From 80650446bda3c2cc707629309dba508b7e536021 Mon Sep 17 00:00:00 2001
From: Gabriel Girard <girard.gabriel@gmail.com>
Date: Tue, 3 Dec 2024 14:51:45 -0500
Subject: [PATCH 1/9] NF - added input options for multiple ROI masks

---
 scripts/scil_volume_stats_in_ROI.py | 103 ++++++++++++++--------------
 1 file changed, 52 insertions(+), 51 deletions(-)

diff --git a/scripts/scil_volume_stats_in_ROI.py b/scripts/scil_volume_stats_in_ROI.py
index 831373fdc..86b311a87 100755
--- a/scripts/scil_volume_stats_in_ROI.py
+++ b/scripts/scil_volume_stats_in_ROI.py
@@ -33,9 +33,9 @@ def _build_arg_parser():
     p = argparse.ArgumentParser(description=__doc__,
                                 formatter_class=argparse.RawTextHelpFormatter)
 
-    p.add_argument('in_mask',
-                   help='Mask volume filename.\nCan be a binary mask or a '
-                        'weighted mask.')
+    p.add_argument('in_masks', nargs='+',
+                   help='Mask volume filenames.\nCan be binary masks or '
+                        'weighted masks.')
 
     g = p.add_argument_group('Metrics input options')
     gg = g.add_mutually_exclusive_group(required=True)
@@ -74,59 +74,60 @@ def main():
         if not os.path.exists(args.metrics_dir):
             parser.error("Metrics directory does not exist: {}"
                          .format(args.metrics_dir))
-        assert_inputs_exist(parser, args.in_mask)
+        assert_inputs_exist(parser, args.in_masks)
 
         tmp_file_list = glob.glob(os.path.join(args.metrics_dir, '*nii.gz'))
         args.metrics_file_list = [os.path.join(args.metrics_dir, f)
                                   for f in tmp_file_list]
     else:
-        assert_inputs_exist(parser, [args.in_mask] + args.metrics_file_list)
-    assert_headers_compatible(parser,
-                              [args.in_mask] + args.metrics_file_list)
-
-    # Loading
-    mask_data = nib.load(args.in_mask).get_fdata(dtype=np.float32)
-    if len(mask_data.shape) > 3:
-        parser.error('Mask should be a 3D image.')
-    if np.min(mask_data) < 0:
-        parser.error('Mask should not contain negative values.')
-    roi_name = split_name_with_nii(os.path.basename(args.in_mask))[0]
-
-    # Discussion about the way the normalization is done.
-    # https://github.com/scilus/scilpy/pull/202#discussion_r411355609
-    # Summary:
-    # 1) We don't want to normalize with data = (data-min) / (max-min) because
-    # it zeroes out the minimal values of the array. This is not a large error
-    # source, but not preferable.
-    # 2) data = data / max(data) or data = data / sum(data): in practice, when
-    # we use them in numpy using their weights argument, leads to the same
-    # result.
-    if args.normalize_weights:
-        mask_data /= np.max(mask_data)
-    elif args.bin:
-        mask_data[np.where(mask_data > 0.0)] = 1.0
-    elif np.min(mask_data) < 0.0 or np.max(mask_data) > 1.0:
-        parser.error('Mask data should only contain values between 0 and 1. '
-                     'Try --normalize_weights.')
-
-    # Load and process all metrics files.
-    json_stats = {roi_name: {}}
-    for f in args.metrics_file_list:
-        metric_img = nib.load(f)
-        metric_name = split_name_with_nii(os.path.basename(f))[0]
-        if len(metric_img.shape) == 3:
-            data = metric_img.get_fdata(dtype=np.float64)
-            if np.any(np.isnan(data)):
-                logging.warning("Metric '{}' contains some NaN. Ignoring "
-                                "voxels with NaN."
-                                .format(os.path.basename(f)))
-            mean, std = weighted_mean_std(mask_data, data)
-            json_stats[roi_name][metric_name] = {'mean': mean,
-                                                 'std': std}
-        else:
-            parser.error(
-                'Metric {} is not a 3D image ({}D shape).'
-                .format(f, len(metric_img.shape)))
+        assert_inputs_exist(parser, args.in_masks + args.metrics_file_list)
+    assert_headers_compatible(parser, args.in_masks + args.metrics_file_list)
+
+    # Computing stats for all masks and metrics files
+    json_stats = {}
+    for mask_filename in args.in_masks:
+        mask_data = nib.load(mask_filename).get_fdata(dtype=np.float32)
+        if len(mask_data.shape) > 3:
+            parser.error('Mask should be a 3D image.')
+        if np.min(mask_data) < 0:
+            parser.error('Mask should not contain negative values.')
+        roi_name = split_name_with_nii(os.path.basename(mask_filename))[0]
+
+        # Discussion about the way the normalization is done.
+        # https://github.com/scilus/scilpy/pull/202#discussion_r411355609
+        # Summary:
+        # 1) We don't want to normalize with data = (data-min) / (max-min) because
+        # it zeroes out the minimal values of the array. This is not a large error
+        # source, but not preferable.
+        # 2) data = data / max(data) or data = data / sum(data): in practice, when
+        # we use them in numpy using their weights argument, leads to the same
+        # result.
+        if args.normalize_weights:
+            mask_data /= np.max(mask_data)
+        elif args.bin:
+            mask_data[np.where(mask_data > 0.0)] = 1.0
+        elif np.min(mask_data) < 0.0 or np.max(mask_data) > 1.0:
+            parser.error('Mask data should only contain values between 0 and 1. '
+                        'Try --normalize_weights.')
+
+        # Load and process all metrics files.
+        json_stats[roi_name] = {}
+        for f in args.metrics_file_list:
+            metric_img = nib.load(f)
+            metric_name = split_name_with_nii(os.path.basename(f))[0]
+            if len(metric_img.shape) == 3:
+                data = metric_img.get_fdata(dtype=np.float64)
+                if np.any(np.isnan(data)):
+                    logging.warning("Metric '{}' contains some NaN. Ignoring "
+                                    "voxels with NaN."
+                                    .format(os.path.basename(f)))
+                mean, std = weighted_mean_std(mask_data, data)
+                json_stats[roi_name][metric_name] = {'mean': mean,
+                                                    'std': std}
+            else:
+                parser.error(
+                    'Metric {} is not a 3D image ({}D shape).'
+                    .format(f, len(metric_img.shape)))
 
