From b8295c70a4916f851ab0b6f83dae76a3fb23da4c Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Tue, 20 Jan 2026 10:07:27 -0500
Subject: [PATCH 1/6] Test_streamlines_in_mask ok

---
 src/scilpy/segment/streamlines.py             |  9 +++-
 src/scilpy/segment/tests/test_bundleseg.py    |  7 +++
 src/scilpy/segment/tests/test_streamlines.py  | 45 +++++++++++++++++++
 .../segment/tests/test_tractogram_from_roi.py |  1 +
 .../tests/test_intersection_finder.py         |  8 ++++
 5 files changed, 69 insertions(+), 1 deletion(-)
 create mode 100644 src/scilpy/segment/tests/test_bundleseg.py
 create mode 100644 src/scilpy/segment/tests/test_streamlines.py
 create mode 100644 src/scilpy/tractograms/tests/test_intersection_finder.py

diff --git a/src/scilpy/segment/streamlines.py b/src/scilpy/segment/streamlines.py
index 5dd461e65..9aec7d8e4 100644
--- a/src/scilpy/segment/streamlines.py
+++ b/src/scilpy/segment/streamlines.py
@@ -17,16 +17,22 @@
 
 def streamlines_in_mask(sft, target_mask, all_in=False):
     """
+    Finds the streamlines that are either touching a mask (if all_in=False) or
+    entirely contained in the mask (if all_in=True).
+
     Parameters
     ----------
     sft : StatefulTractogram
         StatefulTractogram containing the streamlines to segment.
     target_mask : numpy.ndarray
         Binary mask in which the streamlines should pass.
+    all_in: bool
+        If true, finds
+
     Returns
     -------
     ids : list
-        Ids of the streamlines passing through the mask.
+        Ids of the streamlines passing the test.
     """
     sft.to_vox()
     sft.to_corner()
@@ -64,6 +70,7 @@ def filter_grid_roi_both(sft, mask_1, mask_2):
         Binary mask in which the streamlines should start or end.
     mask_2: numpy.ndarray
         Binary mask in which the streamlines should start or end.
+
     Returns
     -------
     new_sft: StatefulTractogram
diff --git a/src/scilpy/segment/tests/test_bundleseg.py b/src/scilpy/segment/tests/test_bundleseg.py
new file mode 100644
index 000000000..f3dbc0a79
--- /dev/null
+++ b/src/scilpy/segment/tests/test_bundleseg.py
@@ -0,0 +1,7 @@
+# -*- coding: utf-8 -*-
+
+def test_recognize():
+    # todo:
+    # bundleseg = BundleSeg(...)
+    # bundleseg.recognize.
+    pass
diff --git a/src/scilpy/segment/tests/test_streamlines.py b/src/scilpy/segment/tests/test_streamlines.py
new file mode 100644
index 000000000..704bd8ed2
--- /dev/null
+++ b/src/scilpy/segment/tests/test_streamlines.py
@@ -0,0 +1,45 @@
+# -*- coding: utf-8 -*-
+from dipy.io.stateful_tractogram import StatefulTractogram, Space, Origin
+import nibabel as nib
+import numpy as np
+from scilpy.segment.streamlines import streamlines_in_mask
+
+
+def test_streamlines_in_mask():
+    # Binary mask: ROI on x=1 and x=2
+    mask = np.zeros((10, 10, 10))
+    mask[1:3, :, :] = 1
+    fake_reference = nib.Nifti1Image(
+        np.zeros((10, 10, 10, 1)), affine=np.eye(4))
+
+    # line 1 entirely in mask. y and z values are random.
+    line1 = [[1.3, 5, 6],
+             [1.5, 5, 7],
+             [2.5, 7, 4],
+             [2.9, 9, 9]]
+
+    # line 2: partially in mask.
+    line2 = [[1.3, 5, 6],
+             [5.5, 5, 7],
+             [2.5, 7, 4],
+             [2.9, 9, 9]]
+
+    # line3: never in mask
+    line3 = [[4.3, 5, 6],
+             [5.5, 5, 7],
+             [7.5, 7, 4],
+             [9.9, 9, 9]]
+
+    sft = StatefulTractogram([line1, line2, line3], fake_reference,
+                             space=Space.VOXMM, origin=Origin('corner'))
+
+    # Test option 'all'
+    ids = streamlines_in_mask(sft, mask, all_in=True)
+    assert len(ids) == 1
+    assert ids[0] == 0
+
+    # Test option 'any'
+    ids = streamlines_in_mask(sft, mask, all_in=False)
+    assert len(ids) == 2
+    assert ids[0] == 0
+    assert ids[1] == 1
diff --git a/src/scilpy/segment/tests/test_tractogram_from_roi.py b/src/scilpy/segment/tests/test_tractogram_from_roi.py
index 2d451bedd..d05c5f14f 100644
--- a/src/scilpy/segment/tests/test_tractogram_from_roi.py
+++ b/src/scilpy/segment/tests/test_tractogram_from_roi.py
@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import os
 import tempfile
 import nibabel as nib
diff --git a/src/scilpy/tractograms/tests/test_intersection_finder.py b/src/scilpy/tractograms/tests/test_intersection_finder.py
new file mode 100644
index 000000000..c39e5aad1
--- /dev/null
+++ b/src/scilpy/tractograms/tests/test_intersection_finder.py
@@ -0,0 +1,8 @@
+# -*- coding: utf-8 -*-
+
+
+def test_find_intersection():
+    # Todo:
+    # finder = IntersectionFinder(...)
+    # finder.find_intersection()
+    pass

