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Copy pathstep_15_inidivdual_tpj_roi_native.m
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step_15_inidivdual_tpj_roi_native.m
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clear all
close all
clc
cf = pwd;
sub = {'AA', 'AB', 'AC', 'AD', 'AE', 'AF', 'AG', 'AH', 'AI', 'AJ', 'AK', 'AL', 'AM', 'AN', 'AO', 'AP', 'AQ', 'AR'};
t_thresh = 1.64;
n_vox = [];
for i = 1:numel(sub)
% Native space
results_dir_c = [cf '/POF_nifti/' sub{i}, filesep, 'Results_native'];
% Contrast Intact vs. Baseline
global_baseline = fullfile(results_dir_c, filesep, 'spmT_0001.nii');
global_baseline_hdr = spm_vol(global_baseline); % get header of image
global_baseline_img = spm_read_vols(global_baseline_hdr); % read image
global_baseline_img(global_baseline_img < t_thresh) = 0;
global_baseline_img(global_baseline_img >= t_thresh) = 1;
% ominbus_mask = fullfile(results_dir_c, filesep, 'Omnibus_GM_Mask_native.nii');
% ominbus_mask_hdr = spm_vol(ominbus_mask); % get header of image
% ominbus_mask_img = spm_read_vols(ominbus_mask_hdr); % read image
%
% global_baseline_img = global_baseline_img .* ominbus_mask_img;
roi_folder = [cf '/POF_nifti/' sub{i}, filesep,'ROIs_native'];
%% TPJ left
tpj_roi_l = fullfile(roi_folder, 'rtpj_anatomy_l.nii');
tpj_roi_l_hdr = spm_vol(tpj_roi_l); % get header of image
tpj_roi_l_img = spm_read_vols(tpj_roi_l_hdr); % read image
tpj_roi_img_c = global_baseline_img .* tpj_roi_l_img;
n_vox(i,1) = sum(sum(sum(tpj_roi_img_c)));
tpj_nonroi_img_c = tpj_roi_l_img - tpj_roi_img_c;
n_vox(i,2) = sum(sum(sum(tpj_nonroi_img_c)));
% ROI as .nii
global_baseline_hdr.fname = [roi_folder, filesep, 'TPJ_Intact_Baseline_L.nii'];
global_baseline_hdr.private.dat.fname = global_baseline_hdr.fname;
spm_write_vol(global_baseline_hdr, tpj_roi_img_c);
global_baseline_hdr.fname = [roi_folder, filesep, 'TPJ_NonROI_L.nii'];
global_baseline_hdr.private.dat.fname = global_baseline_hdr.fname;
spm_write_vol(global_baseline_hdr, tpj_nonroi_img_c);
% Marsbar ROI (mat file)
img_name = [roi_folder, filesep, 'TPJ_Intact_Baseline_L.nii'];
roi_m = maroi_image(struct('vol', spm_vol(img_name), 'binarize',0, 'func', 'img'));
saveroi(roi_m, [roi_folder, filesep, 'TPJ_Intact_Baseline_L_roi.mat']);
img_name = [roi_folder, filesep, 'TPJ_NonROI_L.nii'];
roi_m = maroi_image(struct('vol', spm_vol(img_name), 'binarize',0, 'func', 'img'));
saveroi(roi_m, [roi_folder, filesep, 'TPJ_NonROI_L_roi.mat']);
%% TPJ right
tpj_roi_r = fullfile(roi_folder, 'rtpj_anatomy_r.nii');
tpj_roi_r_hdr = spm_vol(tpj_roi_r); % get header of image
tpj_roi_r_img = spm_read_vols(tpj_roi_r_hdr); % read image
tpj_roi_img_c = global_baseline_img .* tpj_roi_r_img;
n_vox(i,3) = sum(sum(sum(tpj_roi_img_c)));
tpj_nonroi_img_c = tpj_roi_r_img - tpj_roi_img_c;
n_vox(i,4) = sum(sum(sum(tpj_nonroi_img_c)));
% ROI as .nii
global_baseline_hdr.fname = [roi_folder, filesep, 'TPJ_Intact_Baseline_R.nii'];
global_baseline_hdr.private.dat.fname = global_baseline_hdr.fname;
spm_write_vol(global_baseline_hdr, tpj_roi_img_c);
global_baseline_hdr.fname = [roi_folder, filesep, 'TPJ_NonROI_R.nii'];
global_baseline_hdr.private.dat.fname = global_baseline_hdr.fname;
spm_write_vol(global_baseline_hdr, tpj_nonroi_img_c);
% Marsbar ROI (mat file)
img_name = [roi_folder, filesep, 'TPJ_Intact_Baseline_R.nii'];
roi_m = maroi_image(struct('vol', spm_vol(img_name), 'binarize',0, 'func', 'img'));
saveroi(roi_m, [roi_folder, filesep, 'TPJ_Intact_Baseline_R_roi.mat']);
img_name = [roi_folder, filesep, 'TPJ_NonROI_R.nii'];
roi_m = maroi_image(struct('vol', spm_vol(img_name), 'binarize',0, 'func', 'img'));
saveroi(roi_m, [roi_folder, filesep, 'TPJ_NonROI_R_roi.mat']);
end
save('n_vox_native.mat', 'n_vox');