)s].')
 
     g.add_argument('--rel_thr', default=0.01, type=float,
                    help='Value of density maps threshold to obtain density '
                         'masks, as a ratio of the normalized density '
-                        '\nAny normalized density above or equal to '
+                        '\nAny normalized density above '
                         'this value will pass the relative threshold test. '
                         '\nMust be between 0 and 1 [%(default)s].')
 
@@ -255,7 +256,7 @@ def main():
     # Save full fixel density masks, all fixels and bundles combined
     nib.save(nib.Nifti1Image(fixel_density_masks, affine),
              "fixel_density_masks.nii.gz")
-    
+
     # Save full voxel density maps and masks
     if args.norm == "voxel":  # If fixel, the voxel maps do not mean anything
         nib.save(nib.Nifti1Image(voxel_density_maps, affine),

From 24da64a4b05ca2eaef6181799c46313be61468f4 Mon Sep 17 00:00:00 2001
From: Philippe Karan <philippe.karan@usherbrooke.ca>
Date: Fri, 21 Jun 2024 11:46:25 -0400
Subject: [PATCH 10/20] Adding tests

---
 .../tractanalysis/tests/test_fixel_density.py | 11 +++++
 scripts/tests/test_bundle_fixel_analysis.py   | 47 +++++++++++++++++++
 2 files changed, 58 insertions(+)
 create mode 100644 scilpy/tractanalysis/tests/test_fixel_density.py
 create mode 100644 scripts/tests/test_bundle_fixel_analysis.py

diff --git a/scilpy/tractanalysis/tests/test_fixel_density.py b/scilpy/tractanalysis/tests/test_fixel_density.py
new file mode 100644
index 000000000..d1cbe6a3c
--- /dev/null
+++ b/scilpy/tractanalysis/tests/test_fixel_density.py
@@ -0,0 +1,11 @@
+# -*- coding: utf-8 -*-
+
+
+def test_fixel_density():
+    # toDO
+    pass
+
+
+def test_maps_to_masks():
+    # toDO
+    pass
diff --git a/scripts/tests/test_bundle_fixel_analysis.py b/scripts/tests/test_bundle_fixel_analysis.py
new file mode 100644
index 000000000..4bb09febc
--- /dev/null
+++ b/scripts/tests/test_bundle_fixel_analysis.py
@@ -0,0 +1,47 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+import os
+import tempfile
+
+from scilpy import SCILPY_HOME
+from scilpy.io.fetcher import fetch_data, get_testing_files_dict
+
+fetch_data(get_testing_files_dict(), keys=['commit_amico.zip'])
+tmp_dir = tempfile.TemporaryDirectory()
+
+
+def test_help_option(script_runner):
+    ret = script_runner.run('scil_bundle_fixel_analysis.py', '--help')
+    assert ret.success
+
+
+def test_default_parameters(script_runner, monkeypatch):
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    in_peaks = os.path.join(SCILPY_HOME, 'commit_amico', 'peaks.nii.gz')
+    in_bundle = os.path.join(SCILPY_HOME, 'commit_amico', 'tracking.trk')
+
+    ret = script_runner.run('scil_bundle_fixel_analysis.py', in_peaks,
+                            '--in_bundles', in_bundle,
+                            '--processes', '1', '-f')
+    assert ret.success
+
+
+def test_all_parameters(script_runner, monkeypatch):
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    in_peaks = os.path.join(SCILPY_HOME, 'commit_amico', 'peaks.nii.gz')
+    in_bundle = os.path.join(SCILPY_HOME, 'commit_amico', 'tracking.trk')
+
+    ret = script_runner.run('scil_bundle_fixel_analysis.py', in_peaks,
+                            '--in_bundles', in_bundle,
+                            '--in_bundles_names', 'test',
+                            '--abs_thr', '5',
+                            '--rel_thr', '0.05',
+                            '--norm', 'fixel',
+                            '--split_bundles', '--split_fixels',
+                            '--single_bundle',
+                            '--processes', '1', '-f')
+    assert ret.success
+
+# We would need a tractogram with data_per_streamline to test the --dps_key
+# option

From 11caba863c172b4ccf7edd417bfdd4124e71344b Mon Sep 17 00:00:00 2001
From: Philippe Karan <philippe.karan@usherbrooke.ca>
Date: Sat, 6 Jul 2024 08:32:09 -0400
Subject: [PATCH 11/20] Update doc

---
 scripts/scil_bundle_fixel_analysis.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/scil_bundle_fixel_analysis.py b/scripts/scil_bundle_fixel_analysis.py
index ed58e2ac6..2704571b0 100644
--- a/scripts/scil_bundle_fixel_analysis.py
+++ b/scripts/scil_bundle_fixel_analysis.py
@@ -137,11 +137,11 @@ def _build_arg_parser():
 
     p.add_argument('--split_bundles', action='store_true',
                    help='If set, save the density maps for each bundle '
-                        'separately \ninstead of all in one file.')
+                        'separately \nin addition to the all in one version.')
 
