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Update Windows_Installation_Instructions.md
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allucas authored Jan 22, 2024
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# Installing Docker

Please install docker following the instructions found [here](https://github.com/penn-cnt/ieeg-recon/blob/main/python/docs/Docker_Installation.md)

# Installing Miniconda

You need to have Miniconda installed on your system. Follow the instructions below based on your operating system.
Expand All @@ -6,35 +10,37 @@ You need to have Miniconda installed on your system. Follow the instructions bel
2. Run the installer and follow the on-screen instructions.
3. After installation, use the Anaconda Prompt for the following commands.

## Installing Git:
**Note about WSL:** I have tried WSL, and the Anaconda Prompt approach descibed above is a better option. If you get WSL working with this approach, let me know!

# Installing Git:

Install git by typing:

```
conda install git
```

## Clone the repository
# Clone the repository

Clone this repository by doing:

```
git clone https://github.com/penn-cnt/ieeg-recon.git
```

## Install the GUI:
# Install the GUI:

After cloning, install the GUI by running:

```
bash ieeg-recon/python/install_ieeg-recon_gui_linux.sh
bash ieeg-recon/python/install_ieeg-recon_gui_windows.sh
```

## Install VoxTool
# Install VoxTool

Due to differences in package dependencies, the Windows version of iEEG-recon requires a step-by-step installation of VoxTool. It can easily be done by following the instructions [here](https://github.com/penn-cnt/ieeg-recon/blob/main/python/docs/Manual_Voxtool_Installation.md)

## Running iEEG-recon
# Running iEEG-recon

After all the steps above are completed, activate the `ieeg_recon` environment:

Expand All @@ -46,5 +52,5 @@ Then run the GUI by typing:


```
python ieeg-recon/python/ieeg_recon_gui_docker.py
python ieeg-recon/python/ieeg_recon_gui_docker_windows.py
```

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