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astamm authored Jun 7, 2023
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Multiple sclerosis scripts
==========================

This section describes Anima scripts for helping multiple sclerosis (MS) lesions segmentation.
This section describes Anima scripts created to segment lesions from brain MRI images in multiple sclerosis (MS) patients.

MSSEG 2016 prerpocessing script
MSSEG 2016 preprocessing script
-------------------------------

This script (**animaMSExamPreparationMSSEG2016.py**) combines several processing steps to preprocess a single time point containing T1, T2/PD, FLAIR and Gd T1 images using the same script that was used in the MSSEG 2016 challenge [1]. It relies on a precomputed brain mask that may be obtained from `volBrain <https://www.volbrain.upv.es>`_ (as for the challenge) or :doc:`the brain extraction scripts of Anima <segmentation_scripts>`. The script performs denoising, bias correctino, brain masking and registration to the FLAIR image as explained in [1].
This script (**animaMSExamPreparationMSSEG2016.py**) combines several processing steps to preprocess a single time point containing T1, T2/PD, FLAIR and Gd T1 images using the same script that was used in the MSSEG 2016 challenge [1]. It relies on a precomputed brain mask that may be obtained from `volBrain <https://www.volbrain.upv.es>`_ (as for the challenge) or :doc:`the brain extraction scripts of Anima <segmentation_scripts>`. The script performs denoising, bias correction, brain masking and registration to the FLAIR image as explained in [1].

MSSEG-2 longitudinal preprocessing script
-----------------------------------------
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