Code changes

README.md

@@ -22,8 +22,10 @@ A linear PCA model for brain structure T1 MRIs. The models takes in a 3d MRI NIf
 # Example usage
 ```
 # get brain2vec_PCA model repository
+git lfs install  # Ensure Git LFS is installed and enabled
 git clone https://huggingface.co/radiata-ai/brain2vec_PCA
 cd brain2vec_PCA
+git lfs pull
 
 # set up virtual environemt
 python3 -m venv venv_brain2vec_PCA
@@ -51,14 +53,14 @@ python inference_brain2vec_PCA.py \
     --pca_model pca_model.joblib \
     --input_images /path/to/img1.nii.gz /path/to/img2.nii.gz \
     --output_dir pca_output \
-    --embeddings_filename pca_output/pca_embeddings_2 \
+    --embeddings_filename pca_embeddings_2 \
     --save_recons
-    
-# or if you have a CSV with image paths:
+
 python inference_brain2vec_PCA.py \
-    --pca_model /path/to/pca_model.joblib \
-    --csv_input /path/to/input.csv \
-    --output_dir /path/to/out
+    --pca_model pca_model.joblib \
+    --csv_input inputs.csv \
+    --output_dir pca_output \
+    --embeddings_filename pca_embeddings_all
 ```
 
 # Methods

inference_brain2vec_PCA.py

@@ -10,16 +10,19 @@ reconstructions) for each image.
 Example usage:
 
     python inference_brain2vec_PCA.py \
-        --pca_model /path/to/pca_model.joblib \
+        --pca_model pca_model.joblib \
         --input_images /path/to/img1.nii.gz /path/to/img2.nii.gz \
-        --output_dir /path/to/out
+        --output_dir pca_output \
+        --embeddings_filename pca_embeddings_2 \
+        --save_recons
     
 Or, if you have a CSV with image paths:
 
     python inference_brain2vec_PCA.py \
-        --pca_model /path/to/pca_model.joblib \
-        --csv_input /path/to/input.csv \
-        --output_dir /path/to/out
+        --pca_model pca_model.joblib \
+        --csv_input inputs.csv \
+        --output_dir pca_output \
+        --embeddings_filename pca_embeddings_all
 """
 
 import os