     p.add_argument('--split_fixels', action='store_true',
                    help='If set, save the density maps for each fixel '
-                        'separately \ninstead of all in one file.')
+                        'separately \nin addition to the all in one version.')
 
     p.add_argument('--single_bundle', action='store_true',
                    help='If set, will save the single-fiber single-bundle '

From b4a2b736db728ba8f0a0cc46834d78a2aba59279 Mon Sep 17 00:00:00 2001
From: Philippe Karan <philippe.karan@usherbrooke.ca>
Date: Sun, 7 Jul 2024 16:01:10 -0400
Subject: [PATCH 12/20] Adding new saves

---
 scripts/scil_bundle_fixel_analysis.py | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/scripts/scil_bundle_fixel_analysis.py b/scripts/scil_bundle_fixel_analysis.py
index 2704571b0..e98cbad28 100644
--- a/scripts/scil_bundle_fixel_analysis.py
+++ b/scripts/scil_bundle_fixel_analysis.py
@@ -148,6 +148,9 @@ def _build_arg_parser():
                         'masks as well. \nThese are obtained by '
                         'selecting the voxels where only one bundle is '
                         'present \n(and one fiber/fixel).')
+    
+    p.add_argument('--bundles_mask', action='store_true',
+                   help='If set, save the bundle mask for each bundle.')
 
     add_overwrite_arg(p)
     add_processes_arg(p)
@@ -222,6 +225,12 @@ def main():
                      "fixel_density_map_{}.nii.gz".format(bundle_name))
             nib.save(nib.Nifti1Image(fixel_density_masks[..., i], affine),
                      "fixel_density_mask_{}.nii.gz".format(bundle_name))
+            if args.norm == "voxel":  # If fixel, voxel maps mean nothing
+                nib.save(nib.Nifti1Image(voxel_density_maps[..., i], affine),
+                         "voxel_density_map_{}.nii.gz".format(bundle_name))
+            bundle_mask = voxel_density_masks[..., i].astype(np.uint8)
+            nib.save(nib.Nifti1Image(bundle_mask, affine),
+                     "voxel_density_mask_{}.nii.gz".format(bundle_name))
 
         if args.single_bundle:
             # Single-fiber single-bundle voxels
@@ -243,6 +252,13 @@ def main():
                      "fixel_density_map_f{}.nii.gz".format(i + 1))
             nib.save(nib.Nifti1Image(fixel_density_masks[..., i, :], affine),
                      "fixel_density_mask_f{}.nii.gz".format(i + 1))
+            if args.norm == "voxel":  # If fixel, voxel maps mean nothing
+                nib.save(nib.Nifti1Image(voxel_density_maps[..., i, :],
+                                         affine),
+                         "voxel_density_map_f{}.nii.gz".format(i + 1))
+            bundle_mask = voxel_density_masks[..., i, :].astype(np.uint8)
+            nib.save(nib.Nifti1Image(bundle_mask, affine),
+                     "voxel_density_mask_f{}.nii.gz".format(i + 1))
 
     # Save bundles lookup table to know the order of the bundles
     bundles_idx = np.arange(0, len(bundles_names), 1)
@@ -258,7 +274,7 @@ def main():
              "fixel_density_masks.nii.gz")
 
     # Save full voxel density maps and masks
-    if args.norm == "voxel":  # If fixel, the voxel maps do not mean anything
+    if args.norm == "voxel":  # If fixel, voxel maps mean nothing
         nib.save(nib.Nifti1Image(voxel_density_maps, affine),
                  "voxel_density_maps.nii.gz")
     nib.save(nib.Nifti1Image(voxel_density_masks.astype(np.uint8), affine),

From d0b7f4862c4b3416db7e7f9271ef93533d40aabe Mon Sep 17 00:00:00 2001
From: karp2601 <karp2601@dinf-0051-20b.DInf.fsci.usherbrooke.ca>
Date: Tue, 16 Jul 2024 13:46:07 -0400
Subject: [PATCH 13/20] Correct pep8

---
 scripts/scil_bundle_fixel_analysis.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/scil_bundle_fixel_analysis.py b/scripts/scil_bundle_fixel_analysis.py
index e98cbad28..3e0ce0a56 100644
--- a/scripts/scil_bundle_fixel_analysis.py
+++ b/scripts/scil_bundle_fixel_analysis.py
@@ -148,7 +148,7 @@ def _build_arg_parser():
                         'masks as well. \nThese are obtained by '
                         'selecting the voxels where only one bundle is '
                         'present \n(and one fiber/fixel).')
-    
+
     p.add_argument('--bundles_mask', action='store_true',
                    help='If set, save the bundle mask for each bundle.')
 