From 291aaa14c9a29ddfecb6acb82ef3ca8337786b87 Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Tue, 20 Jan 2026 10:12:27 -0500
Subject: [PATCH 2/6] Test filter_grid_roi... ok

---
 src/scilpy/segment/streamlines.py            |  2 +-
 src/scilpy/segment/tests/test_streamlines.py | 45 +++++++++++++++++++-
 src/scilpy/segment/tractogram_from_roi.py    |  6 +--
 3 files changed, 48 insertions(+), 5 deletions(-)

diff --git a/src/scilpy/segment/streamlines.py b/src/scilpy/segment/streamlines.py
index 9aec7d8e4..40c7c440a 100644
--- a/src/scilpy/segment/streamlines.py
+++ b/src/scilpy/segment/streamlines.py
@@ -58,7 +58,7 @@ def streamlines_in_mask(sft, target_mask, all_in=False):
         return np.where(streamlines_case == [0, 1][True])[0].tolist()
 
 
-def filter_grid_roi_both(sft, mask_1, mask_2):
+def filter_grid_roi_both_ends(sft, mask_1, mask_2):
     """ Filters streamlines with one end in a mask and the other in
     another mask.
 
diff --git a/src/scilpy/segment/tests/test_streamlines.py b/src/scilpy/segment/tests/test_streamlines.py
index 704bd8ed2..30c79bd49 100644
--- a/src/scilpy/segment/tests/test_streamlines.py
+++ b/src/scilpy/segment/tests/test_streamlines.py
@@ -2,7 +2,8 @@
 from dipy.io.stateful_tractogram import StatefulTractogram, Space, Origin
 import nibabel as nib
 import numpy as np
-from scilpy.segment.streamlines import streamlines_in_mask
+from scilpy.segment.streamlines import streamlines_in_mask, \
+    filter_grid_roi_both_ends
 
 
 def test_streamlines_in_mask():
@@ -43,3 +44,45 @@ def test_streamlines_in_mask():
     assert len(ids) == 2
     assert ids[0] == 0
     assert ids[1] == 1
+
+
+def test_filter_grid_roi_both_ends():
+    # Binary mask: ROI on x=1 and x=2
+    mask = np.zeros((10, 10, 10))
+    mask[1:3, :, :] = 1
+    fake_reference = nib.Nifti1Image(
+        np.zeros((10, 10, 10, 1)), affine=np.eye(4))
+
+    # line 1 entirely in mask. y and z values are random.
+    line1 = [[1.3, 5, 6],
+             [1.5, 5, 7],
+             [2.5, 7, 4],
+             [2.9, 9, 9]]
+
+    # line 2: both ends in mask but not in the middle
+    line2 = [[1.3, 5, 6],
+             [5.5, 5, 7],
+             [2.5, 7, 4],
+             [2.9, 9, 9]]
+
+    # line 3: Only one end in mask
+    line3 = [[1.3, 5, 6],
+             [5.5, 5, 7],
+             [6.5, 7, 4],
+             [7.9, 9, 9]]
+
+    # line 4: Both ends out of mask
+    line4 = [[1.3, 5, 6],
+             [5.5, 5, 7],
+             [6.5, 7, 4],
+             [7.9, 9, 9]]
+
+    sft = StatefulTractogram([line1, line2, line3, line4], fake_reference,
+                             space=Space.VOXMM, origin=Origin('corner'))
+
+    new_sft, ids = filter_grid_roi_both_ends(sft, mask_1=mask, mask_2=mask)
+    assert len(ids) == 2
+    assert len(new_sft) == 2
+    assert ids[0] == 0
+    assert ids[1] == 1
+    
\ No newline at end of file
diff --git a/src/scilpy/segment/tractogram_from_roi.py b/src/scilpy/segment/tractogram_from_roi.py
index 1ef2f560b..a166803e1 100644
--- a/src/scilpy/segment/tractogram_from_roi.py
+++ b/src/scilpy/segment/tractogram_from_roi.py
@@ -15,7 +15,7 @@
     split_mask_blobs_kmeans
 from scilpy.io.image import get_data_as_mask
 from scilpy.io.streamlines import load_tractogram_with_reference
-from scilpy.segment.streamlines import filter_grid_roi, filter_grid_roi_both
+from scilpy.segment.streamlines import filter_grid_roi, filter_grid_roi_both_ends
 from scilpy.tractograms.streamline_operations import \
     remove_loops_and_sharp_turns
 from scilpy.tractanalysis.streamlines_metrics import compute_tract_counts_map
@@ -363,7 +363,7 @@ def _extract_vb_one_bundle(
             mask_1 = binary_dilation(mask_1, iterations=dilate_endpoints)
             mask_2 = binary_dilation(mask_2, iterations=dilate_endpoints)
 
