updated README with new Zenodo upload

Author: saundersresearch

README.md

@@ -7,7 +7,7 @@ You can set up an environment using [`uv`](https://github.com/astral-sh/uv) by r
 uv sync
 ```
 
-To run the model, download the weights and testing dataset from the following link: [DeepFixel](https://zenodo.org/records/14962758).
+To run the model, download the weights and testing dataset from the following link: [https://zenodo.org/records/16587458](https://zenodo.org/records/16587458).
 
 - Unzip and copy the testing data to `./test_data`
 - Put the weights in `./models/pretrained`

run_deep_fixel.py

@@ -13,6 +13,7 @@
 kappa = 100
 n_fibers = 'both'
 healpix = True
+min_separation_angle = 0
 save_dir = "./models"
 test_dir = "./test_data"
 
@@ -52,4 +53,7 @@
     test_dir=test_dir,
     gpu_id=gpu_id,
     healpix=healpix,
+    use_dipy=True,
+    min_separation_angle=min_separation_angle,
+    is_symmetric=True
 )

run_pretrained_deep_fixel.py

@@ -3,21 +3,22 @@
 
 lr = 1e-3
 batch_size = 512
-n_steps = 10000
-validation_patience = 5
 loss = "MSE"
 model = "mesh_mlp"
-gpu_id = 1
+gpu_id = 0
 seed = 42
-mesh_subdivide = 3
+mesh_subdivide = 1
+healpix = True
 kappa = 100
+min_separation_angle = 0
 n_fibers = 'both'
-model_path = "./models/pretrained/best_model.pth"
+model_path = "./models/pretrained/best_model_mlp.pth"
 test_dir = "./test_data"
-output_dir = './outputs/pretrained'
+output_dir = './outputs/pretrained_mlp'
 amp_threshold = 0.1
 
 deep_fixel.test_mesh_model(
+    model=model,
     model_path=model_path,
     batch_size=batch_size,
     n_fibers=n_fibers,
@@ -27,4 +28,41 @@
     kappa=kappa,
     test_dir=test_dir,
     gpu_id=gpu_id,
+    healpix=healpix,
+    use_dipy=True,
+    min_separation_angle=min_separation_angle,
+    is_symmetric=True
+)
+
+lr = 1e-3
+batch_size = 512
+loss = "MSE"
+model = "mesh_scnn"
+gpu_id = 0
+seed = 42
+mesh_subdivide = 1
+healpix = True
+kappa = 100
+min_separation_angle = 0
+n_fibers = 'both'
+model_path = "./models/pretrained/best_model_scnn.pth"
+test_dir = "./test_data"
+output_dir = './outputs/pretrained_scnn'
+amp_threshold = 0.1
+
+deep_fixel.test_mesh_model(
+    model=model,
+    model_path=model_path,
+    batch_size=batch_size,
+    n_fibers=n_fibers,
+    subdivide_mesh=mesh_subdivide,
+    amp_threshold=amp_threshold,
+    output_dir=output_dir,
+    kappa=kappa,
+    test_dir=test_dir,
+    gpu_id=gpu_id,
+    healpix=healpix,
+    use_dipy=True,
+    min_separation_angle=min_separation_angle,
+    is_symmetric=True
 )