From d29f50675149c602f5399351e3418ccee8dbf7d6 Mon Sep 17 00:00:00 2001
From: karp2601 <karp2601@dinf-0051-20b.DInf.fsci.usherbrooke.ca>
Date: Tue, 23 Jul 2024 10:51:52 -0400
Subject: [PATCH 14/20] Adding output filename options

---
 scripts/scil_bundle_fixel_analysis.py | 172 +++++++++++++++++---------
 1 file changed, 115 insertions(+), 57 deletions(-)

diff --git a/scripts/scil_bundle_fixel_analysis.py b/scripts/scil_bundle_fixel_analysis.py
index 3e0ce0a56..ce5c7521a 100644
--- a/scripts/scil_bundle_fixel_analysis.py
+++ b/scripts/scil_bundle_fixel_analysis.py
@@ -108,49 +108,65 @@ def _build_arg_parser():
                    help='Key to access the data per streamline to use as '
                         'weight when computing the maps, \ninstead of the '
                         'number of streamlines. [%(default)s].')
-
-    g = p.add_argument_group(title='Mask parameters')
-
-    g.add_argument('--abs_thr', default=0, type=float,
-                   help='Value of density maps threshold to obtain density '
-                        'masks, in number of streamlines \nor streamline '
-                        'weighting if --dps_key is given. Any number of '
-                        'streamlines \nor weight above this value will '
-                        'pass the absolute threshold test [%(default)s].')
-
-    g.add_argument('--rel_thr', default=0.01, type=float,
-                   help='Value of density maps threshold to obtain density '
-                        'masks, as a ratio of the normalized density '
-                        '\nAny normalized density above '
-                        'this value will pass the relative threshold test. '
-                        '\nMust be between 0 and 1 [%(default)s].')
-
-    g.add_argument('--norm', default="voxel", choices=["fixel", "voxel"],
-                   help='Way of normalizing the density maps. If fixel, '
-                        'will normalize the maps per fixel, \nin each voxel. '
-                        'If voxel, will normalize the maps per voxel. '
-                        '[%(default)s]')
-
+    
     p.add_argument('--max_theta', default=45,
                    help='Maximum angle between streamline and peak to be '
                         'associated [%(default)s].')
 
-    p.add_argument('--split_bundles', action='store_true',
-                   help='If set, save the density maps for each bundle '
-                        'separately \nin addition to the all in one version.')
-
-    p.add_argument('--split_fixels', action='store_true',
-                   help='If set, save the density maps for each fixel '
-                        'separately \nin addition to the all in one version.')
-
-    p.add_argument('--single_bundle', action='store_true',
-                   help='If set, will save the single-fiber single-bundle '
-                        'masks as well. \nThese are obtained by '
-                        'selecting the voxels where only one bundle is '
-                        'present \n(and one fiber/fixel).')
-
-    p.add_argument('--bundles_mask', action='store_true',
-                   help='If set, save the bundle mask for each bundle.')
+    g1 = p.add_argument_group(title='Mask parameters')
+
+    g1.add_argument('--abs_thr', default=0, type=float,
+                    help='Value of density maps threshold to obtain density '
+                         'masks, in number of streamlines \nor streamline '
+                         'weighting if --dps_key is given. Any number of '
+                         'streamlines \nor weight above this value will '
+                         'pass the absolute threshold test [%(default)s].')
+
+    g1.add_argument('--rel_thr', default=0.01, type=float,
+                    help='Value of density maps threshold to obtain density '
+                         'masks, as a ratio of the normalized density '
+                         '\nAny normalized density above '
+                         'this value will pass the relative threshold test. '
+                         '\nMust be between 0 and 1 [%(default)s].')
+
+    g1.add_argument('--norm', default="voxel", choices=["fixel", "voxel"],
+                    help='Way of normalizing the density maps. If fixel, '
+                         'will normalize the maps per fixel, \nin each voxel. '
+                         'If voxel, will normalize the maps per voxel '
+                         '[%(default)s].')
+    
+    g2 = p.add_argument_group(title='Output options')
+
+    g2.add_argument('--split_bundles', action='store_true',
+                    help='If set, save the density maps for each bundle '
+                         'separately \nin addition to the all in one version.')
+
+    g2.add_argument('--split_fixels', action='store_true',
+                    help='If set, save the density maps for each fixel '
+                         'separately \nin addition to the all in one version.')
+
+    g2.add_argument('--single_bundle', action='store_true',
+                    help='If set, will save the single-fiber single-bundle '
+                         'masks as well. \nThese are obtained by '
+                         'selecting the voxels where only one bundle is '
+                         'present \n(and one fiber/fixel).')
+
+    g2.add_argument('--bundles_mask', action='store_true',
+                    help='If set, save the bundle mask for each bundle.')
+    
+    g2.add_argument('--out_dir', default="./",
+                    help='Path to the output directory where all the output '
+                         'files will be saved [%(default)s].')
+    
+    g2.add_argument('--prefix', default="",
+                    help='Prefix to add to all predetermined output '
+                         'filenames. We recommand finishing with an '
+                         'underscore for better readability [%(default)s].')
+    
+    g2.add_argument('--suffix', default="",
+                    help='Suffix to add to all predetermined output '
+                         'filenames. We recommand starting with an underscore '
+                         'for better readability [%(default)s].')
 
