diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
index fde08ee95..26ad79d8e 100644
--- a/.github/workflows/deploy.yml
+++ b/.github/workflows/deploy.yml
@@ -1,55 +1,88 @@
 name: MAN deploy-docker
 
 on:
-#  release:
-#    types:
-#      - published
+  release:
+    types:
+      - published
   workflow_dispatch:
 
 jobs:
-  deploy-gpu:
-    runs-on: ubuntu-latest
+  deploy-mac:
+    runs-on: macos-14
     timeout-minutes: 120
+    
+    env:
+      RELEASE_ASSETS: true
+    strategy:
+      matrix:
+        arch: [intel, arm]
     steps:
+      - name: Get repository name.
+        run: echo "FASTSURFER_DIR=$GITHUB_WORKSPACE" >> $GITHUB_ENV
       - name: Checkout repository
         uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      - name: Login to Docker
-        uses: docker/login-action@v2
+      - name: Set up python environment
+        uses: actions/setup-python@v6
         with:
-          username: ${{ secrets.DOCKERHUB_USERNAME }}
-          password: ${{ secrets.DOCKERHUB_TOKEN }}
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
-      - name: Build Docker image GPU
-        run: python Docker/build.py --device cuda --tag ${{ secrets.DOCKERHUB_USERNAME }}/fastsurfer:gpu-${{ github.event.release.tag_name }}
-      - name: Add additional tags
+          python-version: '3.10'
+      - name: install dependencies
+        run: python -m pip install py2app pyyaml
+      - name: package app for ${{ matrix.arch }}
+        run: tools/macos_build/build_release_package.sh ${{ matrix.arch }} ${{ env.FASTSURFER_DIR }}
+      - name: Move assets.
+        if: env.RELEASE_ASSETS == 'true'
         run: |
-          docker tag ${{ secrets.DOCKERHUB_USERNAME }}/fastsurfer:gpu-${{ github.event.release.tag_name }} ${{ secrets.DOCKERHUB_USERNAME }}/fastsurfer:gpu-latest
-          docker tag ${{ secrets.DOCKERHUB_USERNAME }}/fastsurfer:gpu-${{ github.event.release.tag_name }} ${{ secrets.DOCKERHUB_USERNAME }}/fastsurfer:latest
-      - name: Push Docker image GPU
-        run: docker push --all-tags ${{ secrets.DOCKERHUB_USERNAME }}/fastsurfer:gpu-${{ github.event.release.tag_name }}
-  deploy-cpu:
-    runs-on: ubuntu-latest
-    timeout-minutes: 120
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v3
+          mkdir assets
+          mv tools/macos_build/installer/* assets/
+      - name: Upload release assets.
+        uses: softprops/action-gh-release@v2
+        if: env.RELEASE_ASSETS == 'true'
         with:
-          fetch-depth: 0
-      - name: Login to Docker
-        uses: docker/login-action@v2
-        with:
-          username: ${{ secrets.DOCKERHUB_USERNAME }}
-          password: ${{ secrets.DOCKERHUB_TOKEN }}
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
-      - name: Build Docker image CPU
-        run: python Docker/build.py --device cpu --tag ${{ secrets.DOCKERHUB_USERNAME }}/fastsurfer:cpu-${{ github.event.release.tag_name }}
-      - name: Add additional tags
-        run: |
-          docker tag ${{ secrets.DOCKERHUB_USERNAME }}/fastsurfer:cpu-${{ github.event.release.tag_name }} ${{ secrets.DOCKERHUB_USERNAME }}/fastsurfer:cpu-latest
-      - name: Push Docker image CPU
-        run: docker push --all-tags ${{ secrets.DOCKERHUB_USERNAME }}/fastsurfer:cpu-${{ github.event.release.tag_name }}
-
+          files: ${{ env.FASTSURFER_DIR }}/assets/*
+  # deploy-gpu:
+  #   runs-on: ubuntu-latest
+  #   timeout-minutes: 120
+  #   steps:
+  #     - name: Checkout repository
+  #       uses: actions/checkout@v3
+  #       with:
+  #         fetch-depth: 0
+  #     - name: Login to Docker
+  #       uses: docker/login-action@v2
+  #       with:
+  #         username: ${{ secrets.DOCKERHUB_USERNAME }}
+  #         password: ${{ secrets.DOCKERHUB_TOKEN }}
+  #     - name: Set up Docker Buildx
+  #       uses: docker/setup-buildx-action@v2
+  #     - name: Build Docker image GPU
+  #       run: python Docker/build.py --device cuda --tag ${{ secrets.DOCKERHUB_USERNAME }}/fastsurfer:gpu-${{ github.event.release.tag_name }}
+  #     - name: Add additional tags
+  #       run: |
+  #         docker tag ${{ secrets.DOCKERHUB_USERNAME }}/fastsurfer:gpu-${{ github.event.release.tag_name }} ${{ secrets.DOCKERHUB_USERNAME }}/fastsurfer:gpu-latest
+  #         docker tag ${{ secrets.DOCKERHUB_USERNAME }}/fastsurfer:gpu-${{ github.event.release.tag_name }} ${{ secrets.DOCKERHUB_USERNAME }}/fastsurfer:latest
+  #     - name: Push Docker image GPU
+  #       run: docker push --all-tags ${{ secrets.DOCKERHUB_USERNAME }}/fastsurfer:gpu-${{ github.event.release.tag_name }}
+  # deploy-cpu:
+  #   runs-on: ubuntu-latest
+  #   timeout-minutes: 120
+  #   steps:
+  #     - name: Checkout repository
+  #       uses: actions/checkout@v3
+  #       with:
+  #         fetch-depth: 0
+  #     - name: Login to Docker
+  #       uses: docker/login-action@v2
+  #       with:
+  #         username: ${{ secrets.DOCKERHUB_USERNAME }}
+  #         password: ${{ secrets.DOCKERHUB_TOKEN }}
+  #     - name: Set up Docker Buildx
+  #       uses: docker/setup-buildx-action@v2
+  #     - name: Build Docker image CPU
+  #       run: python Docker/build.py --device cpu --tag ${{ secrets.DOCKERHUB_USERNAME }}/fastsurfer:cpu-${{ github.event.release.tag_name }}
+  #     - name: Add additional tags
+  #       run: |
+  #         docker tag ${{ secrets.DOCKERHUB_USERNAME }}/fastsurfer:cpu-${{ github.event.release.tag_name }} ${{ secrets.DOCKERHUB_USERNAME }}/fastsurfer:cpu-latest
+  #     - name: Push Docker image CPU
+  #       run: docker push --all-tags ${{ secrets.DOCKERHUB_USERNAME }}/fastsurfer:cpu-${{ github.event.release.tag_name }}
diff --git a/README.md b/README.md
index 379b47134..a178a31dd 100644
--- a/README.md
+++ b/README.md
@@ -76,11 +76,11 @@ All installation methods use the `run_fastsurfer.sh` call interface (replace `*f
    ```
    The `--nv` flag is needed to allow FastSurfer to run on the GPU (otherwise FastSurfer will run on the CPU).
 
