Updates

README.md

@@ -19,28 +19,7 @@ An autoencoder model for brain structure T1 MRIs based on [Brain Latent Progress
 - [PatchAdversarialLoss](https://docs.monai.io/en/stable/losses.html#patchadversarialloss)
 - [PerceptualLoss](https://docs.monai.io/en/stable/losses.html#perceptualloss)
 
-# License
-MIT License
 
-Copyright (c) 2025
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
 
 # Training data
 [Radiata brain-structure](https://huggingface.co/datasets/radiata-ai/brain-structure): 3066 scans from 2085 individuals in the 'train' split. Mean age = 45.1 +- 24.5, including 2847 scans from cognitively normal subjects and 219 scans from individuals with an Alzheimer's disease clinical diagnosis.
@@ -58,7 +37,8 @@ source venv_brain2vec/bin/activate
 # install Python libraries
 pip install -r requirements.txt
 
-# create the csv file listing the scan paths and other info
+# create the csv file inputs.csv listing the scan paths and other info
+# this script loads the radiata-ai/brain-structure dataset
 python create_csv.py
 
 mkdir ae_cache
@@ -97,3 +77,26 @@ Pinaya
   publisher    = {Hugging Face}
 }
 ```
+
+# License
+MIT License
+
+Copyright (c) 2025
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

brain2vec.py

@@ -560,7 +560,7 @@ def inference(
         for image_path in tqdm(df.image_path, total=len(df)):
             destpath = os.path.join(
                 output_dir,
-                os.path.basename(image_path).replace('.nii.gz', '_latent.npz').replace('.nii', '_latent.npz')
+                os.path.basename(image_path).replace('.nii.gz', '_embeddings.npz').replace('.nii', '_embeddings.npz')
             )
             if os.path.exists(destpath):
                 continue