-        _, vs_ids = filter_grid_roi_both(sft, mask_1, mask_2)
+        _, vs_ids = filter_grid_roi_both_ends(sft, mask_1, mask_2)
     else:
         vs_ids = np.array([])
 
@@ -514,7 +514,7 @@ def _extract_ib_one_bundle(sft, mask_1_filename, mask_2_filename,
             mask_1 = binary_dilation(mask_1, iterations=dilate_endpoints)
             mask_2 = binary_dilation(mask_2, iterations=dilate_endpoints)
 
-        _, fc_ids = filter_grid_roi_both(sft, mask_1, mask_2)
+        _, fc_ids = filter_grid_roi_both_ends(sft, mask_1, mask_2)
     else:
         fc_ids = []
 

From dc77a7331570e3cb84ec74828c9dca4a5c2d7f79 Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Tue, 20 Jan 2026 12:57:02 -0500
Subject: [PATCH 3/6] Test_filter_grid_roi ok

---
 src/scilpy/segment/streamlines.py            |  37 +++--
 src/scilpy/segment/tests/test_streamlines.py | 158 +++++++++++--------
 2 files changed, 111 insertions(+), 84 deletions(-)

diff --git a/src/scilpy/segment/streamlines.py b/src/scilpy/segment/streamlines.py
index 40c7c440a..919a87bbc 100644
--- a/src/scilpy/segment/streamlines.py
+++ b/src/scilpy/segment/streamlines.py
@@ -59,8 +59,10 @@ def streamlines_in_mask(sft, target_mask, all_in=False):
 
 
 def filter_grid_roi_both_ends(sft, mask_1, mask_2):
-    """ Filters streamlines with one end in a mask and the other in
-    another mask.
+    """
+    Filters streamlines with one end in a mask and the other in another mask.
+    See also filter_grid_roi, but here we may give two different masks for the
+    endpoints.
 
     Parameters
     ----------
@@ -115,6 +117,9 @@ def filter_grid_roi_both_ends(sft, mask_1, mask_2):
 def filter_grid_roi(sft, mask, filter_type, is_exclude, filter_distance=0,
                     return_sft=False, return_rejected_sft=False):
     """
+    Filters streamlines based on a given criteria (any, all, either_end,
+    both_ends).
+
     Parameters
     ----------
     sft : StatefulTractogram
@@ -206,8 +211,8 @@ def filter_grid_roi(sft, mask, filter_type, is_exclude, filter_distance=0,
     return line_based_indices
 
 
-def pre_filtering_for_geometrical_shape(sft, size, center, filter_type,
-                                        is_in_vox):
+def _pre_filtering_for_geometrical_shape(sft, size, center, filter_type,
+                                         is_in_vox):
     """
     Parameters
     ----------
@@ -261,6 +266,9 @@ def pre_filtering_for_geometrical_shape(sft, size, center, filter_type,
 def filter_ellipsoid(sft, ellipsoid_radius, ellipsoid_center,
                      filter_type, is_exclude, is_in_vox=False):
     """
+    Finds streamlines that respect some criteria in a ROI, where the ROI is
+    a bounding box of ellipsoid type.
+
     Parameters
     ----------
     sft : StatefulTractogram
@@ -287,9 +295,9 @@ def filter_ellipsoid(sft, ellipsoid_radius, ellipsoid_center,
         return np.array([]), sft
 
     pre_filtered_indices, pre_filtered_sft = \
-        pre_filtering_for_geometrical_shape(sft, ellipsoid_radius,
-                                            ellipsoid_center, filter_type,
-                                            is_in_vox)
+        _pre_filtering_for_geometrical_shape(sft, ellipsoid_radius,
+                                             ellipsoid_center, filter_type,
+                                             is_in_vox)
     pre_filtered_sft.to_rasmm()
     pre_filtered_sft.to_center()
     pre_filtered_streamlines = pre_filtered_sft.streamlines
@@ -367,9 +375,11 @@ def filter_ellipsoid(sft, ellipsoid_radius, ellipsoid_center,
     return line_based_indices, new_sft
 
