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Add script for brain processing #2

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Add script for brain processing #2

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32 changes: 32 additions & 0 deletions brain/diff/WM_atlas_registration.m
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Original file line number Diff line number Diff line change
@@ -0,0 +1,32 @@
%%% Registration WM atlas

%% FA template = JHU-ICBM-FA-1mm.nii.gz , Atlas = JHU-ICBM-labels-1mm.nii.gz

list = sct_tools_ls('RAMRI*');
for ilist = 1:length(list)
currentfolder = list{ilist};
subj_name = currentfolder;
currentfolder = strcat('/Volumes/projects/RAMRI/RAMRI_data/RAMRI_data_WM/', currentfolder, '/Processed_data/');
cd(currentfolder)

% Participants are first aligned into a common space. The JHU-ICBM-FA template is used as a reference for all subjects.

% Affine transfo on FA
sct_unix('isct_antsRegistration --dimensionality 3 --transform affine[1] --metric MI[FA.nii.gz,JHU-ICBM-FA-1mm.nii.gz,1,32] --convergence 30x10x5 --shrink-factors 5x3x1 --smoothing-sigmas 0x0x0mm --output [step0,src_regStep0.nii] --verbose 1');
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sct_unix does not seem to be defined anywhere in this repos

% Non-linear
sct_unix('isct_antsRegistration --dimensionality 3 --transform bsplinesyn[0.5,3] --metric MI[FA.nii.gz,JHU-ICBM-FA-1mm.nii.gz,1,32] --convergence 30x10x5 --shrink-factors 5x3x1 --smoothing-sigmas 0x0x0mm --output [step1,src_regStep1.nii] --verbose 1 -r step00GenericAffine.mat');
% Concat + apply warp to labels
sct_unix('sct_concat_transfo -d JHU-ICBM-FA-1mm.nii.gz -w step11InverseWarp.nii.gz,-step00GenericAffine.mat -o warp_FA_to_JHU.nii.gz');
sct_unix('sct_apply_transfo -d JHU-ICBM-labels-1mm.nii.gz -i FA.nii.gz -w warp_FA_to_JHU.nii.gz -o FA_to_JHU.nii.gz -x nn');
% In order to help the convergence of registration, the Laplacian transform is applied on 3D volumes in order to increase the contrast between white and gray matter
sct_unix('sct_maths -i FA_to_JHU.nii.gz -laplacian 2 -o FA_l.nii.gz');
sct_unix('sct_maths -i JHU-ICBM-FA-1mm.nii.gz -laplacian 2 -o JHU_l.nii.gz');
% The resulted images were registered together using Ants non linear registration tools
sct_unix('isct_antsRegistration --dimensionality 3 --transform bsplinesyn[0.5,3] --metric CC[FA_l.nii.gz,JHU_l.nii.gz,1,6] --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output [step2,src_regStep2.nii] --verbose 1');
sct_unix('sct_apply_transfo -i FA_to_JHU.nii.gz -d JHU-ICBM-labels-1mm.nii.gz -w step20InverseWarp.nii.gz -x linear -o FA_2_JHU_2.nii.gz');
% The same transformations were then applied to RD
sct_unix('sct_apply_transfo -d JHU-ICBM-labels-1mm.nii.gz -i RD.nii.gz -w warp_FA_to_JHU.nii.gz -o RD_to_JHU.nii.gz -x nn');
sct_unix('sct_apply_transfo -i RD_to_JHU.nii.gz -d JHU-ICBM-labels-1mm.nii.gz -w step20InverseWarp.nii.gz -x linear -o RD_2_JHU_2.nii.gz');

end