     # Print results
     print(json.dumps(json_stats, indent=args.indent, sort_keys=args.sort_keys))

From 9846bd27bb6b55471eca50e0e3daac5b67f43ffb Mon Sep 17 00:00:00 2001
From: Gabriel Girard <girard.gabriel@gmail.com>
Date: Tue, 3 Dec 2024 15:44:53 -0500
Subject: [PATCH 2/9] RF - removed the roi dict if a single ROI is used

---
 scripts/scil_volume_stats_in_ROI.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/scripts/scil_volume_stats_in_ROI.py b/scripts/scil_volume_stats_in_ROI.py
index 86b311a87..da5257a2b 100755
--- a/scripts/scil_volume_stats_in_ROI.py
+++ b/scripts/scil_volume_stats_in_ROI.py
@@ -129,6 +129,9 @@ def main():
                     'Metric {} is not a 3D image ({}D shape).'
                     .format(f, len(metric_img.shape)))
 
+
+    if len(args.in_masks) == 1:
+        json_stats = json_stats[roi_name]
     # Print results
     print(json.dumps(json_stats, indent=args.indent, sort_keys=args.sort_keys))
 

From 1857abd85ebd5ac6ce1fbc9d6c8d33d4edf32459 Mon Sep 17 00:00:00 2001
From: Gabriel Girard <girard.gabriel@gmail.com>
Date: Tue, 3 Dec 2024 15:45:24 -0500
Subject: [PATCH 3/9] NF - allow for multiple metrics input

---
 scripts/scil_volume_stats_in_labels.py | 54 ++++++++++++++++++++------
 1 file changed, 43 insertions(+), 11 deletions(-)

diff --git a/scripts/scil_volume_stats_in_labels.py b/scripts/scil_volume_stats_in_labels.py
index 07fc290b7..57211b170 100755
--- a/scripts/scil_volume_stats_in_labels.py
+++ b/scripts/scil_volume_stats_in_labels.py
@@ -11,8 +11,10 @@
 """
 
 import argparse
+import glob
 import json
 import logging
+import os
 
 import nibabel as nib
 import numpy as np
@@ -20,6 +22,7 @@
 from scilpy.image.labels import get_data_as_labels, get_stats_in_label
 from scilpy.io.utils import (add_overwrite_arg, add_verbose_arg,
                              assert_inputs_exist, assert_headers_compatible)
+from scilpy.utils.filenames import split_name_with_nii
 
