From 448578b0efac1a6030d9c7ca6c9386b2103e6374 Mon Sep 17 00:00:00 2001
From: Philippe Karan <philippe.karan@usherbrooke.ca>
Date: Wed, 1 Oct 2025 15:17:46 -0400
Subject: [PATCH 01/15] Adding script

---
 .../scil_volume_validate_correct_strides.py   | 96 +++++++++++++++++++
 1 file changed, 96 insertions(+)
 create mode 100644 src/scilpy/cli/scil_volume_validate_correct_strides.py

diff --git a/src/scilpy/cli/scil_volume_validate_correct_strides.py b/src/scilpy/cli/scil_volume_validate_correct_strides.py
new file mode 100644
index 000000000..f52e2a85b
--- /dev/null
+++ b/src/scilpy/cli/scil_volume_validate_correct_strides.py
@@ -0,0 +1,96 @@
+#! /usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Detect when data strides are different from [1, 2, 3] and correct them.
+The script takes as input a nifti file and outputs a nifti file with the
+corrected strides if needed.
+
+Input file can be 3D or 4D. Only the first 3 dimensions are considered
+for the stride correction. In the case of DWI data, we recommand to also input
+the b-values and b-vectors files to correct the b-vectors accordingly. If the
+--validate_bvecs is set, the script first detects sign flips and/or axes swaps
+in the b-vectors from a fiber coherence index [1] and corrects the b-vectors.
+Then, the b-vectors are permuted and sign flipped to match the new strides.
+
+A typical pipeline could be:
+>>> scil_volume_validate_correct_strides t1.nii.gz t1_restride.nii.gz
+>>> scil_volume_validate_correct_strides dwi.nii.gz dwi_restride.nii.gz
+    --in_bvec dwi.bvec --in_bval dwi.bval --out_bvec dwi_restride.bvec
+
+------------------------------------------------------------------------------
+Reference:
+[1] Schilling KG, Yeh FC, Nath V, Hansen C, Williams O, Resnick S, Anderson AW,
+    Landman BA. A fiber coherence index for quality control of B-table
+    orientation in diffusion MRI scans. Magn Reson Imaging. 2019 May;58:82-89.
+    doi: 10.1016/j.mri.2019.01.018.
+------------------------------------------------------------------------------
+"""
+
+import argparse
+import logging
+
+from dipy.io.gradients import read_bvals_bvecs
+import numpy as np
+import nibabel as nib
+
+from scilpy.io.utils import (add_overwrite_arg, assert_inputs_exist,
+                             assert_outputs_exist, add_verbose_arg)
+from scilpy.reconst.fiber_coherence import compute_coherence_table_for_transforms
+from scilpy.version import version_string
+
+
+def _build_arg_parser():
+    p = argparse.ArgumentParser(description=__doc__,
+                                formatter_class=argparse.RawTextHelpFormatter,
+                                epilog=version_string)
+
+    p.add_argument('in_data', 
+                   help='Path to input nifti file.')
+    
+    p.add_argument('out_data',
+                   help='Path to output nifti file with corrected strides.')
+    
+    p.add_argument('--in_bvec',
+                   help='Path to bvec file (FSL format). If provided, the '
+                        'bvecs will be permuted and sign flipped to match the '
+                        'new strides.')
+    
+    p.add_argument('--in_bval',
+                   help='Path to bval file. Must be provided if --in_bvec is '
+                        'used.')
+    
+    p.add_argument('--out_bvec',
+                   help='Path to output bvec file (FSL format). Must be '
+                        'provided if --in_bvec is used.')
+    
+    p.add_argument('--validate_bvecs', action='store_true',
+                   help='If set, the script first detects sign flips and/or '
+                        'axes swaps in the b-vectors from a fiber coherence '
+                        'index [1] and corrects the b-vectors before '
+                        'permuting/sign flipping them to match the new '
+                        'strides. If not set, the b-vectors are only permuted '
+                        'and sign flipped to match the new strides.')
+
+    add_verbose_arg(p)
+    add_overwrite_arg(p)
+    return p
+
+
+def main():
+    parser = _build_arg_parser()
+    args = parser.parse_args()
+    logging.getLogger().setLevel(logging.getLevelName(args.verbose))
+
+    assert_inputs_exist(parser, [args.in_data],
+                        optional=[args.in_bvec, args.in_bval])
+    assert_outputs_exist(parser, args, args.out_data, optional=args.out_bvec)
+
+    img = nib.load(args.in_data)
+    data = img.get_fdata()
+    strides = nib.io_orientation(img.affine)
+    strides = strides[0] * strides[1]
+    print(strides)
+
+
+if __name__ == "__main__":
+    main()

From 9ac122dba2ebad824fcdf4956b8e0b788cce1459 Mon Sep 17 00:00:00 2001
From: Philippe Karan <philippe.karan@usherbrooke.ca>
Date: Wed, 1 Oct 2025 16:20:51 -0400
Subject: [PATCH 02/15] Adding bvec support

---
 .../scil_volume_validate_correct_strides.py   | 74 +++++++++++++++----
 1 file changed, 58 insertions(+), 16 deletions(-)

diff --git a/src/scilpy/cli/scil_volume_validate_correct_strides.py b/src/scilpy/cli/scil_volume_validate_correct_strides.py
index f52e2a85b..d81018903 100644
--- a/src/scilpy/cli/scil_volume_validate_correct_strides.py
+++ b/src/scilpy/cli/scil_volume_validate_correct_strides.py
@@ -33,6 +33,8 @@
 import numpy as np
 import nibabel as nib
 
+from scilpy.gradients.bvec_bval_tools import (flip_gradient_sampling,
+                                              swap_gradient_axis)
 from scilpy.io.utils import (add_overwrite_arg, assert_inputs_exist,
                              assert_outputs_exist, add_verbose_arg)
 from scilpy.reconst.fiber_coherence import compute_coherence_table_for_transforms
@@ -52,24 +54,24 @@ def _build_arg_parser():
     
     p.add_argument('--in_bvec',
                    help='Path to bvec file (FSL format). If provided, the '
-                        'bvecs will be permuted and sign flipped to match the '
-                        'new strides.')
-    
-    p.add_argument('--in_bval',
-                   help='Path to bval file. Must be provided if --in_bvec is '
-                        'used.')
-    
+                        'bvecs will \nbe permuted and sign flipped to match '
+                        'the new strides.')
+
     p.add_argument('--out_bvec',
                    help='Path to output bvec file (FSL format). Must be '
                         'provided if --in_bvec is used.')
     
-    p.add_argument('--validate_bvecs', action='store_true',
+    p.add_argument('--validate_bvec', action='store_true',
                    help='If set, the script first detects sign flips and/or '
-                        'axes swaps in the b-vectors from a fiber coherence '
-                        'index [1] and corrects the b-vectors before '
+                        'axes swaps \nin the b-vectors from a fiber coherence '
+                        'index [1] and corrects \nthe b-vectors before '
                         'permuting/sign flipping them to match the new '
-                        'strides. If not set, the b-vectors are only permuted '
-                        'and sign flipped to match the new strides.')
+                        'strides. \nIf not set, the b-vectors are only '
+                        'permuted and sign flipped to match the new strides.')
+
+    p.add_argument('--in_bval',
+                   help='Path to bval file. Must be provided if '
+                        '--validate_bvecs is used.')
 
     add_verbose_arg(p)
     add_overwrite_arg(p)
@@ -85,11 +87,51 @@ def main():
                         optional=[args.in_bvec, args.in_bval])
     assert_outputs_exist(parser, args, args.out_data, optional=args.out_bvec)
 