     add_overwrite_arg(p)
     add_processes_arg(p)
@@ -195,6 +211,13 @@ def main():
     if args.in_bundles_names:  # If names are given
         bundles_names = args.in_bundles_names[0]
 
+    # Set up saving filename options
+    out_dir = args.out_dir
+    prefix = args.prefix
+    suffix = args.suffix
+    if out_dir[-1] != "/":
+        out_dir += "/"
+
     # Compute fixel density maps and masks
     fixel_density_maps = fixel_density(peaks, bundles, args.dps_key,
                                        args.max_theta,
@@ -219,18 +242,30 @@ def main():
     nb_bundles_per_voxel = np.sum(voxel_density_masks, axis=-1)
 
     # Save all results
-    for i, bundle_name in enumerate(bundles_names):
+    for i, bundle_n in enumerate(bundles_names):
         if args.split_bundles:  # Save the maps and masks for each bundle
             nib.save(nib.Nifti1Image(fixel_density_maps[..., i], affine),
-                     "fixel_density_map_{}.nii.gz".format(bundle_name))
+                     "{}{}fixel_density_map_{}{}.nii.gz".format(out_dir,
+                                                                prefix,
+                                                                bundle_n,
+                                                                suffix))
             nib.save(nib.Nifti1Image(fixel_density_masks[..., i], affine),
-                     "fixel_density_mask_{}.nii.gz".format(bundle_name))
+                     "{}{}fixel_density_mask_{}{}.nii.gz".format(out_dir,
+                                                                 prefix,
+                                                                 bundle_n,
+                                                                 suffix))
             if args.norm == "voxel":  # If fixel, voxel maps mean nothing
                 nib.save(nib.Nifti1Image(voxel_density_maps[..., i], affine),
-                         "voxel_density_map_{}.nii.gz".format(bundle_name))
+                         "{}{}voxel_density_map_{}{}.nii.gz".format(out_dir,
+                                                                    prefix,
+                                                                    bundle_n,
+                                                                    suffix))
             bundle_mask = voxel_density_masks[..., i].astype(np.uint8)
             nib.save(nib.Nifti1Image(bundle_mask, affine),
-                     "voxel_density_mask_{}.nii.gz".format(bundle_name))
+                     "{}{}voxel_density_mask_{}{}.nii.gz".format(out_dir,
+                                                                 prefix,
+                                                                 bundle_n,
+                                                                 suffix))
 
         if args.single_bundle:
             # Single-fiber single-bundle voxels
@@ -240,51 +275,74 @@ def main():
             # Save a single-fiber single-bundle mask for the whole WM
             nib.save(nib.Nifti1Image(one_bundle_per_voxel.astype(np.uint8),
                                      affine),
-                     "single_bundle_mask_WM.nii.gz")
+                     "{}{}single_bundle_mask_WM{}.nii.gz".format(out_dir,
+                                                                 prefix,
+                                                                 suffix))
             # Save a single-fiber single-bundle mask for each bundle
             bundle_mask = fixel_density_masks[..., 0, i] * one_bundle_per_voxel
             nib.save(nib.Nifti1Image(bundle_mask.astype(np.uint8), affine),
-                     "single_bundle_mask_{}.nii.gz".format(bundle_name))
+                     "{}{}single_bundle_mask_{}{}.nii.gz".format(out_dir,
+                                                                 prefix,
+                                                                 bundle_n,
+                                                                 suffix))
 
     if args.split_fixels:  # Save the maps and masks for each fixel
         for i in range(5):
             nib.save(nib.Nifti1Image(fixel_density_maps[..., i, :], affine),
-                     "fixel_density_map_f{}.nii.gz".format(i + 1))
+                     "{}{}fixel_density_map_f{}{}.nii.gz".format(out_dir,
+                                                                 prefix,
+                                                                 i + 1,
+                                                                 suffix))
             nib.save(nib.Nifti1Image(fixel_density_masks[..., i, :], affine),
-                     "fixel_density_mask_f{}.nii.gz".format(i + 1))
+                     "{}{}fixel_density_mask_f{}{}.nii.gz".format(out_dir,
+                                                                  prefix,
+                                                                  i + 1,
+                                                                  suffix))
             if args.norm == "voxel":  # If fixel, voxel maps mean nothing
                 nib.save(nib.Nifti1Image(voxel_density_maps[..., i, :],
                                          affine),
-                         "voxel_density_map_f{}.nii.gz".format(i + 1))
+                         "{}{}voxel_density_map_f{}{}.nii.gz".format(out_dir,
+                                                                     prefix,
+                                                                     i + 1,
+                                                                     suffix))
             bundle_mask = voxel_density_masks[..., i, :].astype(np.uint8)
             nib.save(nib.Nifti1Image(bundle_mask, affine),
-                     "voxel_density_mask_f{}.nii.gz".format(i + 1))
+                     "{}{}voxel_density_mask_f{}{}.nii.gz".format(out_dir,
+                                                                  prefix,
+                                                                  i + 1,
+                                                                  suffix))
 