 
 def _build_arg_parser():
@@ -30,8 +33,16 @@ def _build_arg_parser():
     p.add_argument('in_labels_lut',
                    help='Path of the LUT file corresponding to labels,'
                         'used to name the regions of interest.')
-    p.add_argument('in_map',
-                   help='Path of the input map file. Expecting a 3D file.')
+
+    g = p.add_argument_group('Metrics input options')
+    gg = g.add_mutually_exclusive_group(required=True)
+    gg.add_argument('--metrics_dir', metavar='dir',
+                    help='Name of the directory containing metrics files: '
+                         'we will \nload all nifti files.')
+    gg.add_argument('--metrics', dest='metrics_file_list', nargs='+',
+                    metavar='file',
+                    help='Metrics nifti filename. List of the names of the '
+                         'metrics file, \nin nifti format.')
 
     add_verbose_arg(p)
     add_overwrite_arg(p)
@@ -45,21 +56,42 @@ def main():
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
     # Verifications
-    assert_inputs_exist(parser,
-                        [args.in_labels, args.in_map, args.in_labels_lut])
-    assert_headers_compatible(parser, [args.in_labels, args.in_map])
+
+    # Get input list. Either all files in dir or given list.
+    if args.metrics_dir:
+        if not os.path.exists(args.metrics_dir):
+            parser.error("Metrics directory does not exist: {}"
+                         .format(args.metrics_dir))
+        assert_inputs_exist(parser, [args.in_labels, args.in_labels_lut])
+
+        tmp_file_list = glob.glob(os.path.join(args.metrics_dir, '*nii.gz'))
+        args.metrics_file_list = [os.path.join(args.metrics_dir, f)
+                                  for f in tmp_file_list]
+    else:
+        assert_inputs_exist(parser, [args.in_labels] + args.metrics_file_list)
+    assert_headers_compatible(parser, [args.in_labels] + args.metrics_file_list)
+
 
     # Loading
     label_data = get_data_as_labels(nib.load(args.in_labels))
     with open(args.in_labels_lut) as f:
         label_dict = json.load(f)
-    map_data = nib.load(args.in_map).get_fdata(dtype=np.float32)
-    if len(map_data.shape) > 3:
-        parser.error('Mask should be a 3D image.')
 
-    # Process
-    out_dict = get_stats_in_label(map_data, label_data, label_dict)
-    print(json.dumps(out_dict))
+    # Computing stats for all metrics files
+    json_stats = {}
+    for metric_filename in args.metrics_file_list:
+        metric_data = nib.load(metric_filename).get_fdata(dtype=np.float32)
+        metric_name = split_name_with_nii(os.path.basename(metric_filename))[0]
+        if len(metric_data.shape) > 3:
+            parser.error('Mask should be a 3D image.')
+
+        # Process
+        out_dict = get_stats_in_label(metric_data, label_data, label_dict)
+        json_stats[metric_name] = out_dict
+    
+    if len(args.metrics_file_list) == 1:
+        json_stats = json_stats[metric_name]
+    print(json.dumps(json_stats))
 
 
 if __name__ == "__main__":

From 4ac43ea42b920876f2fa437d76421f02489c5f11 Mon Sep 17 00:00:00 2001
From: Gabriel Girard <girard.gabriel@gmail.com>
Date: Tue, 3 Dec 2024 15:55:27 -0500
Subject: [PATCH 4/9] RF - change variable names from mask to roi

---
 scripts/scil_volume_stats_in_ROI.py | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/scripts/scil_volume_stats_in_ROI.py b/scripts/scil_volume_stats_in_ROI.py
index da5257a2b..e6ce2363c 100755
--- a/scripts/scil_volume_stats_in_ROI.py
+++ b/scripts/scil_volume_stats_in_ROI.py
@@ -33,7 +33,7 @@ def _build_arg_parser():
     p = argparse.ArgumentParser(description=__doc__,
                                 formatter_class=argparse.RawTextHelpFormatter)
 
-    p.add_argument('in_masks', nargs='+',
+    p.add_argument('in_rois', nargs='+',
                    help='Mask volume filenames.\nCan be binary masks or '
                         'weighted masks.')
 
@@ -74,24 +74,24 @@ def main():
         if not os.path.exists(args.metrics_dir):
             parser.error("Metrics directory does not exist: {}"
                          .format(args.metrics_dir))
-        assert_inputs_exist(parser, args.in_masks)
+        assert_inputs_exist(parser, args.in_rois)
 
         tmp_file_list = glob.glob(os.path.join(args.metrics_dir, '*nii.gz'))
         args.metrics_file_list = [os.path.join(args.metrics_dir, f)
                                   for f in tmp_file_list]
     else:
-        assert_inputs_exist(parser, args.in_masks + args.metrics_file_list)
-    assert_headers_compatible(parser, args.in_masks + args.metrics_file_list)
+        assert_inputs_exist(parser, args.in_rois + args.metrics_file_list)
+    assert_headers_compatible(parser, args.in_rois + args.metrics_file_list)
 
     # Computing stats for all masks and metrics files
     json_stats = {}
-    for mask_filename in args.in_masks:
-        mask_data = nib.load(mask_filename).get_fdata(dtype=np.float32)
-        if len(mask_data.shape) > 3:
+    for roi_filename in args.in_rois:
+        roi_data = nib.load(roi_filename).get_fdata(dtype=np.float32)
+        if len(roi_data.shape) > 3:
             parser.error('Mask should be a 3D image.')
-        if np.min(mask_data) < 0:
+        if np.min(roi_data) < 0:
             parser.error('Mask should not contain negative values.')
-        roi_name = split_name_with_nii(os.path.basename(mask_filename))[0]
+        roi_name = split_name_with_nii(os.path.basename(roi_filename))[0]
 
         # Discussion about the way the normalization is done.
         # https://github.com/scilus/scilpy/pull/202#discussion_r411355609
@@ -103,10 +103,10 @@ def main():
         # we use them in numpy using their weights argument, leads to the same
         # result.
         if args.normalize_weights:
-            mask_data /= np.max(mask_data)
+            roi_data /= np.max(roi_data)
         elif args.bin:
-            mask_data[np.where(mask_data > 0.0)] = 1.0
-        elif np.min(mask_data) < 0.0 or np.max(mask_data) > 1.0:
+            roi_data[np.where(roi_data > 0.0)] = 1.0
+        elif np.min(roi_data) < 0.0 or np.max(roi_data) > 1.0:
             parser.error('Mask data should only contain values between 0 and 1. '
                         'Try --normalize_weights.')
 
@@ -121,7 +121,7 @@ def main():
                     logging.warning("Metric '{}' contains some NaN. Ignoring "
                                     "voxels with NaN."
                                     .format(os.path.basename(f)))
-                mean, std = weighted_mean_std(mask_data, data)
+                mean, std = weighted_mean_std(roi_data, data)
                 json_stats[roi_name][metric_name] = {'mean': mean,
                                                     'std': std}
             else:
@@ -130,7 +130,7 @@ def main():
                     .format(f, len(metric_img.shape)))
 
 
-    if len(args.in_masks) == 1:
+    if len(args.in_rois) == 1:
         json_stats = json_stats[roi_name]
     # Print results
     print(json.dumps(json_stats, indent=args.indent, sort_keys=args.sort_keys))

From c9819927833ce4d81239574764392ea02d26858f Mon Sep 17 00:00:00 2001
From: Gabriel Girard <girard.gabriel@gmail.com>
Date: Tue, 3 Dec 2024 16:01:13 -0500
Subject: [PATCH 5/9] DOC - updated script documentation

---
 scripts/scil_volume_stats_in_ROI.py | 24 +++++++++++++-----------
 1 file changed, 13 insertions(+), 11 deletions(-)

diff --git a/scripts/scil_volume_stats_in_ROI.py b/scripts/scil_volume_stats_in_ROI.py
index e6ce2363c..6f726277e 100755
--- a/scripts/scil_volume_stats_in_ROI.py
+++ b/scripts/scil_volume_stats_in_ROI.py
@@ -3,11 +3,11 @@
 
 """
 Compute the statistics (mean, std) of scalar maps, which can represent
-diffusion metrics, in a ROI. Prints the results.
+diffusion metrics, in ROIs. Prints the results.
 