-   The `--no-home` flag tells singularity to not mount the home directory (see [Singularity documentation](Singularity/README.md#mounting-home) for more info).
+   The `--no-home` flag tells singularity to not mount the home directory (see [Singularity documentation](tools/Singularity/README.md#mounting-home) for more info).
 
    The `-B` flag is used to tell singularity, which folders FastSurfer can read and write to.
  
-   See also __[Example 2](doc/overview/EXAMPLES.md#example-2-fastsurfer-singularity)__ for a full singularity FastSurfer run command and [the Singularity documentation](Singularity/README.md#fastsurfer-singularity-image-usage) for details on more singularity flags.  
+   See also __[Example 2](doc/overview/EXAMPLES.md#example-2-fastsurfer-singularity)__ for a full singularity FastSurfer run command and [the Singularity documentation](tools/Singularity/README.md#fastsurfer-singularity-image-usage) for details on more singularity flags.  
 
    (b) For __docker__, the syntax is
     ```
@@ -96,7 +96,7 @@ All installation methods use the `run_fastsurfer.sh` call interface (replace `*f
 
    The `-v` flag is used to tell docker, which folders FastSurfer can read and write to.
  
-   See also __[Example 1](doc/overview/EXAMPLES.md#example-1-fastsurfer-docker)__ for a full FastSurfer run inside a Docker container and [the Docker documentation](Docker/README.md#docker-flags) for more details on the docker flags including `--rm` and `--user`.
+   See also __[Example 1](doc/overview/EXAMPLES.md#example-1-fastsurfer-docker)__ for a full FastSurfer run inside a Docker container and [the Docker documentation](tools/Docker/README.md#docker-flags) for more details on the docker flags including `--rm` and `--user`.
 
 2. For a __native install__, you need to activate your FastSurfer environment (e.g. `conda activate fastsurfer_gpu`) and make sure you have added the FastSurfer path to your `PYTHONPATH` variable, e.g. `export PYTHONPATH=$(pwd)`. 
 
diff --git a/doc/images/fastsurfer.png b/doc/images/fastsurfer.png
new file mode 100644
index 000000000..5d74c972b
Binary files /dev/null and b/doc/images/fastsurfer.png differ
diff --git a/doc/overview/EXAMPLES.md b/doc/overview/EXAMPLES.md
index eb082c885..32e9a500d 100644
--- a/doc/overview/EXAMPLES.md
+++ b/doc/overview/EXAMPLES.md
@@ -39,10 +39,10 @@ Note, that the paths following `--fs_license`, `--t1`, and `--sd` are __inside__
 
 A directory with the name as specified in `--sid` (here subjectX) will be created in the output directory if it does not exist. So in this example output will be written to /home/user/my_fastsurfer_analysis/subjectX/ . Make sure the output directory is empty, to avoid overwriting existing files. 
 
-If you do not have a GPU, you can also run our CPU-Docker by dropping the `--gpus all` flag and specifying `--device cpu` at the end as a FastSurfer flag, see also [FastSurfer's docker documentation](../../Docker/README.md) for more details.
+If you do not have a GPU, you can also run our CPU-Docker by dropping the `--gpus all` flag and specifying `--device cpu` at the end as a FastSurfer flag, see also [FastSurfer's docker documentation](../../tools/Docker/README.md) for more details.
 
 ## Example 2: FastSurfer Singularity
-After building the Singularity image (see below or [these instructions](../../Singularity/README.md)), you also need to register at the FreeSurfer website (https://surfer.nmr.mgh.harvard.edu/registration.html) to acquire a valid license (for free) - same as when using Docker. This license needs to be passed to the script via the `--fs_license` flag. This is not necessary if you want to run the segmentation only.
+After building the Singularity image (see below or [these instructions](../../tools/Singularity/README.md)), you also need to register at the FreeSurfer website (https://surfer.nmr.mgh.harvard.edu/registration.html) to acquire a valid license (for free) - same as when using Docker. This license needs to be passed to the script via the `--fs_license` flag. This is not necessary if you want to run the segmentation only.
 
 To run FastSurfer on a given subject using the Singularity image with GPU access, execute the following commands from a directory where you want to store singularity images. This will create a singularity image from our Dockerhub image and execute it:
 
diff --git a/doc/overview/INSTALL.md b/doc/overview/INSTALL.md
index 333646b4a..d86a262b1 100644
--- a/doc/overview/INSTALL.md
+++ b/doc/overview/INSTALL.md
@@ -22,9 +22,9 @@ Assuming you have singularity installed already (by a system admin), you can bui
 ```bash
 singularity build fastsurfer-gpu.sif docker://deepmi/fastsurfer:latest
 ```
-Additionally, [the Singularity README](../../Singularity/README.md) contains detailed directions for building your own Singularity images from Docker.
+Additionally, [the Singularity README](../../tools/Singularity/README.md) contains detailed directions for building your own Singularity images from Docker.
 
-[Example 2](EXAMPLES.md#example-2-fastsurfer-singularity) explains how to run FastSurfer (for the full pipeline you will also need a FreeSurfer .license file!) and you can find details on how to build your own images here: [Docker](../../Docker/README.md) and [Singularity](../../Singularity/README.md). 
+[Example 2](EXAMPLES.md#example-2-fastsurfer-singularity) explains how to run FastSurfer (for the full pipeline you will also need a FreeSurfer .license file!) and you can find details on how to build your own images here: [Docker](../../tools/Docker/README.md) and [Singularity](../../tools/Singularity/README.md). 
 
