Commit 18f8211f authored by Ludovica Griffanti's avatar Ludovica Griffanti
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Update README.md

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# C-MORE QSM pipeline # C-MORE QSM pipeline
* `**QSM.m**` * `QSM.m`: This script is the main QSM processing pipeline. `weightedCombination.m` and `phasevariance_nonlin.m` are supporting functions.
This script is the main QSM processing pipeline. `weightedCombination.m` and `phasevariance_nonlin.m` are supporting functions. * `14_FIRST_IDPs.sh` : This script is to calculate 14 subcortical (FSL-FIRST segmented) IDPs following UKB pipeline and to extract CSF voxels.
* `**14_FIRST_IDPs.sh**` * `Mix_Mod_CSF.py` : This script is to calculate CSF susceptibility values for QSM referencing.
This script is to calculate 14 subcortical (FSL-FIRST segmented) IDPs following UKB pipeline and to extract CSF voxels.
* `**Mix_Mod_CSF.py**`
This script is to calculate CSF susceptibility values for QSM referencing.
## Requirements ## Requirements
MATLAB R2017b or higher - MATLAB R2017b or higher
STI Suite - https://people.eecs.berkeley.edu/~chunlei.liu/software.html - STI Suite - https://people.eecs.berkeley.edu/~chunlei.liu/software.html
FSL - https://fsl.fmrib.ox.ac.uk/fsldownloads_registration - FSL - https://fsl.fmrib.ox.ac.uk/fsldownloads_registration
Mixture Modelling tool - https://github.com/allera/One_Dim_Mixture_Models - Mixture Modelling tool - https://github.com/allera/One_Dim_Mixture_Models
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