 
-def filter_cuboid(sft, cuboid_radius, cuboid_center,
-                  filter_type, is_exclude):
+def filter_cuboid(sft, cuboid_radius, cuboid_center, filter_type, is_exclude):
     """
+    Finds streamlines that respect some criteria in a ROI, where the ROI is
+    a bounding box of cuboid type.
+
     Parameters
     ----------
     sft : StatefulTractogram
@@ -382,8 +392,7 @@ def filter_cuboid(sft, cuboid_radius, cuboid_center,
         One of the 4 following choices: 'any', 'all', 'either_end', 'both_ends'.
     is_exclude: bool
         Value to indicate if the ROI is an AND (false) or a NOT (true).
-    is_in_vox: bool
-        Value to indicate if the ROI is in voxel space.
+
     Returns
     -------
     ids : list
@@ -395,9 +404,9 @@ def filter_cuboid(sft, cuboid_radius, cuboid_center,
         return np.array([]), sft
 
     pre_filtered_indices, pre_filtered_sft = \
-        pre_filtering_for_geometrical_shape(sft, cuboid_radius,
-                                            cuboid_center, filter_type,
-                                            is_in_vox=False)
+        _pre_filtering_for_geometrical_shape(sft, cuboid_radius,
+                                             cuboid_center, filter_type,
+                                             is_in_vox=False)
     pre_filtered_sft.to_rasmm()
     pre_filtered_sft.to_center()
     pre_filtered_streamlines = pre_filtered_sft.streamlines
diff --git a/src/scilpy/segment/tests/test_streamlines.py b/src/scilpy/segment/tests/test_streamlines.py
index 30c79bd49..9424c5bc7 100644
--- a/src/scilpy/segment/tests/test_streamlines.py
+++ b/src/scilpy/segment/tests/test_streamlines.py
@@ -3,86 +3,104 @@
 import nibabel as nib
 import numpy as np
 from scilpy.segment.streamlines import streamlines_in_mask, \
-    filter_grid_roi_both_ends
+    filter_grid_roi_both_ends, filter_grid_roi
+
+# Preparing SFT for all tests here.
+# Binary mask: ROI on x=1 and x=2
+mask = np.zeros((10, 10, 10))
+mask[1:3, :, :] = 1
+
+# line 0 entirely in mask. y and z values are random.
+line0 = [[1.3, 5, 6],
+         [1.5, 5, 7],
+         [2.5, 7, 4],
+         [2.9, 9, 9]]
+
+# line 1: partially in mask (both ends in mask but not in the middle)
+line1 = [[1.3, 5, 6],
+         [5.5, 5, 7],
+         [2.5, 7, 4],
+         [2.9, 9, 9]]
+
+# line 2: Only one end in mask
+line2 = [[1.3, 5, 6],
+         [5.5, 5, 7],
+         [6.5, 7, 4],
+         [7.9, 9, 9]]
+
+# line 3: Both ends out of mask but touches in the middle
+line3 = [[5.3, 5, 6],
+         [1.5, 5, 7],
+         [2.5, 7, 4],
+         [7.9, 9, 9]]
+
+# line 4: never in mask
+line4 = [[4.3, 5, 6],
+         [5.5, 5, 7],
+         [7.5, 7, 4],
+         [9.9, 9, 9]]
+
+# line 5: passes through, but no real point inside.
+line5 = [[0.3, 5, 6],
+         [5.5, 5, 7],
+         [7.5, 7, 4],
+         [9.9, 9, 9]]
+
+fake_reference = nib.Nifti1Image(
+    np.zeros((10, 10, 10, 1)), affine=np.eye(4))
+sft = StatefulTractogram([line0, line1, line2, line3, line4, line5],
+                         fake_reference, space=Space.VOXMM,
+                         origin=Origin('corner'))
 
 
 def test_streamlines_in_mask():
-    # Binary mask: ROI on x=1 and x=2
-    mask = np.zeros((10, 10, 10))
-    mask[1:3, :, :] = 1
-    fake_reference = nib.Nifti1Image(
-        np.zeros((10, 10, 10, 1)), affine=np.eye(4))
-
-    # line 1 entirely in mask. y and z values are random.
-    line1 = [[1.3, 5, 6],
-             [1.5, 5, 7],
-             [2.5, 7, 4],
-             [2.9, 9, 9]]
-
-    # line 2: partially in mask.
-    line2 = [[1.3, 5, 6],
-             [5.5, 5, 7],
-             [2.5, 7, 4],
-             [2.9, 9, 9]]
-
-    # line3: never in mask
-    line3 = [[4.3, 5, 6],
-             [5.5, 5, 7],
-             [7.5, 7, 4],
-             [9.9, 9, 9]]
-
-    sft = StatefulTractogram([line1, line2, line3], fake_reference,
-                             space=Space.VOXMM, origin=Origin('corner'))
-
     # Test option 'all'
     ids = streamlines_in_mask(sft, mask, all_in=True)
-    assert len(ids) == 1
-    assert ids[0] == 0
+    assert np.array_equal(ids, [0])
 