+    if args.in_bvec and not args.out_bvec:
+        parser.error('--out_bvec must be provided if --in_bvec is used.')
+    if args.validate_bvec and (not args.in_bvec or not args.in_bval):
+        parser.error('--in_bvec and --in_bval must be provided if '
+                     '--validate_bvecs is set.')
+
     img = nib.load(args.in_data)
-    data = img.get_fdata()
-    strides = nib.io_orientation(img.affine)
-    strides = strides[0] * strides[1]
-    print(strides)
+    strides = nib.io_orientation(img.affine).astype(np.int8)
+    strides = (strides[:, 0] + 1) * strides[:, 1]
+    if np.array_equal(strides, [1, 2, 3]):
+        logging.warning('Input data already has the correct strides [1, 2, 3].'
+                        ' No correction needed and outputed. If you want to '
+                        'validate b-vectors, please use the script '
+                        'scil_gradients_validate_correct.')
+        return
+    else:
+        logging.warning('Input data has strides {}. '
+                        'Correcting to [1, 2, 3].'.format(strides))
+    n = len(strides)
+    transform = [0]*n
+    for i, m in enumerate(strides):
+        axis = abs(m) - 1
+        sign = 1 if m > 0 else -1
+        transform[axis] = sign * (i+1)
+
+    axes_to_flip = []
+    swapped_order = []
+    for next_axis in transform:
+        if next_axis in [1, 2, 3]:
+            swapped_order.append(next_axis - 1)
+        elif next_axis in [-1, -2, -3]:
+            axes_to_flip.append(abs(next_axis) - 1)
+            swapped_order.append(abs(next_axis) - 1)
+
+    ornt = np.column_stack((np.array(swapped_order, dtype=np.int8),
+                            np.where(np.isin(range(n), axes_to_flip), -1, 1)))
+
+    new_img = img.as_reoriented(ornt)
+    nib.save(new_img, args.out_data)
+
+    if args.in_bvec and not args.validate_bvec:
+        _, bvecs = read_bvals_bvecs(None, args.in_bvec)
+        bvecs = flip_gradient_sampling(bvecs, axes_to_flip, 'fsl')
+        bvecs = swap_gradient_axis(bvecs, swapped_order, 'fsl')
+        np.savetxt(args.out_bvec, bvecs, "%.8f")
 
 
 if __name__ == "__main__":

From b8cbd4bc2f1c33bfa7896ee0acd02226d09568d4 Mon Sep 17 00:00:00 2001
From: Philippe Karan <philippe.karan@usherbrooke.ca>
Date: Wed, 1 Oct 2025 17:21:21 -0400
Subject: [PATCH 03/15] WIP

---
 .../scil_volume_validate_correct_strides.py   | 111 +++++++++++++-----
 1 file changed, 80 insertions(+), 31 deletions(-)

diff --git a/src/scilpy/cli/scil_volume_validate_correct_strides.py b/src/scilpy/cli/scil_volume_validate_correct_strides.py
index d81018903..b4a7c6133 100644
--- a/src/scilpy/cli/scil_volume_validate_correct_strides.py
+++ b/src/scilpy/cli/scil_volume_validate_correct_strides.py
@@ -29,13 +29,19 @@
 import argparse
 import logging
 
+from dipy.core.gradients import gradient_table
 from dipy.io.gradients import read_bvals_bvecs
+from dipy.reconst.dti import TensorModel, fractional_anisotropy
 import numpy as np
 import nibabel as nib
 
-from scilpy.gradients.bvec_bval_tools import (flip_gradient_sampling,
+from scilpy.gradients.bvec_bval_tools import (check_b0_threshold,
+                                              flip_gradient_sampling,
+                                              is_normalized_bvecs,
+                                              normalize_bvecs,
                                               swap_gradient_axis)
-from scilpy.io.utils import (add_overwrite_arg, assert_inputs_exist,
+from scilpy.io.utils import (add_b0_thresh_arg, add_overwrite_arg,
+                             add_skip_b0_check_arg, assert_inputs_exist,
                              assert_outputs_exist, add_verbose_arg)
 from scilpy.reconst.fiber_coherence import compute_coherence_table_for_transforms
 from scilpy.version import version_string
@@ -73,6 +79,8 @@ def _build_arg_parser():
                    help='Path to bval file. Must be provided if '
                         '--validate_bvecs is used.')
 
+    add_b0_thresh_arg(p)
+    add_skip_b0_check_arg(p, will_overwrite_with_min=True)
     add_verbose_arg(p)
     add_overwrite_arg(p)
     return p
@@ -97,39 +105,80 @@ def main():
     strides = nib.io_orientation(img.affine).astype(np.int8)
     strides = (strides[:, 0] + 1) * strides[:, 1]
     if np.array_equal(strides, [1, 2, 3]):
+        correct=True
         logging.warning('Input data already has the correct strides [1, 2, 3].'
-                        ' No correction needed and outputed. If you want to '
-                        'validate b-vectors, please use the script '
-                        'scil_gradients_validate_correct.')
-        return
+                        ' No correction on data needed and outputed.')
     else:
+        correct=False
         logging.warning('Input data has strides {}. '
                         'Correcting to [1, 2, 3].'.format(strides))
-    n = len(strides)
-    transform = [0]*n
-    for i, m in enumerate(strides):
-        axis = abs(m) - 1
-        sign = 1 if m > 0 else -1
-        transform[axis] = sign * (i+1)
-
-    axes_to_flip = []
-    swapped_order = []
-    for next_axis in transform:
-        if next_axis in [1, 2, 3]:
-            swapped_order.append(next_axis - 1)
-        elif next_axis in [-1, -2, -3]:
-            axes_to_flip.append(abs(next_axis) - 1)
-            swapped_order.append(abs(next_axis) - 1)
-
-    ornt = np.column_stack((np.array(swapped_order, dtype=np.int8),
-                            np.where(np.isin(range(n), axes_to_flip), -1, 1)))
-
-    new_img = img.as_reoriented(ornt)
-    nib.save(new_img, args.out_data)
-
-    if args.in_bvec and not args.validate_bvec:
-        _, bvecs = read_bvals_bvecs(None, args.in_bvec)
-        bvecs = flip_gradient_sampling(bvecs, axes_to_flip, 'fsl')
+        n = len(strides)
+        transform = [0]*n
+        for i, m in enumerate(strides):
+            axis = abs(m) - 1
+            sign = 1 if m > 0 else -1
+            transform[axis] = sign * (i+1)
+
+        axes_to_flip = []
+        swapped_order = []
+        for next_axis in transform:
+            if next_axis in [1, 2, 3]:
+                swapped_order.append(next_axis - 1)
+            elif next_axis in [-1, -2, -3]:
+                axes_to_flip.append(abs(next_axis) - 1)
+                swapped_order.append(abs(next_axis) - 1)
+
+        ornt = np.column_stack((np.array(swapped_order, dtype=np.int8),
+                                np.where(np.isin(range(n), axes_to_flip),
+                                         -1, 1)))
+
+        new_img = img.as_reoriented(ornt)
+        nib.save(new_img, args.out_data)
+
+    if args.validate_bvec:
+        logging.info('Validating b-vectors from fiber coherence index [1]...')
+        data = img.get_fdata()
+        bvals, bvecs = read_bvals_bvecs(args.in_bval, args.in_bvec)
+        if not is_normalized_bvecs(bvecs):
+            logging.warning('Your b-vectors do not seem normalized...')
+            bvecs = normalize_bvecs(bvecs)
+        args.b0_threshold = check_b0_threshold(bvals.min(),
+                                               b0_thr=args.b0_threshold,
+                                               skip_b0_check=args.skip_b0_check)
+        gtab = gradient_table(bvals, bvecs=bvecs,
+                              b0_threshold=args.b0_threshold)
+        tenmodel = TensorModel(gtab, fit_method='WLS',
+                               min_signal=np.min(data[data > 0]))
+
+        mask = np.zeros(data.shape[:3], dtype=bool)
+        interval_i = slice(data.shape[0]//2,
+                           data.shape[0]//2 + data.shape[0]//4)
+        interval_j = slice(data.shape[1]//2,
+                           data.shape[1]//2 + data.shape[1]//4)
+        interval_k = slice(data.shape[2]//2,
+                           data.shape[2]//2 + data.shape[2]//4)
+        mask[interval_i, interval_j, interval_k] = 1
+        tenfit = tenmodel.fit(data, mask=mask)
+        fa = fractional_anisotropy(tenfit.evals)
+        evecs = tenfit.evecs.astype(np.float32)[..., 0]
+        evecs[fa < 0.2] = 0
+        coherence, transform = compute_coherence_table_for_transforms(evecs, 
+                                                                      fa)
+
+        best_t = transform[np.argmax(coherence)]
+        if (best_t == np.eye(3)).all():
+            logging.info('The b-vectors are already correct.')
+            bvecs = bvecs
+        else:
+            logging.warning('Applying correction to b-vectors.')
+            bvecs = np.dot(bvecs, best_t)
+        if correct:
+            np.savetxt(args.out_bvec, bvecs.T, "%.8f")
+
+    if args.in_bvec and not correct:
+        if not args.validate_bvec:
+            _, bvecs = read_bvals_bvecs(None, args.in_bvec)
+        bvecs = flip_gradient_sampling(bvecs.T, axes_to_flip, 'fsl')
         bvecs = swap_gradient_axis(bvecs, swapped_order, 'fsl')
         np.savetxt(args.out_bvec, bvecs, "%.8f")
 