 
 ### Docker
@@ -35,7 +35,7 @@ This is very similar to Singularity. Assuming you have Docker installed (by a sy
 docker pull deepmi/fastsurfer:latest
 ```
 
-[Example 1](EXAMPLES.md#example-1-fastsurfer-docker) explains how to run FastSurfer (for the full pipeline you will also need a FreeSurfer .license file!) and you can find details on how to [build your own image](https://github.com/Deep-MI/FastSurfer/blob/dev/Docker/README.md). 
+[Example 1](EXAMPLES.md#example-1-fastsurfer-docker) explains how to run FastSurfer (for the full pipeline you will also need a FreeSurfer .license file!) and you can find details on how to [build your own image](../../tools/Docker/README.md). 
 
 If you are using the **rootless mode**, you have to install the [NVIDIA Container Toolkit](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/latest/install-guide.html) and follow the [configuration for the rootless mode](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/latest/install-guide.html#rootless-mode). Otherwise, running FastSurfer with Docker will give you this error message ```docker: Error response from daemon: could not select device driver "" with capabilities: [[gpu]]```.
 
@@ -97,7 +97,7 @@ conda env create -f ./env/fastsurfer.yml
 conda activate fastsurfer
 ```
 
-If you do not have an NVIDIA GPU, you can create appropriate ymls on the fly with `python ./Docker/install_env.py -m $MODE -i ./env/FastSurfer.yml -o ./fastsurfer_$MODE.yml`. Here `$MODE` can be for example `cpu`, see also `python ./Docker/install_env.py --help` for other options like rocm or cuda versions. Finally, replace `./env/fastsurfer.yml`  with your custom environment file `./fastsurfer_$MODE.yml`.
+If you do not have an NVIDIA GPU, you can create appropriate ymls on the fly with `python ./tools/Docker/install_env.py -m $MODE -i ./env/FastSurfer.yml -o ./fastsurfer_$MODE.yml`. Here `$MODE` can be for example `cpu`, see also `python ./tools/Docker/install_env.py --help` for other options like rocm or cuda versions. Finally, replace `./env/fastsurfer.yml`  with your custom environment file `./fastsurfer_$MODE.yml`.
 If you only want to run the surface pipeline, use `./env/fastsurfer_reconsurf.yml`.
 
 Next, add the fastsurfer directory to the python path (make sure you have changed into it already):
@@ -129,7 +129,7 @@ We have successfully run the segmentation on an AMD GPU (Radeon Pro W6600) using
 Build the Docker container with ROCm support.
 
 ```bash
-python Docker/build.py --device rocm --tag my_fastsurfer:rocm
+python tools/Docker/build.py --device rocm --tag my_fastsurfer:rocm
 ```
 
 You will need to add a couple of flags to your docker run command for AMD, see [Example 1](EXAMPLES.md#example-1-fastsurfer-docker) for `**other-docker-flags**` or `**fastsurfer-flags**`:
diff --git a/doc/overview/MACOS.md b/doc/overview/MACOS.md
new file mode 100644
index 000000000..60d585f21
--- /dev/null
+++ b/doc/overview/MACOS.md
@@ -0,0 +1,10 @@
+Running FastSurfer
+==================
+
+If you want to run only segmentation (replace placeholders starting with "<" and ending with ">", see https://deep-mi.org/FastSurfer/stable):
+`run_fastsurfer.sh --seg_only --sd <path/to/output/dir> --sid <subject_id> --t1 <path/to/subjects/t1/image>`
+To full run fastsurfer:
+`run_fastsurfer.sh --device mps --sd <path/to/output/dir> --sid <subject_id> --t1 <path/to/subjects/t1/image> --fs_license </path/to/freesurfer/license>`
+Some files of **FreeSurfer** binaries require bypassing MacOS security, which is
+significantly easier to do with the following command than manually and one by one. 
+`

xattr -dr com.apple.quarantine /Applications/freesurfer/*`
diff --git a/doc/overview/docker.rst b/doc/overview/docker.rst
index 3cc4057e5..12328cd7a 100644
--- a/doc/overview/docker.rst
+++ b/doc/overview/docker.rst
@@ -1,7 +1,7 @@
 Docker Support
 --------------
 
-.. include:: ../../Docker/README.md
+.. include:: ../../tools/Docker/README.md
     :parser: fix_links.parser
     :relative-docs: .
     :relative-images:
diff --git a/doc/overview/singularity.rst b/doc/overview/singularity.rst
index afb11cb84..de76f9bf5 100644
--- a/doc/overview/singularity.rst
+++ b/doc/overview/singularity.rst
@@ -1,7 +1,7 @@
 Singularity Support
 -------------------
 
-.. include:: ../../Singularity/README.md
+.. include:: ../../tools/Singularity/README.md
     :parser: fix_links.parser
     :relative-docs: .
     :relative-images:
diff --git a/recon_surf/README.md b/recon_surf/README.md
index 281c8bb89..e452eb7dc 100644
--- a/recon_surf/README.md
+++ b/recon_surf/README.md
@@ -92,7 +92,7 @@ Check [Dockerhub](https://hub.docker.com/r/deepmi/fastsurfer/tags) to find out t
 * The `-B` commands mount your output, and directory with the FreeSurfer license file into the Singularity container. 
   Inside the container these are visible under the name following the colon (in this case /data, /output, and /fs_license). 
 
-* The `--no-home` command disables the automatic mount of the users home directory (see [Best Practice](../Singularity/README.md#mounting-home))
+* The `--no-home` command disables the automatic mount of the users home directory (see [Best Practice](../tools/Singularity/README.md#mounting-home))
 
 The `--t1` and `--asegdkt_segfile` flags point to the already existing conformed T1 input and segmentation from the 
 segmentation module. Also other files from that pipeline will be reused (e.g. the `mask.mgz`, `orig_nu.mgz`). The 
diff --git a/Docker/Dockerfile b/tools/Docker/Dockerfile
similarity index 99%
rename from Docker/Dockerfile
rename to tools/Docker/Dockerfile
index 70930c596..48b608576 100644
--- a/Docker/Dockerfile
+++ b/tools/Docker/Dockerfile
@@ -116,7 +116,7 @@ RUN python /install/install_env.py -m ${DEVICE} -i /install/fastsurfer.yml -o /i
 FROM build_base AS build_freesurfer
 
 # get install scripts into docker
-COPY ./Docker/install_fs_pruned.sh /install/
+COPY ./tools/install_fs_pruned.sh /install/
 SHELL ["/bin/bash", "--login", "-c"]
 
 ARG FREESURFER_URL=default
diff --git a/Docker/README.md b/tools/Docker/README.md
similarity index 99%
rename from Docker/README.md
rename to tools/Docker/README.md
index d26dcfcfc..f28cb6e83 100644
--- a/Docker/README.md
+++ b/tools/Docker/README.md
@@ -46,13 +46,13 @@ docker run --gpus all -v /home/user/my_mri_data:/data \
 * The `--t1` points to the t1-weighted MRI image to analyse (full path, with mounted name inside docker: /home/user/my_mri_data => /data)
 * The `--sid` is the subject ID name (output folder name)
 * The `--sd` points to the output directory (its mounted name inside docker: /home/user/my_fastsurfer_analysis => /output)
-* [more flags](../doc/overview/FLAGS.md#fastsurfer-flags)
+* [more flags](../../doc/overview/FLAGS.md#fastsurfer-flags)
 
 Note, that the paths following `--fs_license`, `--t1`, and `--sd` are __inside__ the container, not global paths on your system, so they should point to the places where you mapped these paths above with the `-v` arguments. 
 
