diff --git a/README.md b/README.md index ea9e41a..2d9d9cb 100644 --- a/README.md +++ b/README.md @@ -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 @@ -120,6 +121,27 @@ echo $CR_PAT | docker login ghcr.io -u --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: