From 4fa2e21debba153ed15be066f683b0387459afc5 Mon Sep 17 00:00:00 2001 From: Atef Badji Date: Wed, 3 Oct 2018 03:27:03 -0400 Subject: [PATCH] add script for brain processing --- brain/diff/WM_atlas_registration.m | 32 ++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 brain/diff/WM_atlas_registration.m diff --git a/brain/diff/WM_atlas_registration.m b/brain/diff/WM_atlas_registration.m new file mode 100644 index 0000000..ac467ec --- /dev/null +++ b/brain/diff/WM_atlas_registration.m @@ -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'); + % 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 +