 A directory with the name as specified in `--sid` (here subjectX) will be created in the output directory (specified via `--sd`). So in this example output will be written to /home/user/my_fastsurfer_analysis/subjectX/ . Make sure the output directory is empty, to avoid overwriting existing files. 
 
-All other available flags are identical to the ones explained on the main page [README](../README.md).
+All other available flags are identical to the ones explained on the main page [README](../../README.md).
 
 ### Docker Best Practice
 * Do not mount the user home directory into the docker container as the home directory.
diff --git a/Docker/build.py b/tools/Docker/build.py
similarity index 100%
rename from Docker/build.py
rename to tools/Docker/build.py
diff --git a/Docker/conda_pack.sh b/tools/Docker/conda_pack.sh
similarity index 100%
rename from Docker/conda_pack.sh
rename to tools/Docker/conda_pack.sh
diff --git a/Docker/entrypoint.sh b/tools/Docker/entrypoint.sh
similarity index 100%
rename from Docker/entrypoint.sh
rename to tools/Docker/entrypoint.sh
diff --git a/Docker/install_env.py b/tools/Docker/install_env.py
similarity index 100%
rename from Docker/install_env.py
rename to tools/Docker/install_env.py
diff --git a/Singularity/README.md b/tools/Singularity/README.md
similarity index 100%
rename from Singularity/README.md
rename to tools/Singularity/README.md
diff --git a/tools/config.yaml b/tools/config.yaml
new file mode 100644
index 000000000..3bfd7ed02
--- /dev/null
+++ b/tools/config.yaml
@@ -0,0 +1,6 @@
+FASTSURFER:
+  VERSION: '242'
+  PYTHON_VERSION: '3.10'
+
+FREESURFER_LINK_LINUX: 'https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz'
+FREESURFER_LINK_MACOS: 'https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-macOS-darwin_x86_64-7.4.1.tar.gz'
diff --git a/tools/get_config_value.py b/tools/get_config_value.py
new file mode 100644
index 000000000..55786be4e
--- /dev/null
+++ b/tools/get_config_value.py
@@ -0,0 +1,83 @@
+# Copyright 2024 Image Analysis Lab, German Center for Neurodegenerative Diseases (DZNE), Bonn
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+import argparse
+import sys
+from pathlib import Path
+
+import yaml
+
+
+def make_parser() -> argparse.ArgumentParser:
+    """
+    Create a command line interface and return command line options.
+
+    Returns
+    -------
+    options
+        Namespace object holding options.
+    """
+    parser = argparse.ArgumentParser(
+        description="Tool for extracting values from configuration file",
+    )
+    parser.add_argument(
+        "--file", "-f",
+        type=Path,
+        dest="file",
+        help="configuration file",
+        required=True,
+    )
+    parser.add_argument(
+        "--key", "-k",
+        type=str,
+        dest="key",
+        help="key to lookup",
+        required=True,
+    )
+    return parser
+
+
+def extract_value(config_file: Path | str, key: str) -> str:
+    """
+    Read configuration file and return the value for the given key.
+
+    Parameters
+    ----------
+    config_file : Path, str
+        Path to configuration file.
+    key : str
+        Key to lookup.
+
+    Returns
+    -------
+    value
+        Value under the given key.
+    """
+    with open(config_file) as config:
+        try:
+            conf = yaml.safe_load(config)
+            value = conf[key.split('.')[0]]
+            for k in key.split('.')[1:]:
+                value = value[k]
+            return value
+        except yaml.YAMLError as e:
+            print(e) 
+            sys.exit(1)
+
+    
+if __name__ == "__main__":
+    parser = make_parser()
+    args = parser.parse_args()
+
+    print(extract_value(args.file,args.key))
+    sys.exit(0)
diff --git a/Docker/install_fs_pruned.sh b/tools/install_fs_pruned.sh
similarity index 74%
rename from Docker/install_fs_pruned.sh
rename to tools/install_fs_pruned.sh
index 0346be306..896254c61 100755
--- a/Docker/install_fs_pruned.sh
+++ b/tools/install_fs_pruned.sh
@@ -12,7 +12,7 @@
 
 
 # Link where to find the FreeSurfer tarball: 
-fslink="https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz"
+fslink="https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-macOS-darwin_x86_64-7.4.1.tar.gz"
 
 
 if [[ "$#" -lt 1 ]]; then
@@ -99,57 +99,61 @@ function run_parallel ()
 