     # Save bundles lookup table to know the order of the bundles
     bundles_idx = np.arange(0, len(bundles_names), 1)
     lookup_table = np.array([bundles_names, bundles_idx])
-    np.savetxt("bundles_LUT.txt", lookup_table, fmt='%s')
+    np.savetxt("{}{}bundles_LUT{}.txt".format(out_dir, prefix, suffix),
+               lookup_table, fmt='%s')
 
     # Save full fixel density maps, all fixels and bundles combined
     nib.save(nib.Nifti1Image(fixel_density_maps, affine),
-             "fixel_density_maps.nii.gz")
+             "{}{}fixel_density_maps{}.nii.gz".format(out_dir, prefix, suffix))
 
     # Save full fixel density masks, all fixels and bundles combined
     nib.save(nib.Nifti1Image(fixel_density_masks, affine),
-             "fixel_density_masks.nii.gz")
+             "{}{}fixel_density_masks{}.nii.gz".format(out_dir, prefix,
+                                                       suffix))
 
     # Save full voxel density maps and masks
     if args.norm == "voxel":  # If fixel, voxel maps mean nothing
         nib.save(nib.Nifti1Image(voxel_density_maps, affine),
-                 "voxel_density_maps.nii.gz")
+                 "{}{}voxel_density_maps{}.nii.gz".format(out_dir, prefix,
+                                                          suffix))
     nib.save(nib.Nifti1Image(voxel_density_masks.astype(np.uint8), affine),
-             "voxel_density_masks.nii.gz")
+             "{}{}voxel_density_masks{}.nii.gz".format(out_dir, prefix,
+                                                       suffix))
 
     # Save number of bundles per fixel and per voxel
     nib.save(nib.Nifti1Image(nb_bundles_per_fixel.astype(np.uint8), affine),
-             "nb_bundles_per_fixel.nii.gz")
+             "{}{}nb_bundles_per_fixel{}.nii.gz".format(out_dir, prefix,
+                                                        suffix))
     nib.save(nib.Nifti1Image(nb_bundles_per_voxel.astype(np.uint8), affine),
-             "nb_bundles_per_voxel.nii.gz")
+             "{}{}nb_bundles_per_voxel{}.nii.gz".format(out_dir, prefix,
+                                                        suffix))
 
 
 if __name__ == "__main__":

From 76d3f7d535c14ba3be32d0d63698971eb4b44b4e Mon Sep 17 00:00:00 2001
From: karp2601 <karp2601@dinf-0051-20b.DInf.fsci.usherbrooke.ca>
Date: Tue, 23 Jul 2024 11:04:34 -0400
Subject: [PATCH 15/20] Adding verbose and more doc

---
 scripts/scil_bundle_fixel_analysis.py | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/scripts/scil_bundle_fixel_analysis.py b/scripts/scil_bundle_fixel_analysis.py
index ce5c7521a..670d117ea 100644
--- a/scripts/scil_bundle_fixel_analysis.py
+++ b/scripts/scil_bundle_fixel_analysis.py
@@ -23,7 +23,9 @@
       the sum over a voxel will be higher than 1 (except in the single-fiber
       case). The density maps can be computed using the streamline count, or
       any streamline weighting like COMMIT or SIF, through the
-      data_per_streamline using the --dps_key argument.
+      data_per_streamline using the --dps_key argument. NOTE: This is a 5D file
+      that will not be easily inputed to a regular viewer. Use --split_bundles
+      or --split_fixels options to save the 4D versions for visualization.
 
     - fixel_density_masks.nii.gz : np.ndarray (x, y, z, 5, N)
       For each voxel, it gives whether or not each bundle is associated
@@ -33,6 +35,9 @@
       either on the number of streamlines or the streamline weights. Second,
       after the normalization, the relative threshold (rel_thr) is applied on
       the maps as a minimal value of density to be counted as an association.
+      NOTE: This is a 5D file that will not be easily inputed to a regular
+      viewer. Use --split_bundles or --split_fixels options to save the 4D
+      versions for visualization.
 
     - voxel_density_maps.nii.gz : np.ndarray (x, y, z, N)
       For each voxel, it gives the density of each bundle within the voxel,
@@ -192,6 +197,7 @@ def main():
         parser.error("Argument rel_thr must be a value between 0 and 1.")
 