-The mask can either be a binary mask, or a weighting mask. If the mask is
-a weighting mask it should either contain floats between 0 and 1 or should be
-normalized with --normalize_weights. IMPORTANT: if the mask contains weights
+The ROIs can either be a binary masks, or a weighting masks. If the ROIs are
+ weighting masks it should either contain floats between 0 and 1 or should be
+normalized with --normalize_weights. IMPORTANT: if the ROIs contain weights
 (and not 0 and 1 exclusively), the standard deviation will also be weighted.
 """
 
@@ -34,7 +34,7 @@ def _build_arg_parser():
                                 formatter_class=argparse.RawTextHelpFormatter)
 
     p.add_argument('in_rois', nargs='+',
-                   help='Mask volume filenames.\nCan be binary masks or '
+                   help='ROIs volume filenames.\nCan be binary masks or '
                         'weighted masks.')
 
     g = p.add_argument_group('Metrics input options')
@@ -83,14 +83,15 @@ def main():
         assert_inputs_exist(parser, args.in_rois + args.metrics_file_list)
     assert_headers_compatible(parser, args.in_rois + args.metrics_file_list)
 
-    # Computing stats for all masks and metrics files
+    # Computing stats for all ROIs and metrics files
     json_stats = {}
     for roi_filename in args.in_rois:
         roi_data = nib.load(roi_filename).get_fdata(dtype=np.float32)
         if len(roi_data.shape) > 3:
-            parser.error('Mask should be a 3D image.')
+            parser.error('ROI {} should be a 3D image.'.format(roi_filename))
         if np.min(roi_data) < 0:
-            parser.error('Mask should not contain negative values.')
+            parser.error('ROI {} should not contain negative values.'
+                         .format(roi_filename))
         roi_name = split_name_with_nii(os.path.basename(roi_filename))[0]
 
         # Discussion about the way the normalization is done.
@@ -107,8 +108,9 @@ def main():
         elif args.bin:
             roi_data[np.where(roi_data > 0.0)] = 1.0
         elif np.min(roi_data) < 0.0 or np.max(roi_data) > 1.0:
-            parser.error('Mask data should only contain values between 0 and 1. '
-                        'Try --normalize_weights.')
+            parser.error('ROI {} data should only contain values between 0 and 1. '
+                         'Try --normalize_weights.'
+                         .format(roi_filename))
 
         # Load and process all metrics files.
         json_stats[roi_name] = {}
@@ -129,9 +131,9 @@ def main():
                     'Metric {} is not a 3D image ({}D shape).'
                     .format(f, len(metric_img.shape)))
 
-
     if len(args.in_rois) == 1:
         json_stats = json_stats[roi_name]
+
     # Print results
     print(json.dumps(json_stats, indent=args.indent, sort_keys=args.sort_keys))
 

From 992be21fda532e4c136c3ed1305ff1942f912751 Mon Sep 17 00:00:00 2001
From: Gabriel Girard <girard.gabriel@gmail.com>
Date: Tue, 3 Dec 2024 16:05:30 -0500
Subject: [PATCH 6/9] TST - updated tests, pep8

---
 scripts/scil_volume_stats_in_ROI.py          | 2 +-
 scripts/scil_volume_stats_in_labels.py       | 3 +--
 scripts/tests/test_volume_stats_in_ROI.py    | 4 ++--
 scripts/tests/test_volume_stats_in_labels.py | 2 +-
 4 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/scripts/scil_volume_stats_in_ROI.py b/scripts/scil_volume_stats_in_ROI.py
index 6f726277e..9fc6002bf 100755
--- a/scripts/scil_volume_stats_in_ROI.py
+++ b/scripts/scil_volume_stats_in_ROI.py
@@ -125,7 +125,7 @@ def main():
                                     .format(os.path.basename(f)))
                 mean, std = weighted_mean_std(roi_data, data)
                 json_stats[roi_name][metric_name] = {'mean': mean,
-                                                    'std': std}
+                                                     'std': std}
             else:
                 parser.error(
                     'Metric {} is not a 3D image ({}D shape).'
diff --git a/scripts/scil_volume_stats_in_labels.py b/scripts/scil_volume_stats_in_labels.py
index 57211b170..35d5c6c16 100755
--- a/scripts/scil_volume_stats_in_labels.py
+++ b/scripts/scil_volume_stats_in_labels.py
@@ -71,7 +71,6 @@ def main():
         assert_inputs_exist(parser, [args.in_labels] + args.metrics_file_list)
     assert_headers_compatible(parser, [args.in_labels] + args.metrics_file_list)
 