 # get FreeSurfer and unpack (some of it)
 echo "Downloading FS and unpacking portions ..."
-wget --no-check-certificate -qO- $fslink  | tar zxv --no-same-owner -C $where \
-      --exclude='freesurfer/average/*.gca' \
-      --exclude='freesurfer/average/Buckner_JNeurophysiol11_MNI152' \
-      --exclude='freesurfer/average/Choi_JNeurophysiol12_MNI152' \
-      --exclude='freesurfer/average/mult-comp-cor' \
-      --exclude='freesurfer/average/samseg' \
-      --exclude='freesurfer/average/Yeo_Brainmap_MNI152' \
-      --exclude='freesurfer/average/Yeo_JNeurophysiol11_MNI152' \
-      --exclude='freesurfer/bin/freeview.bin' \
-      --exclude='freesurfer/bin/freeview' \
-      --exclude='freesurfer/bin/fs_spmreg.glnxa64' \
-      --exclude='freesurfer/bin/mris_decimate_gui.bin' \
-      --exclude='freesurfer/bin/mris_decimate_gui' \
-      --exclude='freesurfer/bin/qdec_glmfit' \
-      --exclude='freesurfer/bin/qdec.bin' \
-      --exclude='freesurfer/bin/qdec' \
-      --exclude='freesurfer/bin/SegmentSubfieldsT1Longitudinal' \
-      --exclude='freesurfer/bin/SegmentSubjectT1_autoEstimateAlveusML' \
-      --exclude='freesurfer/bin/SegmentSubjectT1T2_autoEstimateAlveusML' \
-      --exclude='freesurfer/bin/SegmentSubjectT2_autoEstimateAlveusML' \
-      --exclude='freesurfer/diffusion' \
-      --exclude='freesurfer/fsafd' \
-      --exclude='freesurfer/fsfast' \
-      --exclude='freesurfer/lib/cuda' \
-      --exclude='freesurfer/lib/images' \
-      --exclude='freesurfer/lib/qt' \
-      --exclude='freesurfer/lib/tcl' \
-      --exclude='freesurfer/lib/tktools' \
-      --exclude='freesurfer/lib/vtk' \
-      --exclude='freesurfer/matlab' \
-      --exclude='freesurfer/mni-1.4' \
-      --exclude='freesurfer/mni' \
-      --exclude='freesurfer/models' \
-      --exclude='freesurfer/python/bin' \
-      --exclude='freesurfer/python/include' \
-      --exclude='freesurfer/python/lib' \
-      --exclude='freesurfer/python/share' \
-      --exclude='freesurfer/subjects/bert' \
-      --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
-      --exclude='freesurfer/subjects/cvs_avg35' \
-      --exclude='freesurfer/subjects/fsaverage_sym' \
-      --exclude='freesurfer/subjects/fsaverage3' \
-      --exclude='freesurfer/subjects/fsaverage4' \
-      --exclude='freesurfer/subjects/fsaverage5' \
-      --exclude='freesurfer/subjects/fsaverage6' \
-      --exclude='freesurfer/subjects/lh.EC_average' \
-      --exclude='freesurfer/subjects/rh.EC_average' \
-      --exclude='freesurfer/subjects/V1_average' \
-      --exclude='freesurfer/tktools' \
-      --exclude='freesurfer/trctrain'
+aria2c -x 16 -s 16 -c --check-certificate=false -o freesurfer.tar.gz "$fslink"
 
+tar zxv --no-same-owner -C "$where" \
+  --exclude='freesurfer/average/*.gca' \
+  --exclude='freesurfer/average/Buckner_JNeurophysiol11_MNI152' \
+  --exclude='freesurfer/average/Choi_JNeurophysiol12_MNI152' \
+  --exclude='freesurfer/average/mult-comp-cor' \
+  --exclude='freesurfer/average/samseg' \
+  --exclude='freesurfer/average/Yeo_Brainmap_MNI152' \
+  --exclude='freesurfer/average/Yeo_JNeurophysiol11_MNI152' \
+  --exclude='freesurfer/bin/freeview.bin' \
+  --exclude='freesurfer/bin/freeview' \
+  --exclude='freesurfer/bin/fs_spmreg.glnxa64' \
+  --exclude='freesurfer/bin/mris_decimate_gui.bin' \
+  --exclude='freesurfer/bin/mris_decimate_gui' \
+  --exclude='freesurfer/bin/qdec_glmfit' \
+  --exclude='freesurfer/bin/qdec.bin' \
+  --exclude='freesurfer/bin/qdec' \
+  --exclude='freesurfer/bin/SegmentSubfieldsT1Longitudinal' \
+  --exclude='freesurfer/bin/SegmentSubjectT1_autoEstimateAlveusML' \
+  --exclude='freesurfer/bin/SegmentSubjectT1T2_autoEstimateAlveusML' \
+  --exclude='freesurfer/bin/SegmentSubjectT2_autoEstimateAlveusML' \
+  --exclude='freesurfer/diffusion' \
+  --exclude='freesurfer/fsafd' \
+  --exclude='freesurfer/fsfast' \
+  --exclude='freesurfer/lib/cuda' \
+  --exclude='freesurfer/lib/images' \
+  --exclude='freesurfer/lib/qt' \
+  --exclude='freesurfer/lib/tcl' \
+  --exclude='freesurfer/lib/tktools' \
+  --exclude='freesurfer/lib/vtk' \
+  --exclude='freesurfer/matlab' \
+  --exclude='freesurfer/mni-1.4' \
+  --exclude='freesurfer/mni' \
+  --exclude='freesurfer/models' \
+  --exclude='freesurfer/python/bin' \
+  --exclude='freesurfer/python/include' \
+  --exclude='freesurfer/python/lib' \
+  --exclude='freesurfer/python/share' \
+  --exclude='freesurfer/subjects/bert' \
+  --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
+  --exclude='freesurfer/subjects/cvs_avg35' \
+  --exclude='freesurfer/subjects/fsaverage_sym' \
+  --exclude='freesurfer/subjects/fsaverage3' \
+  --exclude='freesurfer/subjects/fsaverage4' \
+  --exclude='freesurfer/subjects/fsaverage5' \
+  --exclude='freesurfer/subjects/fsaverage6' \
+  --exclude='freesurfer/subjects/lh.EC_average' \
+  --exclude='freesurfer/subjects/rh.EC_average' \
+  --exclude='freesurfer/subjects/V1_average' \
+  --exclude='freesurfer/tktools' \
+  --exclude='freesurfer/trctrain' \
+  -f freesurfer.tar.gz
+
+rm -rf freesurfer.tar.gz
 
