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Ludovica Griffanti
C-MORE brain MRI
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18f8211f
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May 08, 2021
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Ludovica Griffanti
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# C-MORE QSM pipeline
*
`**QSM.m**`
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.
*
`**Mix_Mod_CSF.py**`
This script is to calculate CSF susceptibility values for QSM referencing.
*
`QSM.m`
: 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.
*
`Mix_Mod_CSF.py`
: This script is to calculate CSF susceptibility values for QSM referencing.
## Requirements
MATLAB R2017b or higher
STI Suite - https://people.eecs.berkeley.edu/~chunlei.liu/software.html
FSL - https://fsl.fmrib.ox.ac.uk/fsldownloads_registration
Mixture Modelling tool - https://github.com/allera/One_Dim_Mixture_Models
-
MATLAB R2017b or higher
-
STI Suite - https://people.eecs.berkeley.edu/~chunlei.liu/software.html
-
FSL - https://fsl.fmrib.ox.ac.uk/fsldownloads_registration
-
Mixture Modelling tool - https://github.com/allera/One_Dim_Mixture_Models
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