Add setup documentation for data folder structure

README.md

@@ -1,2 +1,98 @@
 # stroke_disconnection
 Project repo for stroke disconnection research project
+
+## Setup Instructions
+
+### Creating the Required Folder Structure
+
+This project analyzes structural connectivity data using the Schaefer 400-parcel atlas. Before running the analysis scripts, you need to create the required folder structure and add your data files.
+
+#### 1. Create the Data Folder
+
+Create a folder named `Schaefer2018-12m` in the project root directory:
+
+```bash
+mkdir Schaefer2018-12m
+```
+
+#### 2. Add Your Data Files
+
+Place your connectivity data files in the `Schaefer2018-12m/` folder. The files should:
+
+- Be in TSV (tab-separated values) format
+- Follow the naming convention: `sub-<ID>_Schaefer2018-12m.tsv`
+  - Example: `sub-K1_Schaefer2018-12m.tsv`, `sub-P001_Schaefer2018-12m.tsv`
+- Contain 400x400 connectivity matrices (Schaefer 400-parcel atlas)
+- Have ROI names as both row and column headers
+
+#### 3. Expected File Structure
+
+```
+stroke_disconnection/
+├── Schaefer2018-12m/              # Data folder (you create this)
+│   ├── sub-K1_Schaefer2018-12m.tsv
+│   ├── sub-P001_Schaefer2018-12m.tsv
+│   ├── sub-P002_Schaefer2018-12m.tsv
+│   └── ... (additional subject files)
+├── 1) Merge_All_Shaeffler.py
+├── 2) Indivudual visualization of binarized shaeffler.py
+├── 3) Create Group_Sum_Binarized_Schaefer400.py
+├── 4) Visualization_Sum_Binarized_AllPatients.py
+├── 5) Check_ROI_Regions.py
+└── README.md
+```
+
+## Usage
+
+Once you have created the `Schaefer2018-12m/` folder and added your data files, run the analysis scripts in order:
+
+1. **Merge All Data**: Compiles all subject data into a single compressed file
+   ```bash
+   python "1) Merge_All_Shaeffler.py"
+   ```
+
+2. **Visualize Individual Subject**: Creates visualization for a single subject
+   ```bash
+   python "2) Indivudual visualization of binarized shaeffler.py"
+   ```
+
+3. **Create Group Summary**: Generates binarized group-level connectivity matrix
+   ```bash
+   python "3) Create Group_Sum_Binarized_Schaefer400.py"
+   ```
+
+4. **Visualize Group Data**: Creates visualization of group-level connectivity
+   ```bash
+   python "4) Visualization_Sum_Binarized_AllPatients.py"
+   ```
+
+5. **Check ROI Regions**: Utility to check which brain region corresponds to a specific ROI number
+   ```bash
+   python "5) Check_ROI_Regions.py"
+   ```
+
+## Data Format
+
+Each TSV file should contain a 400x400 matrix where:
+- Rows and columns represent the 400 regions from the Schaefer atlas
+- Values represent connectivity strength between regions
+- The first row contains column headers (ROI names)
+- The first column contains row indices (ROI names)
+
+Example TSV structure:
+```
+	ROI1	ROI2	ROI3	...	ROI400
+ROI1	0.0	0.5	0.3	...	0.1
+ROI2	0.5	0.0	0.8	...	0.2
+ROI3	0.3	0.8	0.0	...	0.4
+...
+ROI400	0.1	0.2	0.4	...	0.0
+```
+
+## Output Files
+
+The scripts will generate the following output files:
+- `compiled_data_4953.npz` - Compiled data from all subjects
+- `Group_Sum_Binarized_Schaefer400.csv` - Group-level binarized connectivity matrix
+- `sub-K1_400x400_Binarized.png` - Individual subject visualization
+- `Professional_400x400_Matrix_Binarized.png` - Group-level visualization