newMSM - the new version of Multimodal Surface Matching software

The new (BETA) version of MSM is now available.

Major updates

Most of the code from the original version has been replaced or revised, but some were reused. Most of the updates affect performance:

• complete rework of the mesh resampling functionality with an octree based nearest triangle search algorithm (inspired by the wb_command of Connectome Workbench)
• parallelisation of mesh resampling
• application of octree search during registration
• parallelisation of cost calculation during registration

Please note, the current version is 0.5.0-BETA. All feedbacks are much appreciated.

Download and install

NewMSM is available to download from FSL or Github. Please follow the steps described below. (Note: tested on Ubuntu Linux and MacOS.)

Download and install binary

1. Download and install FSL. For more information, please visit the FSL webpage.
2. Download and install newMSM from the FSL developer branch by executing the following command on Terminal:

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

3. Activate this environment:

   conda activate ./msm-env/
   

4. You can test with the newmsm -p command.

Install from source

1. Download and install FSL. For more information, please visit the FSL webpage.
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/
       git checkout v0.5.0
       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.

Most features remained the same as it was in the original MSM implementation. A detailed user guide will be published soon.

Links

FSL download and install instructions.

NewMSM GitHub repository.