newMSM installation guide

Download and install

NewMSM is available to download from FSL conda channels or Github. Please follow the steps described below. (Note: tested on Ubuntu 20.04, 22.04, 24.04 and MacOS Sonoma 14.7.1.)

If you already have FSL installed

1. Install newMSM by executing the following in Terminal:

   update_fsl_package fsl-newmsm
   

2. You can test with newmsm -p.

Download and install binary

1. Download and install a conda distribution, e.g. miniconda.
2. Download and install newMSM from the FSL public conda channels by executing the following command in Terminal:

   conda create -c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/ -c conda-forge -p ./msm-env fsl-newmsm
   

3. (optional) Activate this environment:

   conda activate ./msm-env/
   

4. You can test with the ./msm-env/bin/newmsm -p command (or just newmsm -p, if you activated the environment).

Install from source

1. Download and install FSL and set up a development environment. For more information, please visit the FSL development pages.
2. Create a directoy where you can download sources:

   mkdir newmsm_sources
   cd newmsm_sources
   

3. Download and install newMSM sources.
   1. newMSM application and dependencies

      git clone https://github.com/rbesenczi/newMSM.git
      cd newMSM/libraries/msm-newresampler/src/
      make && make install
      cd ../../msm-newmeshreg/src/
      make && make install
      cd ../../../src/
      make && make install
      

4. The binary newmsm should be in the folder ${FSLDEVDIR}/bin.
5. You can test it with the ${FSLDEVDIR}/bin/newmsm -p command.