From 0ed2f78ceac5e71bccda346622212f906adb68e0 Mon Sep 17 00:00:00 2001
From: Philippe Karan <philippe.karan@usherbrooke.ca>
Date: Wed, 1 Oct 2025 17:24:06 -0400
Subject: [PATCH 04/15] WIP

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

diff --git a/src/scilpy/cli/scil_volume_validate_correct_strides.py b/src/scilpy/cli/scil_volume_validate_correct_strides.py
index b4a7c6133..8f2e0d7dc 100644
--- a/src/scilpy/cli/scil_volume_validate_correct_strides.py
+++ b/src/scilpy/cli/scil_volume_validate_correct_strides.py
@@ -15,7 +15,8 @@
 A typical pipeline could be:
 >>> scil_volume_validate_correct_strides t1.nii.gz t1_restride.nii.gz
 >>> scil_volume_validate_correct_strides dwi.nii.gz dwi_restride.nii.gz
-    --in_bvec dwi.bvec --in_bval dwi.bval --out_bvec dwi_restride.bvec
+    --in_bvec dwi.bvec --out_bvec dwi_restride.bvec --validate_bvec
+    --in_bval dwi.bval
 
 ------------------------------------------------------------------------------
 Reference:

From 722fb39827ab68d46964c5fe0cc191b495a1983f Mon Sep 17 00:00:00 2001
From: Philippe Karan <philippe.karan@usherbrooke.ca>
Date: Wed, 1 Oct 2025 17:36:29 -0400
Subject: [PATCH 05/15] WIP

---
 src/scilpy/cli/scil_volume_validate_correct_strides.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/scilpy/cli/scil_volume_validate_correct_strides.py b/src/scilpy/cli/scil_volume_validate_correct_strides.py
index 8f2e0d7dc..3ed1bf1f7 100644
--- a/src/scilpy/cli/scil_volume_validate_correct_strides.py
+++ b/src/scilpy/cli/scil_volume_validate_correct_strides.py
@@ -137,7 +137,7 @@ def main():
         nib.save(new_img, args.out_data)
 
     if args.validate_bvec:
-        logging.info('Validating b-vectors from fiber coherence index [1]...')
+        logging.info('Validating b-vectors from fiber coherence index...')
         data = img.get_fdata()
         bvals, bvecs = read_bvals_bvecs(args.in_bval, args.in_bvec)
         if not is_normalized_bvecs(bvecs):
@@ -167,20 +167,25 @@ def main():
                                                                       fa)
 
         best_t = transform[np.argmax(coherence)]
+        print(bvecs.T)
         if (best_t == np.eye(3)).all():
             logging.info('The b-vectors are already correct.')
             bvecs = bvecs
         else:
-            logging.warning('Applying correction to b-vectors.')
+            logging.warning('Applying correction to b-vectors.'
+                            'Transform is: \n{0}.'.format(best_t))
             bvecs = np.dot(bvecs, best_t)
         if correct:
             np.savetxt(args.out_bvec, bvecs.T, "%.8f")
+        print(bvecs.T)
 
     if args.in_bvec and not correct:
+        print(axes_to_flip)
         if not args.validate_bvec:
             _, bvecs = read_bvals_bvecs(None, args.in_bvec)
         bvecs = flip_gradient_sampling(bvecs.T, axes_to_flip, 'fsl')
         bvecs = swap_gradient_axis(bvecs, swapped_order, 'fsl')
+        print(bvecs)
         np.savetxt(args.out_bvec, bvecs, "%.8f")
 
 

From 6331b9a41c9548dae4d25e3b98242dba99718eee Mon Sep 17 00:00:00 2001
From: Philippe Karan <philippe.karan@usherbrooke.ca>
Date: Thu, 2 Oct 2025 08:35:17 -0400
Subject: [PATCH 06/15] WIP

---
 src/scilpy/cli/scil_volume_validate_correct_strides.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/scilpy/cli/scil_volume_validate_correct_strides.py b/src/scilpy/cli/scil_volume_validate_correct_strides.py
index 3ed1bf1f7..71cc915e0 100644
--- a/src/scilpy/cli/scil_volume_validate_correct_strides.py
+++ b/src/scilpy/cli/scil_volume_validate_correct_strides.py
@@ -167,6 +167,10 @@ def main():
                                                                       fa)
 
         best_t = transform[np.argmax(coherence)]
+        for i, tr in enumerate(transform):
+            print(tr)
+            print(coherence[i])
+            print(" ")
         print(bvecs.T)
         if (best_t == np.eye(3)).all():
             logging.info('The b-vectors are already correct.')

From 6c6e124a76ddf2f270ed8c49660130798e9a57a0 Mon Sep 17 00:00:00 2001
From: Philippe Karan <philippe.karan@usherbrooke.ca>
Date: Thu, 2 Oct 2025 10:26:25 -0400
Subject: [PATCH 07/15] Adding tests

---
 pyproject.toml                                |  1 +
 .../scil_volume_validate_correct_strides.py   | 18 ++----
 .../test_volume_validate_correct_strides.py   | 56 +++++++++++++++++++
 3 files changed, 62 insertions(+), 13 deletions(-)
 create mode 100644 src/scilpy/cli/tests/test_volume_validate_correct_strides.py

diff --git a/pyproject.toml b/pyproject.toml
index b7a65fe49..d014d254c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -285,3 +285,4 @@ scil_volume_reshape  = "scilpy.cli.scil_volume_reshape:main"
 scil_volume_reslice_to_reference  = "scilpy.cli.scil_volume_reslice_to_reference:main"
 scil_volume_stats_in_labels  = "scilpy.cli.scil_volume_stats_in_labels:main"
 scil_volume_stats_in_ROI  = "scilpy.cli.scil_volume_stats_in_ROI:main"
+scil_volume_validate_correct_strides  = "scilpy.cli.scil_volume_validate_correct_strides:main"
diff --git a/src/scilpy/cli/scil_volume_validate_correct_strides.py b/src/scilpy/cli/scil_volume_validate_correct_strides.py
index 71cc915e0..4c0966b67 100644
--- a/src/scilpy/cli/scil_volume_validate_correct_strides.py
+++ b/src/scilpy/cli/scil_volume_validate_correct_strides.py
@@ -167,29 +167,21 @@ def main():
                                                                       fa)
 
         best_t = transform[np.argmax(coherence)]
-        for i, tr in enumerate(transform):
-            print(tr)
-            print(coherence[i])
-            print(" ")
-        print(bvecs.T)
         if (best_t == np.eye(3)).all():
-            logging.info('The b-vectors are already correct.')
+            logging.info('The b-vectors are aligned with the original data.')
             bvecs = bvecs
         else:
-            logging.warning('Applying correction to b-vectors.'
-                            'Transform is: \n{0}.'.format(best_t))
+            logging.warning('Applying correction to b-vectors.')
+            logging.info('Transform is: \n{0}.'.format(best_t))
             bvecs = np.dot(bvecs, best_t)
-        if correct:
-            np.savetxt(args.out_bvec, bvecs.T, "%.8f")
-        print(bvecs.T)
+            if correct:
+                np.savetxt(args.out_bvec, bvecs.T, "%.8f")
 
     if args.in_bvec and not correct:
-        print(axes_to_flip)
         if not args.validate_bvec:
             _, bvecs = read_bvals_bvecs(None, args.in_bvec)
         bvecs = flip_gradient_sampling(bvecs.T, axes_to_flip, 'fsl')
         bvecs = swap_gradient_axis(bvecs, swapped_order, 'fsl')
-        print(bvecs)
         np.savetxt(args.out_bvec, bvecs, "%.8f")
 
 
diff --git a/src/scilpy/cli/tests/test_volume_validate_correct_strides.py b/src/scilpy/cli/tests/test_volume_validate_correct_strides.py
new file mode 100644
index 000000000..1cba8018e
--- /dev/null
+++ b/src/scilpy/cli/tests/test_volume_validate_correct_strides.py
@@ -0,0 +1,56 @@
+#!/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
+
+# If they already exist, this only takes 5 seconds (check md5sum)
+fetch_data(get_testing_files_dict(), keys=['processing.zip'])
+tmp_dir = tempfile.TemporaryDirectory()
+
+
+def test_help_option(script_runner):
+    ret = script_runner.run(['scil_volume_validate_correct_strides', '--help'])
+    assert ret.success
+
+
+def test_execution_processing_basic(script_runner, monkeypatch):
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    in_dwi = os.path.join(SCILPY_HOME, 'processing',
+                          'dwi_crop_1000.nii.gz')
+
+    ret = script_runner.run(['scil_volume_validate_correct_strides', in_dwi,
+                             'dwi_restride.nii.gz', '-f'])
+    assert ret.success
+
+
+def test_execution_processing_bvecs(script_runner, monkeypatch):
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    in_dwi = os.path.join(SCILPY_HOME, 'processing',
+                          'dwi_crop_1000.nii.gz')
+    in_bvec = os.path.join(SCILPY_HOME, 'processing',
+                           '1000.bvec')
+
+    ret = script_runner.run(['scil_volume_validate_correct_strides', in_dwi,
+                             'dwi_restride.nii.gz', '--in_bvec', in_bvec,
+                             '--out_bvec', 'dwi_restride.bvec', '-f'])
+    assert ret.success
+
+
+def test_execution_processing_bvecs(script_runner, monkeypatch):
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    in_dwi = os.path.join(SCILPY_HOME, 'processing',
+                          'dwi_crop_1000.nii.gz')
+    in_bvec = os.path.join(SCILPY_HOME, 'processing',
+                           '1000.bvec')
+    in_bval = os.path.join(SCILPY_HOME, 'processing',
+                           '1000.bval')
+
+    ret = script_runner.run(['scil_volume_validate_correct_strides', in_dwi,
+                             'dwi_restride.nii.gz', '--in_bvec', in_bvec,
+                             '--out_bvec', 'dwi_restride.bvec',
+                             '--validate_bvec', '--in_bval', in_bval, '-f'])
+    assert ret.success

From 634045b6337b150dbd744479deb5cda02cabaff7 Mon Sep 17 00:00:00 2001
From: Philippe Karan <philippe.karan@usherbrooke.ca>
Date: Thu, 2 Oct 2025 10:33:20 -0400
Subject: [PATCH 08/15] Adding check for 4D data if bvec given

---
 src/scilpy/cli/scil_volume_validate_correct_strides.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/scilpy/cli/scil_volume_validate_correct_strides.py b/src/scilpy/cli/scil_volume_validate_correct_strides.py
index 4c0966b67..632c8c99f 100644
--- a/src/scilpy/cli/scil_volume_validate_correct_strides.py
+++ b/src/scilpy/cli/scil_volume_validate_correct_strides.py
@@ -139,6 +139,9 @@ def main():
     if args.validate_bvec:
         logging.info('Validating b-vectors from fiber coherence index...')
         data = img.get_fdata()
+        if len(data.shape) != 4:
+            parser.error('Input data must be DWI (4D) when --validate_bvec '
+                         'is set.')
         bvals, bvecs = read_bvals_bvecs(args.in_bval, args.in_bvec)
         if not is_normalized_bvecs(bvecs):
             logging.warning('Your b-vectors do not seem normalized...')

From c37b6e19a55dde48a32b047d6bffda74bfa960bc Mon Sep 17 00:00:00 2001
From: Philippe Karan <philippe.karan@usherbrooke.ca>
Date: Thu, 2 Oct 2025 11:23:31 -0400
Subject: [PATCH 09/15] Adding new tests

---
 .../scil_volume_validate_correct_strides.py   |  1 -
 .../test_volume_validate_correct_strides.py   | 78 ++++++++++++++++++-
 2 files changed, 75 insertions(+), 4 deletions(-)

diff --git a/src/scilpy/cli/scil_volume_validate_correct_strides.py b/src/scilpy/cli/scil_volume_validate_correct_strides.py
index 632c8c99f..eabd004d3 100644
--- a/src/scilpy/cli/scil_volume_validate_correct_strides.py
+++ b/src/scilpy/cli/scil_volume_validate_correct_strides.py
@@ -172,7 +172,6 @@ def main():
         best_t = transform[np.argmax(coherence)]
         if (best_t == np.eye(3)).all():
             logging.info('The b-vectors are aligned with the original data.')
-            bvecs = bvecs
         else:
             logging.warning('Applying correction to b-vectors.')
             logging.info('Transform is: \n{0}.'.format(best_t))
diff --git a/src/scilpy/cli/tests/test_volume_validate_correct_strides.py b/src/scilpy/cli/tests/test_volume_validate_correct_strides.py
index 1cba8018e..8981253d9 100644
--- a/src/scilpy/cli/tests/test_volume_validate_correct_strides.py
+++ b/src/scilpy/cli/tests/test_volume_validate_correct_strides.py
@@ -17,7 +17,7 @@ def test_help_option(script_runner):
     assert ret.success
 
 
-def test_execution_processing_basic(script_runner, monkeypatch):
+def test_execution_processing_no_restride(script_runner, monkeypatch):
     monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
     in_dwi = os.path.join(SCILPY_HOME, 'processing',
                           'dwi_crop_1000.nii.gz')
@@ -27,10 +27,20 @@ def test_execution_processing_basic(script_runner, monkeypatch):
     assert ret.success
 
 
+def test_execution_processing_restride(script_runner, monkeypatch):
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    in_dwi = os.path.join(SCILPY_HOME, 'processing',
+                          'dwi_crop_1000_bad_strides.nii.gz')
+
+    ret = script_runner.run(['scil_volume_validate_correct_strides', in_dwi,
+                             'dwi_restride.nii.gz', '-f'])
+    assert ret.success
+
+
 def test_execution_processing_bvecs(script_runner, monkeypatch):
     monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
     in_dwi = os.path.join(SCILPY_HOME, 'processing',
-                          'dwi_crop_1000.nii.gz')
+                          'dwi_crop_1000_bad_strides.nii.gz')
     in_bvec = os.path.join(SCILPY_HOME, 'processing',
                            '1000.bvec')
 
@@ -40,10 +50,28 @@ def test_execution_processing_bvecs(script_runner, monkeypatch):
     assert ret.success
 
 
-def test_execution_processing_bvecs(script_runner, monkeypatch):
+def test_execution_processing_validate_bvecs_v1(script_runner, monkeypatch):
+    # Validate with good data strides and bad bvecs
     monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
     in_dwi = os.path.join(SCILPY_HOME, 'processing',
                           'dwi_crop_1000.nii.gz')
+    in_bvec = os.path.join(SCILPY_HOME, 'processing',
+                           '1000_bad_strides.bvec')
+    in_bval = os.path.join(SCILPY_HOME, 'processing',
+                           '1000.bval')
+
+    ret = script_runner.run(['scil_volume_validate_correct_strides', in_dwi,
+                             'dwi_restride.nii.gz', '--in_bvec', in_bvec,
+                             '--out_bvec', 'dwi_restride.bvec',
+                             '--validate_bvec', '--in_bval', in_bval, '-f'])
+    assert ret.success
+
+
+def test_execution_processing_validate_bvecs_v2(script_runner, monkeypatch):
+    # Validate with bad data strides
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    in_dwi = os.path.join(SCILPY_HOME, 'processing',
+                          'dwi_crop_1000_bad_strides.nii.gz')
     in_bvec = os.path.join(SCILPY_HOME, 'processing',
                            '1000.bvec')
     in_bval = os.path.join(SCILPY_HOME, 'processing',
@@ -54,3 +82,47 @@ def test_execution_processing_bvecs(script_runner, monkeypatch):
                              '--out_bvec', 'dwi_restride.bvec',
                              '--validate_bvec', '--in_bval', in_bval, '-f'])
     assert ret.success
+
+
+def test_execution_processing_validate_bvecs_v3(script_runner, monkeypatch):
+    # Validate with non-DWI data and bad bvecs
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    in_dwi = os.path.join(SCILPY_HOME, 'processing',
+                          'nufo.nii.gz')
+    in_bvec = os.path.join(SCILPY_HOME, 'processing',
+                           '1000_bad_strides.bvec')
+    in_bval = os.path.join(SCILPY_HOME, 'processing',
+                           '1000.bval')
+
+    ret = script_runner.run(['scil_volume_validate_correct_strides', in_dwi,
+                             'dwi_restride.nii.gz', '--in_bvec', in_bvec,
+                             '--out_bvec', 'dwi_restride.bvec',
+                             '--validate_bvec', '--in_bval', in_bval, '-f'])
+    assert not ret.success
+
+
+def test_execution_processing_no_out_bvec(script_runner, monkeypatch):
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    in_dwi = os.path.join(SCILPY_HOME, 'processing',
+                          'dwi_crop_1000_bad_strides.nii.gz')
+    in_bvec = os.path.join(SCILPY_HOME, 'processing',
+                           '1000.bvec')
+
+    ret = script_runner.run(['scil_volume_validate_correct_strides', in_dwi,
+                             'dwi_restride.nii.gz', '--in_bvec', in_bvec,
+                             '-f'])
+    assert not ret.success
+
+
+def test_execution_processing_no_in_bval(script_runner, monkeypatch):
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    in_dwi = os.path.join(SCILPY_HOME, 'processing',
+                          'dwi_crop_1000_bad_strides.nii.gz')
+    in_bvec = os.path.join(SCILPY_HOME, 'processing',
+                           '1000.bvec')
+
+    ret = script_runner.run(['scil_volume_validate_correct_strides', in_dwi,
+                             'dwi_restride.nii.gz', '--in_bvec', in_bvec,
+                             '--out_bvec', 'dwi_restride.bvec',
+                             '--validate_bvec', '-f'])
+    assert not ret.success

From 9146d3a4b2593b3362cc070b013bcfa167f627f7 Mon Sep 17 00:00:00 2001
From: Philippe Karan <philippe.karan@usherbrooke.ca>
Date: Tue, 7 Oct 2025 15:37:51 -0400
Subject: [PATCH 10/15] Update processing.zip hash

---
 src/scilpy/io/fetcher.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/scilpy/io/fetcher.py b/src/scilpy/io/fetcher.py
index 87c62645b..48112872f 100644
--- a/src/scilpy/io/fetcher.py
+++ b/src/scilpy/io/fetcher.py
@@ -56,7 +56,7 @@ def get_testing_files_dict():
         "plot.zip": "a1dc54cad7e1d17e55228c2518a1b34e",
         "others.zip": "82248b4888a63b0aeffc8070cc206995",
         "fodf_filtering.zip": "5985c0644321ecf81fd694fb91e2c898",
-        "processing.zip": "1ba6869c9d8b58a9b911ba71fdd50a07",
+        "processing.zip": "0417df00d97272f5887c31acb8948604",
         "surface_vtk_fib.zip": "241f3afd6344c967d7176b43e4a99a41",
         "tractograms.zip": "964113f307213523d784b3dbf3a5117a",
         "mrds.zip": "5abe6092400e11e9bb2423e2c387e774",

From e6c444fe311030c4685b15ccbc046b9222a0a19d Mon Sep 17 00:00:00 2001
From: Philippe Karan <philippe.karan@usherbrooke.ca>
Date: Wed, 8 Oct 2025 13:41:12 -0400
Subject: [PATCH 11/15] Update test data names

---
 src/scilpy/cli/tests/test_volume_validate_correct_strides.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/scilpy/cli/tests/test_volume_validate_correct_strides.py b/src/scilpy/cli/tests/test_volume_validate_correct_strides.py
index 8981253d9..709a95700 100644
--- a/src/scilpy/cli/tests/test_volume_validate_correct_strides.py
+++ b/src/scilpy/cli/tests/test_volume_validate_correct_strides.py
@@ -56,7 +56,7 @@ def test_execution_processing_validate_bvecs_v1(script_runner, monkeypatch):
     in_dwi = os.path.join(SCILPY_HOME, 'processing',
                           'dwi_crop_1000.nii.gz')
     in_bvec = os.path.join(SCILPY_HOME, 'processing',
-                           '1000_bad_strides.bvec')
+                           'dwi_crop_1000_bad_strides.bvec')
     in_bval = os.path.join(SCILPY_HOME, 'processing',
                            '1000.bval')
 
@@ -90,7 +90,7 @@ def test_execution_processing_validate_bvecs_v3(script_runner, monkeypatch):
     in_dwi = os.path.join(SCILPY_HOME, 'processing',
                           'nufo.nii.gz')
     in_bvec = os.path.join(SCILPY_HOME, 'processing',
-                           '1000_bad_strides.bvec')
+                           'dwi_crop_1000_bad_strides.bvec')
     in_bval = os.path.join(SCILPY_HOME, 'processing',
                            '1000.bval')
 

From fd359658d3227065cc6e9321a4692a634da72deb Mon Sep 17 00:00:00 2001
From: Philippe Karan <philippe.karan@usherbrooke.ca>
Date: Thu, 9 Oct 2025 10:48:16 -0400
Subject: [PATCH 12/15] Adding comments and cleaning

---
 .../scil_volume_validate_correct_strides.py   | 30 ++++++++++++-------
 1 file changed, 20 insertions(+), 10 deletions(-)

diff --git a/src/scilpy/cli/scil_volume_validate_correct_strides.py b/src/scilpy/cli/scil_volume_validate_correct_strides.py
index eabd004d3..a3b95a0b0 100644
--- a/src/scilpy/cli/scil_volume_validate_correct_strides.py
+++ b/src/scilpy/cli/scil_volume_validate_correct_strides.py
@@ -55,19 +55,16 @@ def _build_arg_parser():
 
     p.add_argument('in_data', 
                    help='Path to input nifti file.')
-    
     p.add_argument('out_data',
                    help='Path to output nifti file with corrected strides.')
-    
+
     p.add_argument('--in_bvec',
                    help='Path to bvec file (FSL format). If provided, the '
                         'bvecs will \nbe permuted and sign flipped to match '
                         'the new strides.')
-
     p.add_argument('--out_bvec',
                    help='Path to output bvec file (FSL format). Must be '
                         'provided if --in_bvec is used.')
-    
     p.add_argument('--validate_bvec', action='store_true',
                    help='If set, the script first detects sign flips and/or '
                         'axes swaps \nin the b-vectors from a fiber coherence '
@@ -75,7 +72,6 @@ def _build_arg_parser():
                         'permuting/sign flipping them to match the new '
                         'strides. \nIf not set, the b-vectors are only '
                         'permuted and sign flipped to match the new strides.')
-
     p.add_argument('--in_bval',
                    help='Path to bval file. Must be provided if '
                         '--validate_bvecs is used.')
@@ -102,9 +98,11 @@ def main():
         parser.error('--in_bvec and --in_bval must be provided if '
                      '--validate_bvecs is set.')
 
+    # Get the current strides
     img = nib.load(args.in_data)
     strides = nib.io_orientation(img.affine).astype(np.int8)
     strides = (strides[:, 0] + 1) * strides[:, 1]
+    # Check if the strides are correct ([1, 2, 3])
     if np.array_equal(strides, [1, 2, 3]):
         correct=True
         logging.warning('Input data already has the correct strides [1, 2, 3].'
@@ -113,15 +111,20 @@ def main():
         correct=False
         logging.warning('Input data has strides {}. '
                         'Correcting to [1, 2, 3].'.format(strides))
+        # Compute the required transform to get to [1, 2, 3]
         n = len(strides)
         transform = [0]*n
         for i, m in enumerate(strides):
+            # Get the axis (0, 1, 2) and the sign of the current stride
             axis = abs(m) - 1
             sign = 1 if m > 0 else -1
-            transform[axis] = sign * (i+1)
+            # Set the transform for this axis
+            transform[axis] = sign * (i + 1)
 
         axes_to_flip = []
         swapped_order = []
+        # Write the transform in a format compatible with the
+        # flip_gradient_sampling and swap_gradient_axis functions (for bvecs)
         for next_axis in transform:
             if next_axis in [1, 2, 3]:
                 swapped_order.append(next_axis - 1)
@@ -129,16 +132,19 @@ def main():
                 axes_to_flip.append(abs(next_axis) - 1)
                 swapped_order.append(abs(next_axis) - 1)
 
+        # Write the transform in a format compatible with the nibabel
+        # as_reoriented function (for image)
         ornt = np.column_stack((np.array(swapped_order, dtype=np.int8),
                                 np.where(np.isin(range(n), axes_to_flip),
                                          -1, 1)))
-
+        # Apply the transform to the image and save it
         new_img = img.as_reoriented(ornt)
         nib.save(new_img, args.out_data)
 
     if args.validate_bvec:
         logging.info('Validating b-vectors from fiber coherence index...')
-        data = img.get_fdata()
+        # Load and validate the data and bvals/bvecs
+        data = img.get_fdata().astype(np.float32)
         if len(data.shape) != 4:
             parser.error('Input data must be DWI (4D) when --validate_bvec '
                          'is set.')
@@ -153,8 +159,9 @@ def main():
                               b0_threshold=args.b0_threshold)
         tenmodel = TensorModel(gtab, fit_method='WLS',
                                min_signal=np.min(data[data > 0]))
-
+        # Generate a mask to avoid fitting tensor on the whole image
         mask = np.zeros(data.shape[:3], dtype=bool)
+        # Use a small cubic ROI at the center of the volume
         interval_i = slice(data.shape[0]//2,
                            data.shape[0]//2 + data.shape[0]//4)
         interval_j = slice(data.shape[1]//2,
@@ -162,13 +169,14 @@ def main():
         interval_k = slice(data.shape[2]//2,
                            data.shape[2]//2 + data.shape[2]//4)
         mask[interval_i, interval_j, interval_k] = 1
+        # Compute the necessary DTI metrics to compute the coherence of bvecs
         tenfit = tenmodel.fit(data, mask=mask)
         fa = fractional_anisotropy(tenfit.evals)
         evecs = tenfit.evecs.astype(np.float32)[..., 0]
         evecs[fa < 0.2] = 0
         coherence, transform = compute_coherence_table_for_transforms(evecs, 
                                                                       fa)
-
+        # Find the best transform and apply it to the bvecs if needed
         best_t = transform[np.argmax(coherence)]
         if (best_t == np.eye(3)).all():
             logging.info('The b-vectors are aligned with the original data.')
@@ -176,9 +184,11 @@ def main():
             logging.warning('Applying correction to b-vectors.')
             logging.info('Transform is: \n{0}.'.format(best_t))
             bvecs = np.dot(bvecs, best_t)
+            # If the data strides were correct, save the bvecs now
             if correct:
                 np.savetxt(args.out_bvec, bvecs.T, "%.8f")
 
+    # Apply the permutation and sign flip to the bvecs and save them
     if args.in_bvec and not correct:
         if not args.validate_bvec:
             _, bvecs = read_bvals_bvecs(None, args.in_bvec)

From 4d1289004907b843519d840e784fd9582068dfa3 Mon Sep 17 00:00:00 2001
From: Philippe Karan <philippe.karan@usherbrooke.ca>
Date: Thu, 9 Oct 2025 12:46:18 -0400
Subject: [PATCH 13/15] Address some comments part 1

---
 .../scil_volume_validate_correct_strides.py   | 21 +++++++++++--------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/src/scilpy/cli/scil_volume_validate_correct_strides.py b/src/scilpy/cli/scil_volume_validate_correct_strides.py
index a3b95a0b0..733fb9c39 100644
--- a/src/scilpy/cli/scil_volume_validate_correct_strides.py
+++ b/src/scilpy/cli/scil_volume_validate_correct_strides.py
@@ -104,11 +104,11 @@ def main():
     strides = (strides[:, 0] + 1) * strides[:, 1]
     # Check if the strides are correct ([1, 2, 3])
     if np.array_equal(strides, [1, 2, 3]):
-        correct=True
+        is_stride_correct=True
         logging.warning('Input data already has the correct strides [1, 2, 3].'
                         ' No correction on data needed and outputed.')
     else:
-        correct=False
+        is_stride_correct=False
         logging.warning('Input data has strides {}. '
                         'Correcting to [1, 2, 3].'.format(strides))
         # Compute the required transform to get to [1, 2, 3]
@@ -183,18 +183,21 @@ def main():
         else:
             logging.warning('Applying correction to b-vectors.')
             logging.info('Transform is: \n{0}.'.format(best_t))
-            bvecs = np.dot(bvecs, best_t)
+            valid_bvecs = np.dot(bvecs, best_t)
             # If the data strides were correct, save the bvecs now
-            if correct:
-                np.savetxt(args.out_bvec, bvecs.T, "%.8f")
+            if is_stride_correct:
+                np.savetxt(args.out_bvec, valid_bvecs.T, "%.8f")
 
     # Apply the permutation and sign flip to the bvecs and save them
-    if args.in_bvec and not correct:
+    if args.in_bvec and not is_stride_correct:
         if not args.validate_bvec:
             _, bvecs = read_bvals_bvecs(None, args.in_bvec)
-        bvecs = flip_gradient_sampling(bvecs.T, axes_to_flip, 'fsl')
-        bvecs = swap_gradient_axis(bvecs, swapped_order, 'fsl')
-        np.savetxt(args.out_bvec, bvecs, "%.8f")
+        else:
+            bvecs = valid_bvecs
+        flipped_bvecs = flip_gradient_sampling(bvecs.T, axes_to_flip, 'fsl')
+        swapped_flipped_bvecs = swap_gradient_axis(flipped_bvecs,
+                                                   swapped_order, 'fsl')
+        np.savetxt(args.out_bvec, swapped_flipped_bvecs, "%.8f")
 
 
 if __name__ == "__main__":

From 56194b93ef4104897577d7d3e7c73ed8b1340620 Mon Sep 17 00:00:00 2001
From: Philippe Karan <philippe.karan@usherbrooke.ca>
Date: Thu, 9 Oct 2025 14:22:04 -0400
Subject: [PATCH 14/15] Adding function for flip/swap format

---
 src/scilpy/cli/scil_gradients_modify_axes.py  | 19 +++--------
 .../scil_volume_validate_correct_strides.py   | 27 ++++++---------
 src/scilpy/gradients/bvec_bval_tools.py       | 34 ++++++++++++++++++-
 .../gradients/tests/test_bvec_bval_tools.py   | 15 +++++---
 4 files changed, 60 insertions(+), 35 deletions(-)

diff --git a/src/scilpy/cli/scil_gradients_modify_axes.py b/src/scilpy/cli/scil_gradients_modify_axes.py
index a34acf715..8ccc93b2d 100755
--- a/src/scilpy/cli/scil_gradients_modify_axes.py
+++ b/src/scilpy/cli/scil_gradients_modify_axes.py
@@ -12,7 +12,8 @@
 
 import numpy as np
 
-from scilpy.gradients.bvec_bval_tools import (flip_gradient_sampling,
+from scilpy.gradients.bvec_bval_tools import (find_flip_swap_from_order,
+                                              flip_gradient_axis,
                                               swap_gradient_axis)
 from scilpy.io.utils import (add_overwrite_arg, assert_inputs_exist,
                              assert_outputs_exist, add_verbose_arg)
@@ -70,17 +71,7 @@ def main():
                      "input's. We do not support conversion in this script.")
 