     # Test option 'any'
     ids = streamlines_in_mask(sft, mask, all_in=False)
-    assert len(ids) == 2
-    assert ids[0] == 0
-    assert ids[1] == 1
+    assert np.array_equal(ids, [0, 1, 2, 3, 5])
 
 
 def test_filter_grid_roi_both_ends():
-    # Binary mask: ROI on x=1 and x=2
-    mask = np.zeros((10, 10, 10))
-    mask[1:3, :, :] = 1
-    fake_reference = nib.Nifti1Image(
-        np.zeros((10, 10, 10, 1)), affine=np.eye(4))
-
-    # line 1 entirely in mask. y and z values are random.
-    line1 = [[1.3, 5, 6],
-             [1.5, 5, 7],
-             [2.5, 7, 4],
-             [2.9, 9, 9]]
-
-    # line 2: both ends in mask but not in the middle
-    line2 = [[1.3, 5, 6],
-             [5.5, 5, 7],
-             [2.5, 7, 4],
-             [2.9, 9, 9]]
-
-    # line 3: Only one end in mask
-    line3 = [[1.3, 5, 6],
-             [5.5, 5, 7],
-             [6.5, 7, 4],
-             [7.9, 9, 9]]
-
-    # line 4: Both ends out of mask
-    line4 = [[1.3, 5, 6],
-             [5.5, 5, 7],
-             [6.5, 7, 4],
-             [7.9, 9, 9]]
-
-    sft = StatefulTractogram([line1, line2, line3, line4], fake_reference,
-                             space=Space.VOXMM, origin=Origin('corner'))
-
+    # Pretending to have two masks
+    # Test option 'both ends'
     new_sft, ids = filter_grid_roi_both_ends(sft, mask_1=mask, mask_2=mask)
-    assert len(ids) == 2
+    assert np.array_equal(ids, [0, 1])
     assert len(new_sft) == 2
-    assert ids[0] == 0
-    assert ids[1] == 1
-    
\ No newline at end of file
+
+
+def test_filter_grid_roi():
+    # Note. Distance not tested yet. (toDo)
+    # Testing the returned SFT only the first time.
+    # Parameter is "is_exclude", so:
+    include=False
+    exclude=True
+
+    # Test 'any'
+    ids, new_sft, rejected_sft = filter_grid_roi(
+        sft, mask, 'any', include,
+        return_sft=True, return_rejected_sft=True)
+    assert np.array_equal(ids, [0, 1, 2, 3, 5])
+    assert len(new_sft) == 5
+    ids = filter_grid_roi(sft, mask, 'any', exclude)
+    assert np.array_equal(ids, [4])
+
+    # Test 'all'
+    ids = filter_grid_roi(sft, mask, 'all', include)
+    assert np.array_equal(ids, [0])
+    ids = filter_grid_roi(sft, mask, 'all', exclude)
+    assert np.array_equal(ids, [1, 2, 3, 4, 5])
+
+    # Test 'either_end'
+    ids = filter_grid_roi(sft, mask, 'either_end', include)
+    assert np.array_equal(ids, [0, 1, 2])
+    ids = filter_grid_roi(sft, mask, 'either_end', exclude)
+    assert np.array_equal(ids, [3, 4, 5])
+
+    # Test 'both_ends'
+    ids = filter_grid_roi(sft, mask, 'both_ends', include)
+    assert np.array_equal(ids, [0, 1])
+    ids = filter_grid_roi(sft, mask, 'both_ends', exclude)
+    assert np.array_equal(ids, [2, 3, 4, 5])
\ No newline at end of file

From 0e46b34f0d97e9930932d8cf1fb971ec14e2d3f8 Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Tue, 20 Jan 2026 15:07:53 -0500
Subject: [PATCH 4/6] filter_ellipsoid and filter_cuboid ok

---
 src/scilpy/segment/streamlines.py            |  10 +-
 src/scilpy/segment/tests/test_streamlines.py | 129 ++++++++++++-------
 2 files changed, 83 insertions(+), 56 deletions(-)

diff --git a/src/scilpy/segment/streamlines.py b/src/scilpy/segment/streamlines.py
index 919a87bbc..dc14a84bc 100644
--- a/src/scilpy/segment/streamlines.py
+++ b/src/scilpy/segment/streamlines.py
@@ -259,8 +259,7 @@ def _pre_filtering_for_geometrical_shape(sft, size, center, filter_type,
 
     pre_mask[min_x:max_x, min_y:max_y, min_z:max_z] = 1
 
-    return filter_grid_roi(sft, pre_mask, filter_type, is_exclude=False,
-                           return_sft=True)
+    return filter_grid_roi(sft, pre_mask, filter_type, is_exclude=False)
 