 # rename download to tmp
 mv $where/freesurfer $fss
@@ -415,66 +419,5 @@ do
   touch $fsd/$file 
 done
 
-# FS calls these for version info, but we don't need them
-# so we link them to mri_info to save space. 
-link_files="
-  bin/mri_and
-  bin/mri_aparc2aseg
-  bin/mri_ca_label
-  bin/mri_ca_normalize
-  bin/mri_ca_register
-  bin/mri_compute_overlap
-  bin/mri_compute_seg_overlap
-  bin/mri_em_register
-  bin/mri_fwhm
-  bin/mri_gcut
-  bin/mri_log_likelihood
-  bin/mri_motion_correct.fsl
-  bin/mri_normalize_tp2
-  bin/mri_or
-  bin/mri_relabel_nonwm_hypos
-  bin/mri_remove_neck
-  bin/mri_stats2seg
-  bin/mri_surf2vol
-  bin/mri_surfcluster
-  bin/mri_voldiff
-  bin/mri_watershed
-  bin/mris_divide_parcellation
-  bin/mris_left_right_register
-  bin/mris_surface_stats
-  bin/mris_thickness
-  bin/mris_thickness_diff
-  bin/nu_correct
-  bin/tkregister2_cmdl"
-
-# create target for link with ERROR message if called
-ltrg=$fsd/bin/not-here.sh
-echo '#!/bin/bash
-if [ "$1" == "-all-info" ]; then
-  echo "$0 not included ..."
-  exit 0
-fi
-echo
-echo "ERROR: The binary $0 is not included, your call is forwarded to not-here.sh"
-echo
-exit 1
-' > $ltrg
-chmod a+x $ltrg
-echo
-for file in $link_files
-do
-  echo "linking $file"
-  ln -s $ltrg $fsd/$file 
-done
-
-# use our python (not really needed in recon-all anyway)
-p3=$(which python3)
-if [ "$p3" == "" ]; then
-  echo "No python3 found, please install first!"
-  echo
-  exit 1
-fi
-ln -s $p3 $fsd/bin/fspython
-
 #cleanup
 rm -rf $fss
diff --git a/tools/macos_build/.gitignore b/tools/macos_build/.gitignore
new file mode 100644
index 000000000..97da6dcc5
--- /dev/null
+++ b/tools/macos_build/.gitignore
@@ -0,0 +1,11 @@
+raw_package/
+installer/
+*.pkg
+*.gz
+
+.eggs
+build
+scripts/postinstall
+scripts_intell/postinstall
+dist/
+resources/
\ No newline at end of file
diff --git a/tools/macos_build/FastSurfer.py.template b/tools/macos_build/FastSurfer.py.template
new file mode 100644
index 000000000..0c8bd2225
--- /dev/null
+++ b/tools/macos_build/FastSurfer.py.template
@@ -0,0 +1,12 @@
+from subprocess import run
+
+proc = run(["/usr/bin/osascript", 
+"-e",
+"tell app \"Terminal\"", 
+"-e",
+"do script \"source /Applications/<fastsurfer>/macos_setup_fastsurfer.sh\"",
+"-e",
+"activate",
+"-e",
+"end tell"
+])
diff --git a/tools/macos_build/README.md b/tools/macos_build/README.md
new file mode 100644
index 000000000..b785b5fa1
--- /dev/null
+++ b/tools/macos_build/README.md
@@ -0,0 +1,40 @@
+# FastSurfer MacOS packaging
+## Create MacOS package
+
+In order to build the MacOS package of FastSurfer, simply run:
+
+```bash
+./build_release_package.sh <version> <architecture> <path_to_fastsurfer_to_package> [<link_to_freesurfer>]
+```
+
+Script creates release package for MacOS, where `<version>` is the release version, `<architecture>` is `arm` for arm64 arch based chips and `intel` for `x86_64` arch based chips.
+`<path_to_fastsurfer_to_package>` is the directory with the fastsurfer to package.
+Link to specific freesurfer distribution might be provided with `<link_to_freesurfer>` argument.
+
+### Dependencies for the script
+
+Script is using py2app python dependency, which isn't installed through any requirements file of FastSurfer, so in order to run the script, make sure that py2app is installed.
+
+### Running the package
+
+After the script is executed, `installer` folder will be created along with the MacOS package of FastSurfer inside.
+Run the package by opening it and follow instructions.
+
+After successful installation, FastSurfer applet and its source code will appear under the `/Applications` folder.
+
+### Run FastSurfer
+
+If you would want to run FastSurfer, you could either use terminal or FastSurfer applet. Though, running applet is recommended as it opens shell terminal and sets up environment for FastSurfer.
+
+#### FastSurfer Flags
+* The `--fs_license` points to your FreeSurfer license which needs to be available on your computer in the `my_fs_license_dir` that was mapped above. 
+* The `--t1` points to the t1-weighted MRI image to analyse (full path, with mounted name inside docker: /home/user/my_mri_data => /data)
+* The `--sid` is the subject ID name (output folder name)
+* The `--sd` points to the output directory (its mounted name inside docker: /home/user/my_fastsurfer_analysis => /output)
+* [more flags](../../doc/overview/FLAGS.md#fastsurfer-flags)
+
+Note, that the paths following `--fs_license`, `--t1`, and `--sd` are __inside__ the container, not global paths on your system, so they should point to the places where you mapped these paths above with the `-v` arguments. 
+
+A directory with the name as specified in `--sid` (here subjectX) will be created in the output directory (specified via `--sd`). So in this example output will be written to /home/user/my_fastsurfer_analysis/subjectX/ . Make sure the output directory is empty, to avoid overwriting existing files. 
+
+All other available flags are identical to the ones explained on the main page [README](../../README.md).
diff --git a/tools/macos_build/build_release_package.sh b/tools/macos_build/build_release_package.sh
new file mode 100755
index 000000000..7bc7d30cf
--- /dev/null
+++ b/tools/macos_build/build_release_package.sh
@@ -0,0 +1,116 @@
+#!/bin/bash
+
+if [ "$#" -lt 2 ] ; then
+  echo
+  echo "Usage:  build_release_package.sh <arm|intel> <dir_to_fastsurfer> "
+  echo
+  exit
+fi
+
+# cd into directory with this script 
+dir=${0%/*}
+if [ -d "$dir" ]; then