     # Format final order
-    # Our scripts use axes as 0, 1, 2 rather than 1, 2, 3: adding -1.
-    axes_to_flip = []
-    swapped_order = []
-    for next_axis in args.final_order:
-        if next_axis in [1, 2, 3]:
-            swapped_order.append(next_axis - 1)
-        elif next_axis in [-1, -2, -3]:
-            axes_to_flip.append(abs(next_axis) - 1)
-            swapped_order.append(abs(next_axis) - 1)
-        else:
-            parser.error("Sorry, final order not understood.")
+    axes_to_flip, swapped_order = find_flip_swap_from_order(args.final_order)
 
     # Verifying that user did not ask for, ex, -xxy
     if len(np.unique(swapped_order)) != 3:
@@ -95,7 +86,7 @@ def main():
             parser.error("b-vectors format for a .b file should be FSL, "
                          "and contain 3 lines (x, y, z), but got {}"
                          .format(bvecs.shape[0]))
-        bvecs = flip_gradient_sampling(bvecs, axes_to_flip, 'fsl')
+        bvecs = flip_gradient_axis(bvecs, axes_to_flip, 'fsl')
         bvecs = swap_gradient_axis(bvecs, swapped_order, 'fsl')
         np.savetxt(args.out_gradient_sampling_file, bvecs, "%.8f")
     else:  # ext == '.b':
@@ -104,7 +95,7 @@ def main():
             parser.error("b-vectors format for a .b file should be mrtrix, "
                          "and contain 4 columns (x, y, z, bval), but got {}"
                          .format(bvecs.shape[1]))
-        bvecs = flip_gradient_sampling(bvecs, axes_to_flip, 'mrtrix')
+        bvecs = flip_gradient_axis(bvecs, axes_to_flip, 'mrtrix')
         bvecs = swap_gradient_axis(bvecs, swapped_order, 'mrtrix')
         np.savetxt(args.out_gradient_sampling_file, bvecs,
                    "%.8f %.8f %.8f %0.6f")
diff --git a/src/scilpy/cli/scil_volume_validate_correct_strides.py b/src/scilpy/cli/scil_volume_validate_correct_strides.py
index 733fb9c39..b8a571d16 100644
--- a/src/scilpy/cli/scil_volume_validate_correct_strides.py
+++ b/src/scilpy/cli/scil_volume_validate_correct_strides.py
@@ -37,7 +37,8 @@
 import nibabel as nib
 
 from scilpy.gradients.bvec_bval_tools import (check_b0_threshold,
-                                              flip_gradient_sampling,
+                                              find_flip_swap_from_order,
+                                              flip_gradient_axis,
                                               is_normalized_bvecs,
                                               normalize_bvecs,
                                               swap_gradient_axis)
@@ -104,11 +105,11 @@ def main():
     strides = (strides[:, 0] + 1) * strides[:, 1]
     # Check if the strides are correct ([1, 2, 3])
     if np.array_equal(strides, [1, 2, 3]):
-        is_stride_correct=True
+        is_stride_correct = True
         logging.warning('Input data already has the correct strides [1, 2, 3].'
                         ' No correction on data needed and outputed.')
     else:
-        is_stride_correct=False
+        is_stride_correct = False
         logging.warning('Input data has strides {}. '
                         'Correcting to [1, 2, 3].'.format(strides))
         # Compute the required transform to get to [1, 2, 3]
@@ -121,16 +122,9 @@ def main():
             # Set the transform for this axis
             transform[axis] = sign * (i + 1)
 
-        axes_to_flip = []
-        swapped_order = []
         # Write the transform in a format compatible with the
-        # flip_gradient_sampling and swap_gradient_axis functions (for bvecs)
-        for next_axis in transform:
-            if next_axis in [1, 2, 3]:
-                swapped_order.append(next_axis - 1)
-            elif next_axis in [-1, -2, -3]:
-                axes_to_flip.append(abs(next_axis) - 1)
-                swapped_order.append(abs(next_axis) - 1)
+        # flip_gradient_axis and swap_gradient_axis functions (for bvecs)
+        axes_to_flip, swapped_order = find_flip_swap_from_order(transform)
 
         # Write the transform in a format compatible with the nibabel
         # as_reoriented function (for image)
@@ -162,11 +156,11 @@ def main():
         # Generate a mask to avoid fitting tensor on the whole image
         mask = np.zeros(data.shape[:3], dtype=bool)
         # Use a small cubic ROI at the center of the volume
-        interval_i = slice(data.shape[0]//2,
+        interval_i = slice(data.shape[0]//2 - data.shape[0]//4,
                            data.shape[0]//2 + data.shape[0]//4)
-        interval_j = slice(data.shape[1]//2,
+        interval_j = slice(data.shape[1]//2 - data.shape[1]//4,
                            data.shape[1]//2 + data.shape[1]//4)
-        interval_k = slice(data.shape[2]//2,
+        interval_k = slice(data.shape[2]//2 - data.shape[2]//4,
                            data.shape[2]//2 + data.shape[2]//4)
         mask[interval_i, interval_j, interval_k] = 1
         # Compute the necessary DTI metrics to compute the coherence of bvecs
@@ -180,6 +174,7 @@ def main():
         best_t = transform[np.argmax(coherence)]
         if (best_t == np.eye(3)).all():
             logging.info('The b-vectors are aligned with the original data.')
+            valid_bvecs = bvecs
         else:
             logging.warning('Applying correction to b-vectors.')
             logging.info('Transform is: \n{0}.'.format(best_t))
@@ -194,7 +189,7 @@ def main():
             _, bvecs = read_bvals_bvecs(None, args.in_bvec)
         else:
             bvecs = valid_bvecs
-        flipped_bvecs = flip_gradient_sampling(bvecs.T, axes_to_flip, 'fsl')
+        flipped_bvecs = flip_gradient_axis(bvecs.T, axes_to_flip, 'fsl')
         swapped_flipped_bvecs = swap_gradient_axis(flipped_bvecs,
                                                    swapped_order, 'fsl')
         np.savetxt(args.out_bvec, swapped_flipped_bvecs, "%.8f")
diff --git a/src/scilpy/gradients/bvec_bval_tools.py b/src/scilpy/gradients/bvec_bval_tools.py
index ba99c3e3a..ec8014d94 100644
--- a/src/scilpy/gradients/bvec_bval_tools.py
+++ b/src/scilpy/gradients/bvec_bval_tools.py
@@ -228,7 +228,39 @@ def str_to_axis_index(axis):
     return None
 