 
 def filter_ellipsoid(sft, ellipsoid_radius, ellipsoid_center,
@@ -276,7 +275,7 @@ def filter_ellipsoid(sft, ellipsoid_radius, ellipsoid_center,
     ellipsoid_radius : numpy.ndarray (3)
         Size in mm, x/y/z of the ellipsoid.
     ellipsoid_center: numpy.ndarray (3)
-        Center x/y/z of the ellipsoid.
+        Center x/y/z of the ellipsoid, in RASMM space, center origin.
     filter_type: str
         One of the 4 following choices, 'any', 'all', 'either_end', 'both_ends'.
     is_exclude: bool
@@ -300,7 +299,6 @@ def filter_ellipsoid(sft, ellipsoid_radius, ellipsoid_center,
                                              is_in_vox)
     pre_filtered_sft.to_rasmm()
     pre_filtered_sft.to_center()
-    pre_filtered_streamlines = pre_filtered_sft.streamlines
     transfo, _, res, _ = sft.space_attributes
 
     if is_in_vox:
@@ -318,7 +316,7 @@ def filter_ellipsoid(sft, ellipsoid_radius, ellipsoid_center,
     ellipsoid_radius = np.asarray(ellipsoid_radius, dtype=float)
     ellipsoid_center = np.asarray(ellipsoid_center, dtype=float)
 
-    for i, line in enumerate(pre_filtered_streamlines):
+    for i, line in enumerate(pre_filtered_sft.streamlines):
         if filter_type in ['any', 'all']:
             # Resample to 1/10 of the voxel size
             nb_points = max(int(length(line) / np.average(res) * 10), 2)
@@ -387,7 +385,7 @@ def filter_cuboid(sft, cuboid_radius, cuboid_center, filter_type, is_exclude):
     cuboid_radius : numpy.ndarray (3)
         Size in mm, x/y/z of the cuboid.
     cuboid_center: numpy.ndarray (3)
-        Center x/y/z of the cuboid.
+        Center x/y/z of the cuboid, in RASMM space, center origin.
     filter_type: str
         One of the 4 following choices: 'any', 'all', 'either_end', 'both_ends'.
     is_exclude: bool
diff --git a/src/scilpy/segment/tests/test_streamlines.py b/src/scilpy/segment/tests/test_streamlines.py
index 9424c5bc7..93bcd93df 100644
--- a/src/scilpy/segment/tests/test_streamlines.py
+++ b/src/scilpy/segment/tests/test_streamlines.py
@@ -3,48 +3,59 @@
 import nibabel as nib
 import numpy as np
 from scilpy.segment.streamlines import streamlines_in_mask, \
-    filter_grid_roi_both_ends, filter_grid_roi
+    filter_grid_roi_both_ends, filter_grid_roi, filter_ellipsoid, filter_cuboid
 
 # Preparing SFT for all tests here.
-# Binary mask: ROI on x=1 and x=2
+# 3 ways to crete ROI, all ~voxels 1 and 2 in x, y, z
+# - mask
+# - bdo_ellipsoid
+# - bdo_cuboid
+
+# Binary mask
 mask = np.zeros((10, 10, 10))
-mask[1:3, :, :] = 1
-
-# line 0 entirely in mask. y and z values are random.
-line0 = [[1.3, 5, 6],
-         [1.5, 5, 7],
-         [2.5, 7, 4],
-         [2.9, 9, 9]]
-
-# line 1: partially in mask (both ends in mask but not in the middle)
-line1 = [[1.3, 5, 6],
-         [5.5, 5, 7],
-         [2.5, 7, 4],
-         [2.9, 9, 9]]
-
-# line 2: Only one end in mask
-line2 = [[1.3, 5, 6],
-         [5.5, 5, 7],
-         [6.5, 7, 4],
-         [7.9, 9, 9]]
-
-# line 3: Both ends out of mask but touches in the middle
-line3 = [[5.3, 5, 6],
-         [1.5, 5, 7],
-         [2.5, 7, 4],
-         [7.9, 9, 9]]
-
-# line 4: never in mask
-line4 = [[4.3, 5, 6],
-         [5.5, 5, 7],
-         [7.5, 7, 4],
-         [9.9, 9, 9]]
-
-# line 5: passes through, but no real point inside.
-line5 = [[0.3, 5, 6],
-         [5.5, 5, 7],
-         [7.5, 7, 4],
-         [9.9, 9, 9]]
+mask[1:3, 1:3, 1:3] = 1
+
+# bdo.
+# Note. Everything else here is in vox, corner, except bdo_center
+bdo_center_rasmm_centerorigin = np.asarray([1.5, 1.5, 1.5])
+bdo_radius_mm = 1.5
+
+# Preparing streamlines fitting criteria.
+# line 0 'all': entirely in mask.
+line0 = [[1.5, 1.5, 1.5],
+         [1.6, 1.6, 1.6],
+         [1.7, 1.7, 1.7],
+         [2.5, 2.5, 2.5]]
+
+# line 1 'both_ends': both ends in mask but not in the middle.
+line1 = [[1.5, 1.5, 1.5],
+         [9, 9, 9],
+         [1.7, 1.7, 1.7],
+         [2.5, 2.5, 2.5]]
+
+# line 2 'any': Only one end in mask
+line2 = [[1.5, 1.5, 1.5],
+         [1.6, 1.6, 1.6],
+         [1.7, 1.7, 1.7],
+         [9, 9, 9]]
+
+# line 3 'any': Both ends out of mask but touches in the middle
+line3 = [[9, 9, 9],
+         [1.6, 1.6, 1.6],
+         [1.7, 1.7, 1.7],
+         [9, 9, 9]]
+
+# line 4 (exclude): never in mask
+line4 = [[9, 9, 9.0],
+         [8, 8, 8.0],
+         [7, 7, 7.0],
+         [9, 9, 9.0]]
+
+# line 5 'any': passes through, but no real point inside.
+line5 = [[0.1, 0.1, 0.1],
+         [8, 8, 8.0],
+         [7, 7, 7.0],
+         [9, 9, 9.0]]
 
