From 5424c1638111e870f7b1cee6a4797beada379d2b Mon Sep 17 00:00:00 2001
From: Ashley Stewart <a.stewart.au@gmail.com>
Date: Thu, 17 Oct 2024 14:46:27 -0500
Subject: [PATCH] Critical bug fix + included label.json

---
 MANIFEST.in                |   1 +
 label.json                 | 131 +++++++++++++++++++++++++++++++++++++
 qsm_forward/qsm_forward.py |   2 +-
 setup.py                   |   4 +-
 4 files changed, 136 insertions(+), 2 deletions(-)
 create mode 100644 MANIFEST.in
 create mode 100644 label.json

diff --git a/MANIFEST.in b/MANIFEST.in
new file mode 100644
index 0000000..ecceb50
--- /dev/null
+++ b/MANIFEST.in
@@ -0,0 +1 @@
+include qsm_forward/label.json
\ No newline at end of file
diff --git a/label.json b/label.json
new file mode 100644
index 0000000..c2d1cc3
--- /dev/null
+++ b/label.json
@@ -0,0 +1,131 @@
+[
+    {
+        "name": "Caudate",
+        "label": "1",
+        "voxel_value": 1,
+        "r": 202,
+        "g": 116,
+        "b": 198
+    },
+    {
+        "name": "Globus pallidus",
+        "label": "2",
+        "voxel_value": 2,
+        "r": 145,
+        "g": 167,
+        "b": 62
+    },
+    {
+        "name": "Putamen",
+        "label": "3",
+        "voxel_value": 3,
+        "r": 106,
+        "g": 112,
+        "b": 215
+    },
+    {
+        "name": "Red nucleus",
+        "label": "4",
+        "voxel_value": 4,
+        "r": 205,
+        "g": 156,
+        "b": 46
+    },
+    {
+        "name": "Dentate nucleus",
+        "label": "5",
+        "voxel_value": 5,
+        "r": 92,
+        "g": 55,
+        "b": 136
+    },
+    {
+        "name": "Substantia nigra & subthalamic nucleus",
+        "label": "6",
+        "voxel_value": 6,
+        "r": 125,
+        "g": 186,
+        "b": 94
+    },
+    {
+        "name": "Thalamus",
+        "label": "7",
+        "voxel_value": 7,
+        "r": 178,
+        "g": 69,
+        "b": 124
+    },
+    {
+        "name": "White matter",
+        "label": "8",
+        "voxel_value": 8,
+        "r": 89,
+        "g": 190,
+        "b": 121
+    },
+    {
+        "name": "Gray matter",
+        "label": "9",
+        "voxel_value": 9,
+        "r": 186,
+        "g": 71,
+        "b": 88
+    },
+    {
+        "name": "CSF",
+        "label": "10",
+        "voxel_value": 10,
+        "r": 67,
+        "g": 200,
+        "b": 172
+    },
+    {
+        "name": "Blood",
+        "label": "11",
+        "voxel_value": 11,
+        "r": 191,
+        "g": 70,
+        "b": 58
+    },
+    {
+        "name": "Fat",
+        "label": "12",
+        "voxel_value": 12,
+        "r": 109,
+        "g": 141,
+        "b": 215
+    },
+    {
+        "name": "Bone",
+        "label": "13",
+        "voxel_value": 13,
+        "r": 189,
+        "g": 151,
+        "b": 64
+    },
+    {
+        "name": "Air",
+        "label": "14",
+        "voxel_value": 14,
+        "r": 73,
+        "g": 115,
+        "b": 39
+    },
+    {
+        "name": "Muscle",
+        "label": "15",
+        "voxel_value": 15,
+        "r": 181,
+        "g": 95,
+        "b": 50
+    },
+    {
+        "name": "Calcification",
+        "label": "16",
+        "voxel_value": 16,
+        "r": 170,
+        "g": 140,
+        "b": 72
+    }
+]
+
diff --git a/qsm_forward/qsm_forward.py b/qsm_forward/qsm_forward.py
index 1988d37..8eb1f36 100644
--- a/qsm_forward/qsm_forward.py
+++ b/qsm_forward/qsm_forward.py
@@ -391,7 +391,7 @@ def generate_bids(tissue_params: TissueParams, recon_params: ReconParams, bids_d
         json_dict = {
             'Subject': recon_params.subject,
             'Session': recon_params.session,
-            'Acquisition': recon_params.acquisition,
+            'Acquisition': recon_params.acq,
             'Run': recon_params.run,
             'EchoTime': recon_params.TEs[i],
             'MagneticFieldStrength': recon_params.B0,
diff --git a/setup.py b/setup.py
index d35ec80..d3f8b39 100644
--- a/setup.py
+++ b/setup.py
@@ -2,8 +2,10 @@
 
 setup(
     name='qsm-forward',
-    version='0.23',
+    version='0.24',
     packages=find_packages(),
+    include_package_data=True,
+    package_data={ 'qsm_forward': ['label.json'] },
     url='https://github.com/astewartau/qsm-forward',
     author='Ashley Stewart',
     author_email='a.stewart.au@gmail.com',