From 75a42d12b71e77c79ad6a79bf3c955624b6b7d5e Mon Sep 17 00:00:00 2001 From: WillForan Date: Sat, 2 Mar 2024 21:05:58 -0500 Subject: [PATCH] =?UTF-8?q?=E2=9C=A8=20add=20skullstripping?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- readme.md | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/readme.md b/readme.md index 2c6df16..f059581 100644 --- a/readme.md +++ b/readme.md @@ -16,6 +16,7 @@ - [Raw Data](#raw-data) - [Provenance and Automation](#provenance-and-automation) - [Imaging Tools](#imaging-tools) + - [Skullstripping](#skullstripping) - [Warping](#warping) - [Manipulation](#manipulation) - [Modeling](#modeling) @@ -117,6 +118,14 @@ Dealing with DICOM and k-space images ## Imaging Tools Software to read, write, and manipulate volumetric and/or surface data. +### Skullstripping +- [optibet](https://montilab.psych.ucla.edu/fmri-wiki/optibet/) - Shell script to combine afni and fsl tools for more robust skull stripping in patient populations. +- [`3dSkullStrip`](https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dSkullStrip.html) - [AFNI](https://afni.nimh.nih.gov/)'s skull stripping utility with many parameters. +- [`bet`](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET/UserGuide) - [FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki)'s brain exraction tool. +- [`antsBrainExtraction.sh`](https://dpaniukov.github.io/2016/06/06/brain-extraction-with-ants.html) - [ANTs](http://stnava.github.io/ANTs/) version. +- [`mri-watershed`](https://surfer.nmr.mgh.harvard.edu/fswiki/mri_watershed) - Part of the [Freesurfer](https://freesurfer.net/) pipeline. +- [ROBEX](https://www.nitrc.org/projects/robex) - Robust Brain Extraction without parameter tweaking. + ### Warping Spatial normalization