-
     # Loading
     label_data = get_data_as_labels(nib.load(args.in_labels))
     with open(args.in_labels_lut) as f:
@@ -88,7 +87,7 @@ def main():
         # Process
         out_dict = get_stats_in_label(metric_data, label_data, label_dict)
         json_stats[metric_name] = out_dict
-    
+
     if len(args.metrics_file_list) == 1:
         json_stats = json_stats[metric_name]
     print(json.dumps(json_stats))
diff --git a/scripts/tests/test_volume_stats_in_ROI.py b/scripts/tests/test_volume_stats_in_ROI.py
index af3dd29ec..71eb2bc8d 100644
--- a/scripts/tests/test_volume_stats_in_ROI.py
+++ b/scripts/tests/test_volume_stats_in_ROI.py
@@ -19,10 +19,10 @@ def test_help_option(script_runner):
 
 def test_execution_tractometry(script_runner, monkeypatch):
     monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
-    in_mask = os.path.join(SCILPY_HOME, 'tractometry',
+    in_roi = os.path.join(SCILPY_HOME, 'tractometry',
                            'IFGWM.nii.gz')
     in_ref = os.path.join(SCILPY_HOME, 'tractometry',
                           'mni_masked.nii.gz')
     ret = script_runner.run('scil_volume_stats_in_ROI.py',
-                            in_mask, '--metrics', in_ref)
+                            in_roi, '--metrics', in_ref)
     assert ret.success
diff --git a/scripts/tests/test_volume_stats_in_labels.py b/scripts/tests/test_volume_stats_in_labels.py
index 83bd07b8f..df1ea8064 100644
--- a/scripts/tests/test_volume_stats_in_labels.py
+++ b/scripts/tests/test_volume_stats_in_labels.py
@@ -21,5 +21,5 @@ def test_execution(script_runner, monkeypatch):
     in_atlas = os.path.join(SCILPY_HOME, 'plot', 'atlas_brainnetome.nii.gz')
     atlas_lut = os.path.join(SCILPY_HOME, 'plot', 'atlas_brainnetome.json')
     ret = script_runner.run('scil_volume_stats_in_labels.py',
-                            in_atlas, atlas_lut, in_map)
+                            in_atlas, atlas_lut, "--metrics", in_map)
     assert ret.success

From 78def7a691706ba0632dfe7721fdf5a81debaa6a Mon Sep 17 00:00:00 2001
From: Gabriel Girard <girard.gabriel@gmail.com>
Date: Tue, 3 Dec 2024 16:15:53 -0500
Subject: [PATCH 7/9] NF - added add_json_args to the arguments, format the
 output json

---
 scripts/scil_volume_stats_in_ROI.py    | 16 ++++++++--------
 scripts/scil_volume_stats_in_labels.py |  9 +++++----
 2 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/scripts/scil_volume_stats_in_ROI.py b/scripts/scil_volume_stats_in_ROI.py
index 9fc6002bf..4382a4a9c 100755
--- a/scripts/scil_volume_stats_in_ROI.py
+++ b/scripts/scil_volume_stats_in_ROI.py
@@ -97,19 +97,19 @@ def main():
         # Discussion about the way the normalization is done.
         # https://github.com/scilus/scilpy/pull/202#discussion_r411355609
         # Summary:
-        # 1) We don't want to normalize with data = (data-min) / (max-min) because
-        # it zeroes out the minimal values of the array. This is not a large error
-        # source, but not preferable.
-        # 2) data = data / max(data) or data = data / sum(data): in practice, when
-        # we use them in numpy using their weights argument, leads to the same
-        # result.
+        # 1) We don't want to normalize with data = (data-min) / (max-min)
+        # because it zeroes out the minimal values of the array. This is
+        # not a large error source, but not preferable.
+        # 2) data = data / max(data) or data = data / sum(data): in practice,
+        # when we use them in numpy using their weights argument, leads to the
+        # same result.
         if args.normalize_weights:
             roi_data /= np.max(roi_data)
         elif args.bin:
             roi_data[np.where(roi_data > 0.0)] = 1.0
         elif np.min(roi_data) < 0.0 or np.max(roi_data) > 1.0:
-            parser.error('ROI {} data should only contain values between 0 and 1. '
-                         'Try --normalize_weights.'
+            parser.error('ROI {} data should only contain values between 0 '
+                         'and 1. Try --normalize_weights.'
                          .format(roi_filename))
 