+  cd "$dir"
+fi 
+
+VERSION=$(python3 ../get_config_value.py --file ../config.yaml --key FASTSURFER.VERSION) # version of the project
+URL_TO_FREESURFER=$(python3 ../get_config_value.py --file ../config.yaml --key FREESURFER_LINK_MACOS) # freesurfer install url 
+ARCH_TYPE=$1 # chip architecture - arm or intel
+DIR_TO_FASTSURFER=$2 # directory to fastsurfer
+
+ARCH_TYPE_NAME="arm64"
+if [ "$ARCH_TYPE" = "intel" ]; then
+    ARCH_TYPE_NAME="x86_64"
+fi
+
+PACKAGE_NAME=FastSurfer$VERSION-macos-darwin_${ARCH_TYPE_NAME} # name of the package displayed in the installer
+ID="ord.deep-mi.FastSurfer.${VERSION}_${ARCH_TYPE_NAME}" # package identifier (f.e. com.mycompany.productid)
+INSTALLATION_DIR="/Applications" # install location for the content of the package
+OUTPUT_PKG="raw_package/$PACKAGE_NAME.pkg" # raw package file to be created
+INSTALLER_PKG="installer/$PACKAGE_NAME.pkg" # installer to be created
+
+# create temporary folder to package and copy FastSurfer over
+STAGED_DIR="FastSurferPackageContent"
+FASTSURFER_TO_PACKAGE="$STAGED_DIR/FastSurfer$VERSION"
+mkdir $STAGED_DIR
+rsync -av --progress $DIR_TO_FASTSURFER/ $FASTSURFER_TO_PACKAGE \
+      --exclude requirements.txt \
+      --exclude requirements.cpu.txt \
+      --exclude tools
+
+# install freesurfer into temp folder
+../install_fs_pruned.sh $STAGED_DIR --upx --url $URL_TO_FREESURFER
+
+SCRIPTS_DIR="./scripts" # directory with scripts executed during installation process (f.e. preinsatll postinstall)
+PYTHON_VERSION=$(python3 ../get_config_value.py --file ../config.yaml --key FASTSURFER.PYTHON_VERSION)
+
+# substitute values in postinstall script
+PATH_TO_FASTSURFER="$INSTALLATION_DIR/FastSurfer$VERSION"
+cp $SCRIPTS_DIR/postinstall.template $SCRIPTS_DIR/postinstall
+
+sed -i '' -e "s|<fastsurfer_home_dir>|${PATH_TO_FASTSURFER}|g" $SCRIPTS_DIR/postinstall
+sed -i '' -e "s|<python_version>|${PYTHON_VERSION}|g" $SCRIPTS_DIR/postinstall  
+if [ "$ARCH_TYPE" = "arm" ]; then
+    sed -i '' -e "s|<homebrew_dir>|/opt/homebrew|g" $SCRIPTS_DIR/postinstall
+else
+    sed -i '' -e "s|<homebrew_dir>|/usr/local|g" $SCRIPTS_DIR/postinstall
+fi
+
+# assemble resources
+mkdir resources
+cp $DIR_TO_FASTSURFER/doc/images/fastsurfer.png resources/
+cp $DIR_TO_FASTSURFER/doc/overview/MACOS.md resources/
+cp $DIR_TO_FASTSURFER/LICENSE resources/LICENSE.txt
+
+# create fastsurfer applet
+cp FastSurfer.py.template FastSurfer.py
+sed -i '' -e "s|<fastsurfer>|FastSurfer${VERSION}|g" FastSurfer.py
+
+cp macos_setup_fastsurfer.sh.template macos_setup_fastsurfer.sh
+sed -i '' -e "s|<fastsurfer>|FastSurfer${VERSION}|g" macos_setup_fastsurfer.sh
+sed -i '' -e "s|<python_version>|${PYTHON_VERSION}|g" macos_setup_fastsurfer.sh
+if [ "$ARCH_TYPE" = "arm" ]; then
+    sed -i '' -e "s|<mps_fallback_value>|1|g" macos_setup_fastsurfer.sh
+else
+    sed -i '' -e "s|<mps_fallback_value>|0|g" macos_setup_fastsurfer.sh
+fi
+mv macos_setup_fastsurfer.sh $FASTSURFER_TO_PACKAGE/
+
+python3 setup.py py2app --iconfile resources/fastsurfer.png
+mv dist/FastSurfer.app $STAGED_DIR/FastSurfer$VERSION.app
+
+rm -f FastSurfer.py
+chmod -R 755 $STAGED_DIR/*
+
+# create raw package
+mkdir raw_package
+pkgbuild \
+    --root $STAGED_DIR \
+    --version $VERSION \
+    --identifier $ID \
+    --install-location $INSTALLATION_DIR \
+    --scripts $SCRIPTS_DIR \
+    $OUTPUT_PKG
+
+rm -f $SCRIPTS_DIR/postinstall
+
+# create distribution file template based on provided package
+RESOURCES="./resources"
+DISTRIBUTION_FILE="resources/distribution.xml"
+productbuild --synthesize --package $OUTPUT_PKG $DISTRIBUTION_FILE
+
+# edit the distribution file
+# set title to package name (f.e. package_name.pkg -> <title>package_name</title>)
+python3 edit_distribution.py --file "$DISTRIBUTION_FILE" --title "$PACKAGE_NAME"
+
+# create installer package
+mkdir installer
+productbuild \
+    --distribution $DISTRIBUTION_FILE \
+    --resources $RESOURCES \
+    --package-path raw_package \
+    $INSTALLER_PKG
+
+# get rid of temporary folder
+rm -rf $STAGED_DIR
+rm -rf resources
diff --git a/tools/macos_build/edit_distribution.py b/tools/macos_build/edit_distribution.py
new file mode 100644
index 000000000..a634c4e8d
--- /dev/null
+++ b/tools/macos_build/edit_distribution.py
@@ -0,0 +1,95 @@
+# Copyright 2024 Image Analysis Lab, German Center for Neurodegenerative Diseases (DZNE), Bonn
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+import argparse
+import sys
+from pathlib import Path
+from xml.etree import ElementTree
+
+
+def make_parser() -> argparse.ArgumentParser:
+    """
+    Create a command line interface and return command line options.
+
+    Returns
+    -------
+    options
+        Namespace object holding options.
+    """
+    parser = argparse.ArgumentParser(
+        description="Script to edit provided distribution.xml file.",
+    )
+    parser.add_argument(
+        "--file", "-f",
+        type=Path,
+        dest="file",
+        help="path to distribution file to edit",
+        required=True,
+    )
+    parser.add_argument(
+        "--title", "-t",
+        type=str,
+        dest="title",
+        help="value for the title of the distribution file",
+        required=True
+    )
+    return parser
+
+
+def edit_distribution(distribution_file: Path | str, title: str) -> None:
+    """
+    Take path to distribution file and edit it.
+
+    Parameters
+    ----------
+    distribution_file : Path, str
+        Path to distribution file.
+    title : str
