This is the main repository of the reimplemented MSM software. The code and licenses of the original version can be found at this link. The user guide of that version can be found here.
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 0.6.3-BETA. All feedbacks are much appreciated.
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 FSL. For more information, please visit the FSL webpage.
- 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
- Activate this environment:
conda activate ./msm-env/
- You can test with the
newmsm -p
command.
- Download and install FSL. For more information, please visit the FSL webpage.
- Create a directoy where you can download sources:
mkdir newmsm_sources cd newmsm_sources
- Download and install newMSM sources.
- 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
- newMSM application and dependencies
- The binary
newmsm
should be in the folder${FSLDEVDIR}/bin
. - 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.
FSL download and install instructions.