     # Load the data
+    logging.info("Loading data.")
     peaks_img = nib.load(args.in_peaks)
     peaks = peaks_img.get_fdata()
     affine = peaks_img.affine
@@ -203,12 +209,16 @@ def main():
         nufo_sf = np.logical_and(is_first_peak, is_second_peak)
 
     # Extract bundles and names
+    logging.info("Extracting bundles.")
     bundles = []
     bundles_names = []
     for bundle in args.in_bundles[0]:
         bundles.append(bundle)
         bundles_names.append(Path(bundle).name.split(".")[0])
     if args.in_bundles_names:  # If names are given
+        if len(args.in_bundles_names) != len(bundles):
+            parser.error("""--in_bundles_names must contain the same number of
+                         element as in --in_bundles.""")
         bundles_names = args.in_bundles_names[0]
 
     # Set up saving filename options
@@ -219,16 +229,19 @@ def main():
         out_dir += "/"
 
     # Compute fixel density maps and masks
+    logging.info("Computing fixel density for all bundles.")
     fixel_density_maps = fixel_density(peaks, bundles, args.dps_key,
                                        args.max_theta,
                                        nbr_processes=args.nbr_processes)
 
+    logging.info("Computing density masks from density maps.")
     fixel_density_masks, fixel_density_maps = maps_to_masks(fixel_density_maps,
                                                             args.abs_thr,
                                                             args.rel_thr,
                                                             args.norm,
                                                             len(bundles))
 
+    logging.info("Computing additional derivatives.")
     # Compute number of bundles per fixel
     nb_bundles_per_fixel = np.sum(fixel_density_masks, axis=-1)
     # Compute voxel density maps
@@ -242,6 +255,7 @@ def main():
     nb_bundles_per_voxel = np.sum(voxel_density_masks, axis=-1)
 
     # Save all results
+    logging.info("Saving all results.")
     for i, bundle_n in enumerate(bundles_names):
         if args.split_bundles:  # Save the maps and masks for each bundle
             nib.save(nib.Nifti1Image(fixel_density_maps[..., i], affine),

From 9054323ba8f49e6343850f6a889a23db94dc75ba Mon Sep 17 00:00:00 2001
From: karp2601 <karp2601@dinf-0051-20b.DInf.fsci.usherbrooke.ca>
Date: Tue, 23 Jul 2024 11:30:34 -0400
Subject: [PATCH 16/20] Fixing prints and bundles names extraction

---
 scripts/scil_bundle_fixel_analysis.py | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/scripts/scil_bundle_fixel_analysis.py b/scripts/scil_bundle_fixel_analysis.py
index 670d117ea..7b923e2e2 100644
--- a/scripts/scil_bundle_fixel_analysis.py
+++ b/scripts/scil_bundle_fixel_analysis.py
@@ -165,13 +165,13 @@ def _build_arg_parser():
     
     g2.add_argument('--prefix', default="",
                     help='Prefix to add to all predetermined output '
-                         'filenames. We recommand finishing with an '
+                         'filenames. \nWe recommand finishing with an '
                          'underscore for better readability [%(default)s].')
     
     g2.add_argument('--suffix', default="",
                     help='Suffix to add to all predetermined output '
-                         'filenames. We recommand starting with an underscore '
-                         'for better readability [%(default)s].')
+                         'filenames. \nWe recommand starting with an '
+                         'underscore for better readability [%(default)s].')
 
     add_overwrite_arg(p)
     add_processes_arg(p)
@@ -209,17 +209,17 @@ def main():
         nufo_sf = np.logical_and(is_first_peak, is_second_peak)
 
     # Extract bundles and names
-    logging.info("Extracting bundles.")
-    bundles = []
-    bundles_names = []
-    for bundle in args.in_bundles[0]:
-        bundles.append(bundle)
-        bundles_names.append(Path(bundle).name.split(".")[0])
+    bundles = args.in_bundles[0]
     if args.in_bundles_names:  # If names are given
-        if len(args.in_bundles_names) != len(bundles):
-            parser.error("""--in_bundles_names must contain the same number of
-                         element as in --in_bundles.""")
+        if len(args.in_bundles_names[0]) != len(bundles):
+            parser.error("--in_bundles_names must contain the same number of "
+                         "elements as in --in_bundles.")
         bundles_names = args.in_bundles_names[0]
+    else:
+      logging.info("Extracting bundles names.")
+      bundles_names = []
+      for bundle in bundles:
+          bundles_names.append(Path(bundle).name.split(".")[0])
 
     # Set up saving filename options
     out_dir = args.out_dir

From 8b55a63f63b93ecb624a831e1573c98fa603d1ad Mon Sep 17 00:00:00 2001
From: karp2601 <karp2601@dinf-0051-20b.DInf.fsci.usherbrooke.ca>
Date: Tue, 23 Jul 2024 11:31:39 -0400
Subject: [PATCH 17/20] Fix pep8

