From ec30ac64ba555f50bcd603deb292e9233d2921c2 Mon Sep 17 00:00:00 2001 From: Renato Besenczi Date: Fri, 13 Oct 2023 13:50:45 +0100 Subject: [PATCH] Updated newMSM page with new installation instructions and added major changes. --- _pages/newmsm.md | 45 ++++++++++++++++++++------------------------- 1 file changed, 20 insertions(+), 25 deletions(-) diff --git a/_pages/newmsm.md b/_pages/newmsm.md index fac5dad1f40..8ccd1fd714d 100644 --- a/_pages/newmsm.md +++ b/_pages/newmsm.md @@ -6,7 +6,19 @@ sitemap: false permalink: /newMSM/ --- -# newMSM - the new, reworked version of Multimodal Surface Matching software +# 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 0.4.3-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.) @@ -33,41 +45,24 @@ conda activate ./msm-env/ cd newmsm_sources ``` 3. Download and install newMSM sources. - 1. newresampler library + 1. newMSM application and dependencies ```console - git clone https://github.com/rbesenczi/msm-newresampler.git - cd msm-newresampler/src - git checkout tags/v0.4.1 + git clone https://github.com/rbesenczi/newMSM.git + cd newMSM/libraries/msm-newresampler/src/ + git checkout v0.4.3 make && make install - cd ../.. - ``` - 2. newmesreg library - ```console - git clone https://github.com/rbesenczi/msm-newmeshreg.git - cd msm-newmeshreg/src - git checkout tags/v0.4.1 + cd ../../msm-newmeshreg/src/ make && make install - cd ../.. - ``` - 3. newMSM application - ```console - git clone https://github.com/rbesenczi/newMSM.git - cd newMSM/src - git checkout tags/v0.4.1 + cd ../../../src/ make && make install - cd ../.. ``` 3. The binary `newmsm` should be in the folder `${FSLDEVDIR}/bin`. 4. You can test it with the `${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. +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](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation). -Newresampler GitHub [repository](https://github.com/rbesenczi/msm-newresampler). - -Newmeshreg GitHub [repository](https://github.com/rbesenczi/msm-newmeshreg). - NewMSM GitHub [repository](https://github.com/rbesenczi/newMSM).