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Adds dcm2niix build instructions to README #37

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Adds dcm2niix build instructions to README #37

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22 changes: 22 additions & 0 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,7 @@ with the segmentations generated by TotalSegmentator
- GPU-enabled machine
- Docker
- Required for running the MAP. Not required for running source code
- dcm2niix ([see build instructions](#dcm2niix-install))

## Setup

Expand Down Expand Up @@ -120,6 +121,27 @@ echo $CR_PAT | docker login ghcr.io -u <github-username> --password-stdin
docker push ghcr.io/gstt-csc/totalsegmentator-aide/map-init:0.2.0
```

## dcm2niix install

This MAP requires [dcm2niix](https://github.com/rordenlab/dcm2niix). For best performance, we build from source
following the [guidelines here](https://github.com/rordenlab/dcm2niix#build-from-source).

Instructions in short (assuming Ubuntu):
```shell
# install dcm2niix dependencies
sudo apt-get install cmake pkg-config

# build and install dcm2niix
git clone https://github.com/rordenlab/dcm2niix.git
cd dcm2niix
mkdir build && cd build
cmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON ..
sudo make install # creates dcm2niix inside /usr/local/bin

# test install
dcm2niix -h
```

## GitHub Packages

Note: two containers are present under GitHub Packages:
Expand Down