 
-def flip_gradient_sampling(bvecs, axes, sampling_type):
+def find_flip_swap_from_order(order):
+    """
+    Find the flip and swap necessary to get the bvecs to the given order. This
+    assumes the original order of the bvecs is 1,2,3.
+
+    Parameters
+    ----------
+    order: list of int
+        List of axes to flip and swap.
+        Ex: to only flip y: [1, -2, 3]
+        Ex: to only swap x and y: [2, 1, 3]
+        Ex: to first flip x, then permute all three axes: [3, -1, 2]
+
+    Returns
+    -------
+    axes_to_flip: list of int
+        List of axes to flip (e.g. [0, 1]).
+    swapped_order: list of int
+        List of axes in the given order (e.g. [1, 0, 2]).
+    """
+    # Our scripts use axes as 0, 1, 2 rather than 1, 2, 3: adding -1.
+    axes_to_flip = []
+    swapped_order = []
+    for next_axis in order:
+        if next_axis in [1, 2, 3]:
+            swapped_order.append(next_axis - 1)
+        elif next_axis in [-1, -2, -3]:
+            axes_to_flip.append(abs(next_axis) - 1)
+            swapped_order.append(abs(next_axis) - 1)
+    return(axes_to_flip, swapped_order)
+
+
+def flip_gradient_axis(bvecs, axes, sampling_type):
     """
     Flip bvecs on chosen axis.
 
diff --git a/src/scilpy/gradients/tests/test_bvec_bval_tools.py b/src/scilpy/gradients/tests/test_bvec_bval_tools.py
index 4085dd5d3..f119411be 100644
--- a/src/scilpy/gradients/tests/test_bvec_bval_tools.py
+++ b/src/scilpy/gradients/tests/test_bvec_bval_tools.py
@@ -3,8 +3,8 @@
 
 from scilpy.gradients.bvec_bval_tools import (
     check_b0_threshold, identify_shells, is_normalized_bvecs,
-    flip_gradient_sampling, normalize_bvecs, round_bvals_to_shell,
-    str_to_axis_index, swap_gradient_axis)
+    flip_gradient_axis, find_flip_swap_from_order, normalize_bvecs,
+    round_bvals_to_shell, str_to_axis_index, swap_gradient_axis)
 
 bvecs = np.asarray([[1.0, 1.0, 1.0],
                     [1.0, 0.0, 1.0],
@@ -79,9 +79,16 @@ def test_str_to_axis_index():
     assert str_to_axis_index('v') is None
 
 
-def test_flip_gradient_sampling():
+def test_find_flip_swap_from_order():
+    order = [1, -3, -2]
+    axes_to_flip, swapped_order = find_flip_swap_from_order(order)
+    assert np.array_equal(axes_to_flip, [2, 1])
+    assert np.array_equal(swapped_order, [0, 2, 1])
+
+
+def test_flip_gradient_axis():
     fsl_bvecs = bvecs.T
-    b = flip_gradient_sampling(fsl_bvecs, axes=[0], sampling_type='fsl')
+    b = flip_gradient_axis(fsl_bvecs, axes=[0], sampling_type='fsl')
     assert np.array_equal(b, np.asarray([[-1.0, 1.0, 1.0],
                                          [-1.0, 0.0, 1.0],
                                          [-0.0, 1.0, 0.0],

From d29c07e5158d5bcff47c8b8516e509eadc3da77f Mon Sep 17 00:00:00 2001
From: Philippe Karan <philippe.karan@usherbrooke.ca>
Date: Thu, 9 Oct 2025 14:36:07 -0400
Subject: [PATCH 15/15] Adding other functions

---
 .../scil_volume_validate_correct_strides.py   | 26 +++------
 src/scilpy/image/utils.py                     | 54 +++++++++++++++++++
 2 files changed, 60 insertions(+), 20 deletions(-)

diff --git a/src/scilpy/cli/scil_volume_validate_correct_strides.py b/src/scilpy/cli/scil_volume_validate_correct_strides.py
index b8a571d16..5efd2469d 100644
--- a/src/scilpy/cli/scil_volume_validate_correct_strides.py
+++ b/src/scilpy/cli/scil_volume_validate_correct_strides.py
@@ -42,6 +42,7 @@
                                               is_normalized_bvecs,
                                               normalize_bvecs,
                                               swap_gradient_axis)
+from scilpy.image.utils import verify_strides, find_strides_transform
 from scilpy.io.utils import (add_b0_thresh_arg, add_overwrite_arg,
                              add_skip_b0_check_arg, assert_inputs_exist,
                              assert_outputs_exist, add_verbose_arg)
@@ -101,26 +102,10 @@ def main():
 
     # Get the current strides
     img = nib.load(args.in_data)
-    strides = nib.io_orientation(img.affine).astype(np.int8)
-    strides = (strides[:, 0] + 1) * strides[:, 1]
-    # Check if the strides are correct ([1, 2, 3])
-    if np.array_equal(strides, [1, 2, 3]):
-        is_stride_correct = True
-        logging.warning('Input data already has the correct strides [1, 2, 3].'
-                        ' No correction on data needed and outputed.')
-    else:
-        is_stride_correct = False
-        logging.warning('Input data has strides {}. '
-                        'Correcting to [1, 2, 3].'.format(strides))
+    strides, is_stride_correct = verify_strides(img)
+    if not is_stride_correct:
         # Compute the required transform to get to [1, 2, 3]
-        n = len(strides)
-        transform = [0]*n
-        for i, m in enumerate(strides):
-            # Get the axis (0, 1, 2) and the sign of the current stride
-            axis = abs(m) - 1
-            sign = 1 if m > 0 else -1
-            # Set the transform for this axis
-            transform[axis] = sign * (i + 1)
+        transform = find_strides_transform(strides)
 
         # Write the transform in a format compatible with the
         # flip_gradient_axis and swap_gradient_axis functions (for bvecs)
@@ -129,7 +114,8 @@ def main():
         # Write the transform in a format compatible with the nibabel
         # as_reoriented function (for image)
         ornt = np.column_stack((np.array(swapped_order, dtype=np.int8),
-                                np.where(np.isin(range(n), axes_to_flip),
+                                np.where(np.isin(range(len(strides)),
+                                                 axes_to_flip),
                                          -1, 1)))
         # Apply the transform to the image and save it
         new_img = img.as_reoriented(ornt)
diff --git a/src/scilpy/image/utils.py b/src/scilpy/image/utils.py
index d05a87280..3400fb57a 100644
--- a/src/scilpy/image/utils.py
+++ b/src/scilpy/image/utils.py
@@ -74,6 +74,60 @@ def extract_affine(input_files):
             return vol.affine
 
 
+def verify_strides(vol_img):
+    """Verify if the strides of the given volume are [1, 2, 3].
+
+    Parameters
+    ----------
+    vol_img : nib.Nifti1Image
+        Volume image.
+
+    Returns
+    -------
+    strides : np.array
+        Current strides of the volume.
+    is_stride_correct : bool
+        True if the strides are [1, 2, 3], false otherwise.
+    """
+    strides = nib.io_orientation(vol_img.affine).astype(np.int8)
+    strides = (strides[:, 0] + 1) * strides[:, 1]
+    # Check if the strides are correct ([1, 2, 3])
+    if np.array_equal(strides, [1, 2, 3]):
+        is_stride_correct = True
+        logging.warning('Input data already has the correct strides [1, 2, 3].'
+                        ' No correction on data needed and outputed.')
+    else:
+        is_stride_correct = False
+        logging.warning('Input data has strides {}. '
+                        'Correcting to [1, 2, 3].'.format(strides))
+    return strides, is_stride_correct
+
+
+def find_strides_transform(strides):
+    """Find the transform required to get to [1, 2, 3] from the current
+    strides.
+
+    Parameters
+    ----------
+    strides : np.array
+        Current strides of the volume.
+
+    Returns
+    -------
+    transform : list of int
+        Transform to apply to get to [1, 2, 3].
+    """
+    n = len(strides)
+    transform = [0]*n
+    for i, m in enumerate(strides):
+        # Get the axis (0, 1, 2) and the sign of the current stride
+        axis = abs(m) - 1
+        sign = 1 if m > 0 else -1
+        # Set the transform for this axis
+        transform[axis] = sign * (i + 1)
+    return transform
+
+
 def check_slice_indices(vol_img, axis_name, slice_ids):
     """Check that the given volume can be sliced at the given slice indices
     along the requested axis.