         # Load and process all metrics files.
diff --git a/scripts/scil_volume_stats_in_labels.py b/scripts/scil_volume_stats_in_labels.py
index 35d5c6c16..6a311459f 100755
--- a/scripts/scil_volume_stats_in_labels.py
+++ b/scripts/scil_volume_stats_in_labels.py
@@ -20,7 +20,7 @@
 import numpy as np
 
 from scilpy.image.labels import get_data_as_labels, get_stats_in_label
-from scilpy.io.utils import (add_overwrite_arg, add_verbose_arg,
+from scilpy.io.utils import (add_json_args, add_overwrite_arg, add_verbose_arg,
                              assert_inputs_exist, assert_headers_compatible)
 from scilpy.utils.filenames import split_name_with_nii
 
@@ -43,7 +43,7 @@ def _build_arg_parser():
                     metavar='file',
                     help='Metrics nifti filename. List of the names of the '
                          'metrics file, \nin nifti format.')
-
+    add_json_args(p)
     add_verbose_arg(p)
     add_overwrite_arg(p)
 
@@ -69,7 +69,8 @@ def main():
                                   for f in tmp_file_list]
     else:
         assert_inputs_exist(parser, [args.in_labels] + args.metrics_file_list)
-    assert_headers_compatible(parser, [args.in_labels] + args.metrics_file_list)
+    assert_headers_compatible(parser,
+                              [args.in_labels] + args.metrics_file_list)
 
     # Loading
     label_data = get_data_as_labels(nib.load(args.in_labels))
@@ -90,7 +91,7 @@ def main():
 
     if len(args.metrics_file_list) == 1:
         json_stats = json_stats[metric_name]
-    print(json.dumps(json_stats))
+    print(json.dumps(json_stats, indent=args.indent, sort_keys=args.sort_keys))
 
 
 if __name__ == "__main__":

From cc2dc8d2d6230a83f458b88d222262b88b9e6992 Mon Sep 17 00:00:00 2001
From: Gabriel Girard <girard.gabriel@gmail.com>
Date: Thu, 19 Dec 2024 15:50:41 -0500
Subject: [PATCH 8/9] TST - Scripts inputs

---
 scripts/tests/test_volume_stats_in_ROI.py    | 26 +++++++++++++++++++-
 scripts/tests/test_volume_stats_in_labels.py | 19 ++++++++++++--
 2 files changed, 42 insertions(+), 3 deletions(-)

diff --git a/scripts/tests/test_volume_stats_in_ROI.py b/scripts/tests/test_volume_stats_in_ROI.py
index 71eb2bc8d..c03593858 100644
--- a/scripts/tests/test_volume_stats_in_ROI.py
+++ b/scripts/tests/test_volume_stats_in_ROI.py
@@ -20,9 +20,33 @@ def test_help_option(script_runner):
 def test_execution_tractometry(script_runner, monkeypatch):
     monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
     in_roi = os.path.join(SCILPY_HOME, 'tractometry',
-                           'IFGWM.nii.gz')
+                          'IFGWM.nii.gz')
     in_ref = os.path.join(SCILPY_HOME, 'tractometry',
                           'mni_masked.nii.gz')
+
+    # Test with a single ROI input
     ret = script_runner.run('scil_volume_stats_in_ROI.py',
                             in_roi, '--metrics', in_ref)
     assert ret.success
+
+    # Test with multiple ROIs input
+    ret = script_runner.run('scil_volume_stats_in_ROI.py',
+                            in_roi, in_roi, in_roi, '--metrics', in_ref)
+    assert ret.success
+
+    # Test with multiple metric input
+    ret = script_runner.run('scil_volume_stats_in_ROI.py',
+                            in_roi, '--metrics', in_ref, in_ref, in_ref)
+    assert ret.success
+
+    # Test with multiple metric and ROIs input
+    ret = script_runner.run('scil_volume_stats_in_ROI.py',
+                            in_roi, in_roi, '--metrics', in_ref, in_ref)
+    assert ret.success
+
+    # Test with a metric folder
+    metrics_dir = os.path.join(SCILPY_HOME, 'plot')
+    in_roi = os.path.join(SCILPY_HOME, 'plot', 'mask_wm.nii.gz')
+    ret = script_runner.run('scil_volume_stats_in_ROI.py',
+                            in_roi, '--metrics_dir', metrics_dir)
+    assert ret.success
diff --git a/scripts/tests/test_volume_stats_in_labels.py b/scripts/tests/test_volume_stats_in_labels.py
index df1ea8064..4a4471384 100644
--- a/scripts/tests/test_volume_stats_in_labels.py
+++ b/scripts/tests/test_volume_stats_in_labels.py
@@ -17,9 +17,24 @@ def test_help_option(script_runner):
 
