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hMRI-toolbox-public/tbx_scfg_hmri_proc.m
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function proc = tbx_scfg_hmri_proc | |
% Configuration file for the "histological MRI" (hMRI) toolbox | |
% Previously named "Voxel-Based Quantification" (VBQ) | |
% -> Dealing with the processign of the maps | |
% This include 3 main processing steps: | |
% - Unified Segmentation (US) -> produces individual tissue maps + warping | |
% into MNI space | |
% - DARTEL -> improves the warping into a common space of multiple | |
% subjects, based on their tissue maps | |
% - Smoothing -> tissue specific weighted averaging | |
% These steps are split into 3 sub-modules. | |
% | |
% For simplicity, 2 standard pipelines are also set up: | |
% - US+Smooth -> applies US, warps into MNI, then smoothes | |
% (weighted-average) | |
% - US+Dartel+Smooth -> applies US, builds Dartel template and warps into | |
% MNI, then smoothes (weighted-average) | |
%_______________________________________________________________________ | |
% Copyright (C) 2017 Cyclotron Research Centre | |
% Written by Christophe Phillips | |
% NOTE: | |
% Only the Dartel tool is made available. Shoot could be added later on if | |
% needed or wanted... | |
% --------------------------------------------------------------------- | |
% proc_modul Preprocess maps -> individual steps | |
% --------------------------------------------------------------------- | |
proc_modul = cfg_choice; | |
proc_modul.tag = 'proc_modul'; | |
proc_modul.name = 'Proc. hMRI -> Individual modules'; | |
proc_modul.help = { | |
['Parameter maps are spatially processed and brought into standard space',... | |
'for furhter statistical analysis.'] | |
['This include 3 main processing steps:'] | |
['- Unified Segmentation (US) -> produces individual tissue maps' ... | |
'+ warping into MNI space'] | |
['- DARTEL -> improves the warping into a common space of multiple' ... | |
'subjects, based on their tissue maps'] | |
['- Smoothing -> tissue specific weighted averaging'] | |
}'; %#ok<*NBRAK> | |
proc_modul.values = {tbx_scfg_hmri_proc_US tbx_scfg_hmri_proc_Dartel tbx_scfg_hmri_proc_smooth}; | |
% --------------------------------------------------------------------- | |
% proc Preprocess maps | |
% --------------------------------------------------------------------- | |
proc = cfg_choice; | |
proc.tag = 'proc'; | |
proc.name = 'Process hMRI maps'; | |
proc.help = { | |
['Parameter maps are spatially processed and brought into standard space',... | |
'for furhter statistical analysis.'] | |
['This include 3 main processing steps:'] | |
['- Unified Segmentation (US) -> produces individual tissue maps' ... | |
'+ warping into MNI space'] | |
['- DARTEL -> improves the warping into a common space of multiple' ... | |
'subjects, based on their tissue maps'] | |
['- Smoothing -> tissue specific weighted averaging'] | |
[' '] | |
['For simplicity, 2 standard pipelines are also set up:'] | |
['- US+Smooth -> applies US, warps into MNI, then smoothes (weighted-average)'] | |
['US+Dartel+Smooth -> applies US, builds Dartel template and warps' ... | |
'into MNI, then smoothes (weighted-average)'] | |
}'; %#ok<*NBRAK> | |
proc.values = {tbx_scfg_hmri_proc_pipeline proc_modul}; | |
end |