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Adjusted create_Group_MNI_plots #22

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merged 3 commits into from
Jun 21, 2023
Merged

Adjusted create_Group_MNI_plots #22

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1286e50
Added additional outcome measures and adjusted it to incorporate both…
KTZ228 Jun 6, 2023
2e9bd07
Adjusted documentation
KTZ228 Jun 6, 2023
ca0d60c
Revert "Adjusted documentation"
KTZ228 Jun 6, 2023
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43 changes: 32 additions & 11 deletions functions/create_group_MNI_plots.m
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Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
function create_group_MNI_plots(outputs_path, subject_list, parameters, options)
function create_group_MNI_plots(subject_list, parameters, options)
arguments
outputs_path string
subject_list
parameters struct
options.ROI_MNI_mask (:,:,:)
Expand All @@ -20,10 +19,10 @@ function create_group_MNI_plots(outputs_path, subject_list, parameters, options)
slice_labels = {'x','y','z'};



outputs_path = parameters.temp_output_dir;
bg_range_to_use = [];
isppa_range_to_use = [5, 6];
temp_range_to_use = [37, 37.5];
temp_range_to_use = [parameters.thermal.temp_0, parameters.thermal.temp_0 + 0.5];

full_subject_list = subject_list;
% first pass: get background intensity at the target slice & isppa range
Expand All @@ -43,8 +42,12 @@ function create_group_MNI_plots(outputs_path, subject_list, parameters, options)
segmented_image_mni_file = fullfile(outputs_path, sprintf('%s_final_medium_masks_MNI%s.nii.gz', results_prefix, parameters.results_filename_affix));
max_pressure_mni_file = fullfile(outputs_path, sprintf('%s_final_pressure_MNI%s.nii.gz', results_prefix, parameters.results_filename_affix));
output_pressure_file = fullfile(outputs_path,sprintf('%s_%s_isppa%s.csv', results_prefix, parameters.simulation_medium, parameters.results_filename_affix));
if strcmp(parameters.segmentation_software, 'headreco')
t1_mni_file = fullfile(headreco_folder, 'toMNI','T1fs_nu_12DOF_MNI.nii.gz');
else
t1_mni_file = fullfile(headreco_folder, 'toMNI','final_tissues_MNI.nii.gz');
end

t1_mni_file = fullfile(headreco_folder, 'toMNI','T1fs_nu_12DOF_MNI.nii.gz');
files_to_check = {t1_mni_file , segmented_image_mni_file, isppa_map_mni_file, max_pressure_mni_file, output_pressure_file};

if options.plot_heating
Expand Down Expand Up @@ -146,8 +149,12 @@ function create_group_MNI_plots(outputs_path, subject_list, parameters, options)
isppa_map_mni_file = fullfile(outputs_path, sprintf('%s_final_isppa_MNI%s.nii.gz', results_prefix, parameters.results_filename_affix));
segmented_image_mni_file = fullfile(outputs_path, sprintf('%s_final_medium_masks_MNI%s.nii.gz', results_prefix, parameters.results_filename_affix));
max_pressure_mni_file = fullfile(outputs_path, sprintf('%s_final_pressure_MNI%s.nii.gz', results_prefix, parameters.results_filename_affix));
t1_mni_file = fullfile(headreco_folder, 'toMNI','T1fs_nu_12DOF_MNI.nii.gz');
output_pressure_file = fullfile(outputs_path,sprintf('%s_%s_isppa%s.csv', results_prefix, parameters.simulation_medium, parameters.results_filename_affix));
if strcmp(parameters.segmentation_software, 'headreco')
t1_mni_file = fullfile(headreco_folder, 'toMNI','T1fs_nu_12DOF_MNI.nii.gz');
else
t1_mni_file = fullfile(headreco_folder, 'toMNI','final_tissues_MNI.nii.gz');
end

% get T1 in MNI space
t1_mni = niftiread(t1_mni_file);
Expand Down Expand Up @@ -191,6 +198,8 @@ function create_group_MNI_plots(outputs_path, subject_list, parameters, options)
end

fwhm_size = sum(max_pressure_map_mni >= max_pressure/2,'all');
fwhm_mask(max_pressure_map_mni ~= 0) = 1;

curTable = readtable(output_pressure_file);
curTable.('fwhm_size_MNI_based_on_pressure') = fwhm_size;

Expand All @@ -199,8 +208,17 @@ function create_group_MNI_plots(outputs_path, subject_list, parameters, options)

if isfield(options,'ROI_MNI_mask')
roi_size = sum(options.ROI_MNI_mask,'all');
avg_isppa_within_roi = mean(Isppa_map_mni(options.ROI_MNI_mask),'all');
avg_isppa_within_roi = mean(Isppa_map_mni(logical(options.ROI_MNI_mask)),'all');
if ~isequal((logical(options.ROI_MNI_mask.*fwhm_mask)), zeros(size(options.ROI_MNI_mask)))
avg_isppa_within_fwhm_and_roi_overlap = mean(Isppa_map_mni(logical(options.ROI_MNI_mask.*fwhm_mask)),'all');
else
avg_isppa_within_fwhm_and_roi_overlap = mean(avg_isppa_within_roi, 'all');
end
curTable.(sprintf('avg_isppa_within_fwhm_and_roi_overlap%s', options.outputs_suffix)) = avg_isppa_within_fwhm_and_roi_overlap;
n_voxels_within_roi_above_thresh = sum(options.ROI_MNI_mask & (max_pressure_map_mni >= max_pressure/2),'all');
props = regionprops(true(size(options.ROI_MNI_mask)), options.ROI_MNI_mask, 'WeightedCentroid');
dist_between_Isppa_and_center_of_ROI = norm(max_focus_MNI_grid - props.WeightedCentroid);
curTable.(sprintf('dist_between_Isppa_and_center_of_ROI%s', options.outputs_suffix)) = dist_between_Isppa_and_center_of_ROI;
curTable.(sprintf('avg_isppa_within_roi%s', options.outputs_suffix)) = avg_isppa_within_roi;
curTable.(sprintf('perc_voxels_within_roi%s', options.outputs_suffix)) = n_voxels_within_roi_above_thresh/roi_size;
curTable.(sprintf('perc_voxels_within_fwhm%s', options.outputs_suffix)) = n_voxels_within_roi_above_thresh/fwhm_size;
Expand Down Expand Up @@ -251,10 +269,13 @@ function create_group_MNI_plots(outputs_path, subject_list, parameters, options)
end

% combine individual images in a single image

suffix_list = {sprintf('maxT_MNI%s%s', parameters.results_filename_affix, options.outputs_suffix),...
sprintf('final_isppa_MNI%s%s', parameters.results_filename_affix, options.outputs_suffix)
};
if options.plot_heating == 1
suffix_list = {sprintf('maxT_MNI%s%s', parameters.results_filename_affix, options.outputs_suffix),...
sprintf('final_isppa_MNI%s%s', parameters.results_filename_affix, options.outputs_suffix)
};
else
suffix_list = sprintf('final_isppa_MNI%s%s', parameters.results_filename_affix, options.outputs_suffix);
end

for suffix_cell = suffix_list
suffix = suffix_cell{:};
Expand Down