Add MacOS build packaging tool

.github/workflows/deploy.yml

@@ -1,55 +1,94 @@
 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:
+      VERSION: 242
+      FREESURFER_URL: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-macOS-darwin_x86_64-7.4.1.tar.gz
+      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: |
-          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 }}
+          python -m pip install py2app
 
+          brew update
+          brew upgrade || true
+      - name: package app for ${{ matrix.arch }}
+        run: tools/macos_build/build_release_package.sh ${{ env.VERSION }} ${{ matrix.arch }} ${{ env.FASTSURFER_DIR }} ${{ env.FREESURFER_URL }}
+      - name: Move assets.
+        if: env.RELEASE_ASSETS == 'true'
+        run: |
+          mkdir assets
+          mv tools/macos_build/installer/* assets/
+      - name: Upload release assets.
+        uses: softprops/action-gh-release@v2
+        if: env.RELEASE_ASSETS == 'true'
+        with:
+          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 }}

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)`. 
 

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:
 

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**`:

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/*`

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:

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:

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 

Docker/Dockerfile → 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

Docker/README.md → 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.