+        Value for the title tag.
+    """
+    dist_elementtree = ElementTree.parse(distribution_file)
+
+    root_tag = dist_elementtree.getroot()
+    
+    title_tag = ElementTree.SubElement(root_tag, "title")
+    title_tag.text = title
+    
+    background_tag = ElementTree.SubElement(root_tag, "background")
+    background_tag.attrib["file"] = "fastsurfer.png"
+    background_tag.attrib["uti"] = "public.png"
+    background_tag.attrib["scaling"] = "proportional"
+    background_tag.attrib["alignment"] = "bottomleft"
+
+    background_darkAqua_tag = ElementTree.SubElement(root_tag, "background-darkAqua")
+    background_darkAqua_tag.attrib = background_tag.attrib
+
+    license_tag = ElementTree.SubElement(root_tag, "license")
+    license_tag.attrib["file"] = "LICENSE.txt"
+    license_tag.attrib["mime-type"] = "text/txt"
+
+    conclusion_tag = ElementTree.SubElement(root_tag, "conclusion")
+    conclusion_tag.attrib["file"] = "MACOS.md"
+    conclusion_tag.attrib["mime-type"] = "text/txt"
+    
+    ElementTree.indent(dist_elementtree, '    ')
+
+    dist_elementtree.write(distribution_file,  encoding="utf-8", xml_declaration=True)
+
+    
+if __name__ == "__main__":
+    parser = make_parser()
+    args = parser.parse_args()
+
+    print(f"Editing distribution file: {args.file} ...")
+    edit_distribution(args.file, args.title)
+    sys.exit(0)
diff --git a/tools/macos_build/macos_setup_fastsurfer.sh.template b/tools/macos_build/macos_setup_fastsurfer.sh.template
new file mode 100644
index 000000000..f0cff739a
--- /dev/null
+++ b/tools/macos_build/macos_setup_fastsurfer.sh.template
@@ -0,0 +1,27 @@
+#!/bin/bash
+
+export FASTSURFER_HOME=/Applications/<fastsurfer>
+source $FASTSURFER_HOME/venv/bin/activate
+export PYTHONPATH=$FASTSURFER_HOME/venv/lib/python<python_version>/site-packages:$PYTHONPATH
+export PYTORCH_ENABLE_MPS_FALLBACK=<mps_fallback_value>
+export FREESURFER_HOME=/Applications/freesurfer
+source $FREESURFER_HOME/SetUpFreeSurfer.sh > /dev/null
+echo
+echo "This is the FastSurfer console. Call \`run_fastsurfer.sh -t1 ...\` in here! " 
+echo "See also https://deep-mi.org/FastSurfer/stable/overview/MACOS.html"
+
+if ! grep -q "export PATH=\"$(brew --prefix)/opt/grep/libexec/gnubin:\$PATH\"" ~/.bash_profile; then 
+    echo "export PATH=\"$(brew --prefix)/opt/grep/libexec/gnubin:\$PATH\"" >> ~/.bash_profile;
+    export PATH="$(brew --prefix)/opt/grep/libexec/gnubin:$PATH" 
+    echo "GNU grep has been added to path"
+fi
+
+if ! grep -q "export PATH=\"$FASTSURFER_HOME:\$PATH\"" ~/.bash_profile; then 
+    echo "export PATH=\"$FASTSURFER_HOME:\$PATH\"" >> ~/.bash_profile; 
+    export PATH="$FASTSURFER_HOME:$PATH"
+    echo "FastSurfer dir has been added to path"
+fi
+
+if [[ -z "${FS_LICENSE}" ]]; then 
+    echo "Set FS_LICENSE environmental variable"
+fi
diff --git a/tools/macos_build/scripts/postinstall.template b/tools/macos_build/scripts/postinstall.template
new file mode 100755
index 000000000..2e4c9b6e6
--- /dev/null
+++ b/tools/macos_build/scripts/postinstall.template
@@ -0,0 +1,77 @@
+#!/bin/bash
+
+FASTSURFER_HOME="<fastsurfer_home_dir>"
+PYTHON="python<python_version>"
+
+if [[ ! -f "$FASTSURFER_HOME/venv" ]]
+then
+  echo "Creating FastSurfer run environment"
+  <homebrew_dir>/bin/$PYTHON -m venv --copies $FASTSURFER_HOME/venv
+fi
+
+source $FASTSURFER_HOME/venv/bin/activate
+$PYTHON -m pip install --upgrade pip
+
+export PYTHONPATH=${FASTSURFER_HOME}:${PYTHONPATH}
+
+$PYTHON -m pip install -r $FASTSURFER_HOME/requirements.mac.txt
+
+$PYTHON $FASTSURFER_HOME/FastSurferCNN/download_checkpoints.py --all
+
+sed -i '' -e "s|(venv)|($(basename $FASTSURFER_HOME))|g" $FASTSURFER_HOME/venv/bin/activate  
+
+FREESURFER_HOME="/Applications/freesurfer"
+
+ln -sf $FASTSURFER_HOME/venv/bin/$PYTHON $FREESURFER_HOME/bin/fspython
+
+# FS calls these for version info, but we don't need them
+# so we link them to mri_info to save space.
+link_files="
+  bin/mri_and
+  bin/mri_aparc2aseg
+  bin/mri_ca_label
+  bin/mri_ca_normalize
+  bin/mri_ca_register
+  bin/mri_compute_overlap
+  bin/mri_compute_seg_overlap
+  bin/mri_em_register
+  bin/mri_fwhm
+  bin/mri_gcut
+  bin/mri_log_likelihood
+  bin/mri_motion_correct.fsl
+  bin/mri_normalize_tp2
+  bin/mri_or
+  bin/mri_relabel_nonwm_hypos
+  bin/mri_remove_neck
+  bin/mri_stats2seg
+  bin/mri_surf2vol
+  bin/mri_surfcluster
+  bin/mri_voldiff
+  bin/mri_watershed
+  bin/mris_divide_parcellation
+  bin/mris_left_right_register
+  bin/mris_surface_stats
+  bin/mris_thickness
+  bin/mris_thickness_diff
+  bin/nu_correct
+  bin/tkregister2_cmdl"
+
+# create target for link with ERROR message if called
+ltrg=$FREESURFER_HOME/bin/not-here.sh
+echo '#!/bin/bash
+if [ "$1" == "-all-info" ]; then
+  echo "$0 not included ..."
+  exit 0
+fi
+echo
+echo "ERROR: The binary $0 is not included, your call is forwarded to not-here.sh"
+echo
+exit 1
+' > $ltrg
+chmod a+x $ltrg
+echo
+for file in $link_files
+do
+  echo "linking $file"
+  ln -sf $ltrg $FREESURFER_HOME/$file 
+done
diff --git a/tools/macos_build/setup.py b/tools/macos_build/setup.py
new file mode 100644
index 000000000..dea6d97d3
--- /dev/null
+++ b/tools/macos_build/setup.py
@@ -0,0 +1,19 @@
+"""
+This is a setup.py script generated by py2applet
+
+Usage:
+    python setup.py py2app
+"""
+
+from setuptools import setup
+
+APP = ['FastSurfer.py']
+DATA_FILES = []
+OPTIONS = {}
+
+setup(
+    app=APP,
+    data_files=DATA_FILES,
+    options={'py2app': OPTIONS},
+    setup_requires=['py2app'],
+)