# Running AutoAFIDs with Conda

AutoAFIDs can be installed and run using Conda on **Linux and macOS** systems.

> **Note:** Conda installation is **not supported on Windows and M1 chip** at this time.  
> If you are on Windows or M1 chip on Mac, please refer to the [Docker instructions](docker.md) instead.

---

## For Users: Installing AutoAFIDs via Conda

These steps are intended for **end users** who simply want to run AutoAFIDs and get their AFIDs (+ other derivative apps).

### 1. Install Conda (if not already installed)

Follow the instructions at the official Conda documentation:  
[https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html)

---

### 2. Create and activate a new Conda environment

```bash
conda install mamba -c conda-forge
mamba create --name autoafids-env -c khanlab -c conda-forge -c bioconda autoafids
eval "$(mamba shell hook --shell zsh)"
mamba activate autoafids-env
```

---

### 3. Test the installation

Run the following command to verify the installation:

```bash
autoafids -h
```

You should see a help message listing all available command-line options.  
If this runs successfully, you’re ready to start processing data with AutoAFIDs!

---

## Running an Example

You can try AutoAFIDs on a sample dataset to make sure everything works as expected.

First, download and extract a single-subject BIDS dataset for this test:

```bash
wget "https://www.dropbox.com/scl/fi/phmmofiy4q6o1k01rs6c4/ds003653.tar?rlkey=bpa8fxfl0lyrdc38fs6aowta7&st=zvhpqsga&dl=1" -O ds003653.tar
tar -xvf ds003653.tar
```

This will create a `ds003653/` folder with a single subject that has both T1w and T2w images:

```
ds003653/
├── dataset_description.json
├── README
└── sub-718211
    └── ses-01
        ├── anat
        │   ├── sub-718211_ses-01_T1w.json
        │   ├── sub-718211_ses-01_T1w.nii.gz
        │   ├── sub-718211_ses-01_T2w.json
        │   └── sub-718211_ses-01_T2w.nii.gz
        ├── sub-718211_ses-01_scans.json
        └── sub-718211_ses-01_scans.tsv
```

---

### Run the Full AutoAFIDs BIDS Pipeline

By default (Linux or Intel-based macOS), run:

```bash
autoafids ds003653 ds003653_autoafids participant --cores all
```

This will run the full pipeline and place results in a new `ds003653_autoafids/` folder.

#### For M2 (Apple Silicon) Macs

Prefix with `CONDA_SUBDIR=osx-64` to force compatibility:

```bash
CONDA_SUBDIR=osx-64 autoafids ds003653 ds003653_autoafids participant --cores all
```

> ⚠️ **Note:** AutoAFIDs on Apple Silicon currently only supports the T1w modality.  
> Other modalities (e.g., T2w, FLAIR) are not yet supported on this platform.


## Cache Directory

When running, AutoAFIDs automatically downloads and caches the necessary CNN model to speed up subsequent runs.

By default,  it's stored in the following directory:

```bash
~/.cache/autoafids/
```

You can override this default cache location by setting the `AUTOAFIDS_CACHE_DIR` environment variable:

```bash
export AUTOAFIDS_CACHE_DIR=/path/to/custom/cache
```

This is useful when working on shared systems, when home directory storage is limited, or if you wish to isolate data per project or user.

## For Developers & Contributors

These steps are intended for people who want to contribute to the development of AutoAFIDs or explore its internals.

### 1. Clone the AutoAFIDs GitHub repository

```bash
git clone https://github.com/afids/autoafids.git
cd autoafids
```

---

### 2. Create and activate a new Conda environment

```bash
mamba env create -f autoafids-dev.yml
eval "$(mamba shell hook --shell zsh)"
mamba activate autoafids-dev
```

---

### 3. Run the development version of AutoAFIDs

You can run AutoAFIDs directly from the source directory using:

```bash
./autoafids/run.py -h
```

This should print out the available command-line arguments for the tool.  
You’re now set up for development and contribution!

If you’re on an M-chip mac, prefix with CONDA_SUBDIR=osx-64 to ensure compatibility:

```bash
CONDA_SUBDIR=osx-64 ./autoafids/run.py -h
```

---

## Troubleshooting

If you encounter issues while setting up AutoAFIDs via Conda:

- Make sure you’re using the latest Conda:
  ```bash
  conda update -n base -c defaults conda
  ```
- Double-check that your environment is activated (`mamba activate autoafids-env` or `autoafids-dev`)
- Try creating a fresh environment if problems persist
- Search for similar issues or open a new one in the [GitHub issues](https://github.com/afids/autoafids/issues) page

---