 def test_execution(script_runner, monkeypatch):
     monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
-    in_map = os.path.join(SCILPY_HOME, 'plot', 'fa.nii.gz')
+    in_metric = os.path.join(SCILPY_HOME, 'plot', 'fa.nii.gz')
     in_atlas = os.path.join(SCILPY_HOME, 'plot', 'atlas_brainnetome.nii.gz')
     atlas_lut = os.path.join(SCILPY_HOME, 'plot', 'atlas_brainnetome.json')
+
+    # Test with a single metric
+    ret = script_runner.run('scil_volume_stats_in_labels.py',
+                            in_atlas, atlas_lut, "--metrics", in_metric)
+    assert ret.success
+
+    # Test with multiple metrics
+    ret = script_runner.run('scil_volume_stats_in_labels.py',
+                            in_atlas, atlas_lut, "--metrics",
+                            in_metric, in_metric, in_metric)
+    assert ret.success
+
+    # Test with a metric folder
+    metrics_dir = os.path.join(SCILPY_HOME, 'plot')
     ret = script_runner.run('scil_volume_stats_in_labels.py',
-                            in_atlas, atlas_lut, "--metrics", in_map)
+                            in_atlas, atlas_lut, "--metrics_dir",
+                            metrics_dir)
     assert ret.success

From fe35d8e9adb449eb7e7758e9dcb3bca4a51803d7 Mon Sep 17 00:00:00 2001
From: Gabriel Girard <girard.gabriel@gmail.com>
Date: Wed, 8 Jan 2025 11:24:59 -0500
Subject: [PATCH 9/9] BF - fixed errenous path when using metrics_dir

---
 scripts/scil_volume_stats_in_ROI.py    | 4 +---
 scripts/scil_volume_stats_in_labels.py | 4 +---
 2 files changed, 2 insertions(+), 6 deletions(-)

diff --git a/scripts/scil_volume_stats_in_ROI.py b/scripts/scil_volume_stats_in_ROI.py
index 4382a4a9c..88916becf 100755
--- a/scripts/scil_volume_stats_in_ROI.py
+++ b/scripts/scil_volume_stats_in_ROI.py
@@ -76,9 +76,7 @@ def main():
                          .format(args.metrics_dir))
         assert_inputs_exist(parser, args.in_rois)
 
-        tmp_file_list = glob.glob(os.path.join(args.metrics_dir, '*nii.gz'))
-        args.metrics_file_list = [os.path.join(args.metrics_dir, f)
-                                  for f in tmp_file_list]
+        args.metrics_file_list = glob.glob(os.path.join(args.metrics_dir, '*nii.gz'))
     else:
         assert_inputs_exist(parser, args.in_rois + args.metrics_file_list)
     assert_headers_compatible(parser, args.in_rois + args.metrics_file_list)
diff --git a/scripts/scil_volume_stats_in_labels.py b/scripts/scil_volume_stats_in_labels.py
index 6a311459f..05963e5af 100755
--- a/scripts/scil_volume_stats_in_labels.py
+++ b/scripts/scil_volume_stats_in_labels.py
@@ -64,9 +64,7 @@ def main():
                          .format(args.metrics_dir))
         assert_inputs_exist(parser, [args.in_labels, args.in_labels_lut])
 
-        tmp_file_list = glob.glob(os.path.join(args.metrics_dir, '*nii.gz'))
-        args.metrics_file_list = [os.path.join(args.metrics_dir, f)
-                                  for f in tmp_file_list]
+        args.metrics_file_list = glob.glob(os.path.join(args.metrics_dir, '*nii.gz'))
     else:
         assert_inputs_exist(parser, [args.in_labels] + args.metrics_file_list)
     assert_headers_compatible(parser,