---
 scripts/scil_bundle_fixel_analysis.py | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/scripts/scil_bundle_fixel_analysis.py b/scripts/scil_bundle_fixel_analysis.py
index 7b923e2e2..5c4a5a82a 100644
--- a/scripts/scil_bundle_fixel_analysis.py
+++ b/scripts/scil_bundle_fixel_analysis.py
@@ -113,7 +113,7 @@ def _build_arg_parser():
                    help='Key to access the data per streamline to use as '
                         'weight when computing the maps, \ninstead of the '
                         'number of streamlines. [%(default)s].')
-    
+
     p.add_argument('--max_theta', default=45,
                    help='Maximum angle between streamline and peak to be '
                         'associated [%(default)s].')
@@ -139,7 +139,7 @@ def _build_arg_parser():
                          'will normalize the maps per fixel, \nin each voxel. '
                          'If voxel, will normalize the maps per voxel '
                          '[%(default)s].')
-    
+
     g2 = p.add_argument_group(title='Output options')
 
     g2.add_argument('--split_bundles', action='store_true',
@@ -158,16 +158,16 @@ def _build_arg_parser():
 
     g2.add_argument('--bundles_mask', action='store_true',
                     help='If set, save the bundle mask for each bundle.')
-    
+
     g2.add_argument('--out_dir', default="./",
                     help='Path to the output directory where all the output '
                          'files will be saved [%(default)s].')
-    
+
     g2.add_argument('--prefix', default="",
                     help='Prefix to add to all predetermined output '
                          'filenames. \nWe recommand finishing with an '
                          'underscore for better readability [%(default)s].')
-    
+
     g2.add_argument('--suffix', default="",
                     help='Suffix to add to all predetermined output '
                          'filenames. \nWe recommand starting with an '
@@ -216,10 +216,10 @@ def main():
                          "elements as in --in_bundles.")
         bundles_names = args.in_bundles_names[0]
     else:
-      logging.info("Extracting bundles names.")
-      bundles_names = []
-      for bundle in bundles:
-          bundles_names.append(Path(bundle).name.split(".")[0])
+        logging.info("Extracting bundles names.")
+        bundles_names = []
+        for bundle in bundles:
+            bundles_names.append(Path(bundle).name.split(".")[0])
 
     # Set up saving filename options
     out_dir = args.out_dir

From b190339dc76bc3793d7392cd1c474a1a436b77e5 Mon Sep 17 00:00:00 2001
From: Philippe Karan <philippe.karan@usherbrooke.ca>
Date: Wed, 24 Jul 2024 09:45:02 -0400
Subject: [PATCH 18/20] Fixing out_dir stuff

---
 scripts/scil_bundle_fixel_analysis.py | 40 ++++++++++++++-------------
 1 file changed, 21 insertions(+), 19 deletions(-)

diff --git a/scripts/scil_bundle_fixel_analysis.py b/scripts/scil_bundle_fixel_analysis.py
index 5c4a5a82a..711e6a881 100644
--- a/scripts/scil_bundle_fixel_analysis.py
+++ b/scripts/scil_bundle_fixel_analysis.py
@@ -3,9 +3,14 @@
 """
 Analyze bundles at the fixel level using peaks and bundles (.trk). If the
 bundles files are names as {bundle_name}.trk, simply use the --in_bundles
-argument with --in_bundles_names. If it is not the case or you want other names
-to be saved, please use --in_bundles_names to provide bundles names IN THE SAME
-ORDER as the inputed bundles.
+argument without --in_bundles_names. If it is not the case or you want other
+names to be saved, please use --in_bundles_names to provide bundles names
+IN THE SAME ORDER as the inputed bundles.
+
+The duration of the script depends heavily on the number of bundles, the number
+of streamlines in bundles and the number of processors used. For a standard
+tractoflow/rbx_flow output with ~30 bundles, it should not take over 30
+minutes.
 
 The script produces various output:
 
@@ -87,7 +92,8 @@
 
 from scilpy.io.utils import (add_overwrite_arg, add_processes_arg,
                              assert_headers_compatible, assert_inputs_exist,
-                             assert_outputs_exist, add_verbose_arg)
+                             add_verbose_arg,
+                             assert_output_dirs_exist_and_empty)
 from scilpy.tractanalysis.fixel_density import (fixel_density, maps_to_masks)
 
 
@@ -159,9 +165,10 @@ def _build_arg_parser():
     g2.add_argument('--bundles_mask', action='store_true',
                     help='If set, save the bundle mask for each bundle.')
 
-    g2.add_argument('--out_dir', default="./",
+    g2.add_argument('--out_dir', default="fixel_analysis/",
                     help='Path to the output directory where all the output '
-                         'files will be saved [%(default)s].')
+                         'files will be saved. \nCurrent directory by '
+                         'default.')
 
     g2.add_argument('--prefix', default="",
                     help='Prefix to add to all predetermined output '
@@ -184,13 +191,15 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
+    # Set up saving filename options
+    out_dir = args.out_dir
+    prefix = args.prefix
+    suffix = args.suffix
+    if out_dir[-1] != "/":
+        out_dir += "/"
+
+    assert_output_dirs_exist_and_empty(parser, args, out_dir, create_dir=True)
     assert_inputs_exist(parser, [args.in_peaks] + args.in_bundles[0])
-    assert_outputs_exist(parser, args, ["bundles_LUT.txt",
-                                        "fixel_density_maps.nii.gz",
-                                        "fixel_density_masks.nii.gz",
-                                        "voxel_density_masks.nii.gz",
-                                        "nb_bundles_per_fixel.nii.gz",
-                                        "nb_bundles_per_voxel.nii.gz"])
     assert_headers_compatible(parser, [args.in_peaks] + args.in_bundles[0])
 
     if args.rel_thr < 0 or args.rel_thr > 1:
@@ -221,13 +230,6 @@ def main():
         for bundle in bundles:
             bundles_names.append(Path(bundle).name.split(".")[0])
 