 fake_reference = nib.Nifti1Image(
     np.zeros((10, 10, 10, 1)), affine=np.eye(4))
@@ -73,34 +84,52 @@ def test_filter_grid_roi_both_ends():
 
 def test_filter_grid_roi():
     # Note. Distance not tested yet. (toDo)
-    # Testing the returned SFT only the first time.
+    roi_options = (mask,)
+    _test_all_criteria(filter_grid_roi, roi_options)
+
+
+def test_filter_ellipsoid():
+    roi_options = (bdo_radius_mm, bdo_center_rasmm_centerorigin)
+    _test_all_criteria(filter_ellipsoid, roi_options)
+
+
+def test_filter_cuboid():
+    roi_options = (bdo_radius_mm, bdo_center_rasmm_centerorigin)
+    _test_all_criteria(filter_cuboid, roi_options)
+
+
+def _test_all_criteria(fct, roi_options):
+    """
+    The three filtering methods (filter_grid_roi, filter_ellipsoid,
+    filter_cuboid) test the same criteria, but with a different way to treat
+    the ROI.
+    """
     # Parameter is "is_exclude", so:
     include=False
     exclude=True
 
     # Test 'any'
-    ids, new_sft, rejected_sft = filter_grid_roi(
-        sft, mask, 'any', include,
-        return_sft=True, return_rejected_sft=True)
+    # Testing the returned sft only this once
+    ids, new_sft = fct(sft, *roi_options, 'any', include)
     assert np.array_equal(ids, [0, 1, 2, 3, 5])
     assert len(new_sft) == 5
-    ids = filter_grid_roi(sft, mask, 'any', exclude)
+    ids, _ =  fct(sft, *roi_options, 'any', exclude)
     assert np.array_equal(ids, [4])
 
     # Test 'all'
-    ids = filter_grid_roi(sft, mask, 'all', include)
+    ids, _ =  fct(sft, *roi_options, 'all', include)
     assert np.array_equal(ids, [0])
-    ids = filter_grid_roi(sft, mask, 'all', exclude)
+    ids, _ =  fct(sft, *roi_options, 'all', exclude)
     assert np.array_equal(ids, [1, 2, 3, 4, 5])
 
     # Test 'either_end'
-    ids = filter_grid_roi(sft, mask, 'either_end', include)
+    ids, _ =  fct(sft, *roi_options, 'either_end', include)
     assert np.array_equal(ids, [0, 1, 2])
-    ids = filter_grid_roi(sft, mask, 'either_end', exclude)
+    ids, _ =  fct(sft, *roi_options, 'either_end', exclude)
     assert np.array_equal(ids, [3, 4, 5])
 
     # Test 'both_ends'
-    ids = filter_grid_roi(sft, mask, 'both_ends', include)
+    ids, _ =  fct(sft, *roi_options, 'both_ends', include)
     assert np.array_equal(ids, [0, 1])
-    ids = filter_grid_roi(sft, mask, 'both_ends', exclude)
+    ids, _ =  fct(sft, *roi_options, 'both_ends', exclude)
     assert np.array_equal(ids, [2, 3, 4, 5])
\ No newline at end of file

From cfb3cf0497e1cb945c9d5520d034c7c07babbe6b Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Tue, 20 Jan 2026 15:10:11 -0500
Subject: [PATCH 5/6] Finish docstring

---
 src/scilpy/segment/streamlines.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/scilpy/segment/streamlines.py b/src/scilpy/segment/streamlines.py
index dc14a84bc..2bb8a9c7c 100644
--- a/src/scilpy/segment/streamlines.py
+++ b/src/scilpy/segment/streamlines.py
@@ -27,7 +27,8 @@ def streamlines_in_mask(sft, target_mask, all_in=False):
     target_mask : numpy.ndarray
         Binary mask in which the streamlines should pass.
     all_in: bool
-        If true, finds
+        If true, finds streamlines satisfying the 'all' criteria. Else, finds
+        streamlines satisfying the 'any' criteria.
 
     Returns
     -------

From c2415a2838ae6929520dd4ff0b5d74bc29b97444 Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Wed, 21 Jan 2026 09:34:25 -0500
Subject: [PATCH 6/6] Last fixes

---
 src/scilpy/segment/streamlines.py            |  3 +-
 src/scilpy/segment/tests/test_streamlines.py | 35 +++++++++++---------
 2 files changed, 21 insertions(+), 17 deletions(-)

diff --git a/src/scilpy/segment/streamlines.py b/src/scilpy/segment/streamlines.py
index 2bb8a9c7c..de92dd13e 100644
--- a/src/scilpy/segment/streamlines.py
+++ b/src/scilpy/segment/streamlines.py
@@ -260,7 +260,8 @@ def _pre_filtering_for_geometrical_shape(sft, size, center, filter_type,
 
     pre_mask[min_x:max_x, min_y:max_y, min_z:max_z] = 1
 
-    return filter_grid_roi(sft, pre_mask, filter_type, is_exclude=False)
+    return filter_grid_roi(sft, pre_mask, filter_type, is_exclude=False,
+                           return_sft=True)
 
 
 def filter_ellipsoid(sft, ellipsoid_radius, ellipsoid_center,
diff --git a/src/scilpy/segment/tests/test_streamlines.py b/src/scilpy/segment/tests/test_streamlines.py
index 93bcd93df..82654bea7 100644
--- a/src/scilpy/segment/tests/test_streamlines.py
+++ b/src/scilpy/segment/tests/test_streamlines.py
@@ -85,51 +85,54 @@ def test_filter_grid_roi_both_ends():
 def test_filter_grid_roi():
     # Note. Distance not tested yet. (toDo)
     roi_options = (mask,)
-    _test_all_criteria(filter_grid_roi, roi_options)
+    _test_all_criteria(filter_grid_roi, roi_options, fct_returns_sft=False)
 
 
 def test_filter_ellipsoid():
     roi_options = (bdo_radius_mm, bdo_center_rasmm_centerorigin)
-    _test_all_criteria(filter_ellipsoid, roi_options)
+    _test_all_criteria(filter_ellipsoid, roi_options, fct_returns_sft=True)
 
 
 def test_filter_cuboid():
     roi_options = (bdo_radius_mm, bdo_center_rasmm_centerorigin)
-    _test_all_criteria(filter_cuboid, roi_options)
+    _test_all_criteria(filter_cuboid, roi_options, fct_returns_sft=True)
 
 
-def _test_all_criteria(fct, roi_options):
+def _test_all_criteria(fct, roi_args, fct_returns_sft):
     """
     The three filtering methods (filter_grid_roi, filter_ellipsoid,
     filter_cuboid) test the same criteria, but with a different way to treat
-    the ROI.
+    the ROI. Here are the tests, the roi_args should be different based on fct.
     """
-    # Parameter is "is_exclude", so:
+    # Parameter is "is_exclude" for all three methods. So:
     include=False
     exclude=True
 
+    def get_ids(output):
+        if fct_returns_sft:
+            return output[0]
+        return output
+
     # Test 'any'
-    # Testing the returned sft only this once
-    ids, new_sft = fct(sft, *roi_options, 'any', include)
+    ids = get_ids(fct(sft, *roi_args, 'any', include))
     assert np.array_equal(ids, [0, 1, 2, 3, 5])
-    assert len(new_sft) == 5
-    ids, _ =  fct(sft, *roi_options, 'any', exclude)
+    ids =  get_ids(fct(sft, *roi_args, 'any', exclude))
     assert np.array_equal(ids, [4])
 
     # Test 'all'
-    ids, _ =  fct(sft, *roi_options, 'all', include)
+    ids =  get_ids(fct(sft, *roi_args, 'all', include))
     assert np.array_equal(ids, [0])
-    ids, _ =  fct(sft, *roi_options, 'all', exclude)
+    ids =  get_ids(fct(sft, *roi_args, 'all', exclude))
     assert np.array_equal(ids, [1, 2, 3, 4, 5])
 
     # Test 'either_end'
-    ids, _ =  fct(sft, *roi_options, 'either_end', include)
+    ids =  get_ids(fct(sft, *roi_args, 'either_end', include))
     assert np.array_equal(ids, [0, 1, 2])
-    ids, _ =  fct(sft, *roi_options, 'either_end', exclude)
+    ids =  get_ids(fct(sft, *roi_args, 'either_end', exclude))
     assert np.array_equal(ids, [3, 4, 5])
 
     # Test 'both_ends'
-    ids, _ =  fct(sft, *roi_options, 'both_ends', include)
+    ids =  get_ids(fct(sft, *roi_args, 'both_ends', include))
     assert np.array_equal(ids, [0, 1])
-    ids, _ =  fct(sft, *roi_options, 'both_ends', exclude)
+    ids =  get_ids(fct(sft, *roi_args, 'both_ends', exclude))
     assert np.array_equal(ids, [2, 3, 4, 5])
\ No newline at end of file