-    # Set up saving filename options
-    out_dir = args.out_dir
-    prefix = args.prefix
-    suffix = args.suffix
-    if out_dir[-1] != "/":
-        out_dir += "/"
-
     # Compute fixel density maps and masks
     logging.info("Computing fixel density for all bundles.")
     fixel_density_maps = fixel_density(peaks, bundles, args.dps_key,

From 5727d2668e3bd6057281f1df4d7a65a79403cff9 Mon Sep 17 00:00:00 2001
From: karp2601 <karp2601@dinf-0051-20b.DInf.fsci.usherbrooke.ca>
Date: Thu, 25 Jul 2024 11:52:21 -0400
Subject: [PATCH 19/20] Removing append from parser

---
 scripts/scil_bundle_fixel_analysis.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/scripts/scil_bundle_fixel_analysis.py b/scripts/scil_bundle_fixel_analysis.py
index 5c4a5a82a..2babead08 100644
--- a/scripts/scil_bundle_fixel_analysis.py
+++ b/scripts/scil_bundle_fixel_analysis.py
@@ -100,10 +100,10 @@ def _build_arg_parser():
                         'or SH data, use the script scil_fodf_metrics.py '
                         '\nwith the abs_peaks_and_values option.')
 
-    p.add_argument('--in_bundles', nargs='+', action='append', required=True,
+    p.add_argument('--in_bundles', nargs='+', required=True,
                    help='List of paths of the bundles (.trk) to analyze.')
 
-    p.add_argument('--in_bundles_names', nargs='+', action='append',
+    p.add_argument('--in_bundles_names', nargs='+',
                    help='List of the names of the bundles, in the same order '
                         'as they were given. \nIf this argument is not used, '
                         'the script assumes that the name of the bundle \nis '
@@ -184,14 +184,14 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, [args.in_peaks] + args.in_bundles[0])
+    assert_inputs_exist(parser, [args.in_peaks] + args.in_bundles)
     assert_outputs_exist(parser, args, ["bundles_LUT.txt",
                                         "fixel_density_maps.nii.gz",
                                         "fixel_density_masks.nii.gz",
                                         "voxel_density_masks.nii.gz",
                                         "nb_bundles_per_fixel.nii.gz",
                                         "nb_bundles_per_voxel.nii.gz"])
-    assert_headers_compatible(parser, [args.in_peaks] + args.in_bundles[0])
+    assert_headers_compatible(parser, [args.in_peaks] + args.in_bundles)
 
     if args.rel_thr < 0 or args.rel_thr > 1:
         parser.error("Argument rel_thr must be a value between 0 and 1.")
@@ -209,12 +209,12 @@ def main():
         nufo_sf = np.logical_and(is_first_peak, is_second_peak)
 
     # Extract bundles and names
-    bundles = args.in_bundles[0]
+    bundles = args.in_bundles
     if args.in_bundles_names:  # If names are given
-        if len(args.in_bundles_names[0]) != len(bundles):
+        if len(args.in_bundles_names) != len(bundles):
             parser.error("--in_bundles_names must contain the same number of "
                          "elements as in --in_bundles.")
-        bundles_names = args.in_bundles_names[0]
+        bundles_names = args.in_bundles_names
     else:
         logging.info("Extracting bundles names.")
         bundles_names = []

From 81129743a9e7c553cdf8524f744e1490b7e25564 Mon Sep 17 00:00:00 2001
From: karp2601 <karp2601@dinf-0051-20b.DInf.fsci.usherbrooke.ca>
Date: Thu, 25 Jul 2024 13:08:26 -0400
Subject: [PATCH 20/20] Fixing merge bug

---
 scripts/scil_bundle_fixel_analysis.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/scil_bundle_fixel_analysis.py b/scripts/scil_bundle_fixel_analysis.py
index 5eb51df35..68e69ec41 100644
--- a/scripts/scil_bundle_fixel_analysis.py
+++ b/scripts/scil_bundle_fixel_analysis.py
@@ -199,8 +199,8 @@ def main():
         out_dir += "/"
 
     assert_output_dirs_exist_and_empty(parser, args, out_dir, create_dir=True)
-    assert_inputs_exist(parser, [args.in_peaks] + args.in_bundles[0])
-    assert_headers_compatible(parser, [args.in_peaks] + args.in_bundles[0])
+    assert_inputs_exist(parser, [args.in_peaks] + args.in_bundles)
+    assert_headers_compatible(parser, [args.in_peaks] + args.in_bundles)
 
     if args.rel_thr < 0 or args.rel_thr > 1:
         parser.error("Argument rel_thr must be a value between 0 and 1.")