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markmikkelsenmarkmikkelsen
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Merge pull request #53 from markmikkelsen/dev
Merge with dev
2 parents bfe5574 + 544464f commit d4a1e1f

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9 files changed

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‎CoRegStandAlone/Seg.m‎

Lines changed: 112 additions & 79 deletions
Original file line numberDiff line numberDiff line change
@@ -40,6 +40,8 @@
4040
vox = MRS_struct.p.vox(1);
4141
kk = 1;
4242
setup_spm = 1;
43+
prob_threshold = 0.9; % threshold to reduce partial volume effect and
44+
% improve accuracy of tissue probability maps
4345

4446
for ii = 1:length(MRS_struct.metabfile)
4547

@@ -50,13 +52,13 @@
5052

5153
% Check to see if segmentation has already been done (and all
5254
% probability tissue maps are present)
53-
tmp = {[T1dir filesep 'c1' T1name T1ext]
54-
[T1dir filesep 'c2' T1name T1ext]
55-
[T1dir filesep 'c3' T1name T1ext]
56-
[T1dir filesep 'c6' T1name T1ext]};
57-
filesExist = zeros(1,length(tmp));
58-
for jj = 1:length(tmp)
59-
filesExist(jj) = exist(tmp{jj}, 'file');
55+
tissue_maps = {[T1dir filesep 'c1' T1name T1ext]
56+
[T1dir filesep 'c2' T1name T1ext]
57+
[T1dir filesep 'c3' T1name T1ext]
58+
[T1dir filesep 'c6' T1name T1ext]};
59+
filesExist = zeros(1,length(tissue_maps));
60+
for jj = 1:length(tissue_maps)
61+
filesExist(jj) = exist(tissue_maps{jj}, 'file');
6062
end
6163
if ~all(filesExist)
6264
if setup_spm
@@ -88,89 +90,120 @@
8890
GM = [T1dir filesep 'c1' T1name T1ext];
8991
WM = [T1dir filesep 'c2' T1name T1ext];
9092
CSF = [T1dir filesep 'c3' T1name T1ext];
91-
air = [T1dir filesep 'c6' T1name T1ext];
93+
BG = [T1dir filesep 'c6' T1name T1ext];
9294

93-
GMvol = spm_vol(GM);
94-
WMvol = spm_vol(WM);
95-
CSFvol = spm_vol(CSF);
96-
airvol = spm_vol(air);
97-
98-
% Segmentation quality metrics (Chua et al. JMRI, 2009; Ganzetti et
99-
% al. Front. Neuroinform., 2016; Esteban et al. PLOS One, 2017)
95+
GM_vol = spm_vol(GM);
96+
WM_vol = spm_vol(WM);
97+
CSF_vol = spm_vol(CSF);
98+
BG_vol = spm_vol(BG);
99+
100+
% MRIQC image quality metrics (Esteban et al., 2017,doi:10.1371/journal.pone.0184661;
101+
% also see: Chua et al., 2009, doi:10.1002/jmri.21768; Ganzetti et al., 2016,
102+
% doi:10.3389/fninf.2016.00010)
100103
T1 = spm_vol(struc);
101104
T1_tmp = T1.private.dat(:,:,:);
102-
103-
WMvol_tmp = WMvol.private.dat(:,:,:);
104-
WMvol_tmp(WMvol_tmp < 0.9) = NaN;
105-
WMvol_thresh = WMvol_tmp .* T1_tmp;
106-
WMvol_thresh = WMvol_thresh(:);
107-
108-
GMvol_tmp = GMvol.private.dat(:,:,:);
109-
GMvol_tmp(GMvol_tmp < 0.9) = NaN;
110-
GMvol_thresh = GMvol_tmp .* T1_tmp;
111-
GMvol_thresh = GMvol_thresh(:);
112-
113-
airvol_tmp = airvol.private.dat(:,:,:);
114-
airvol_tmp(airvol_tmp < 0.9) = NaN;
115-
airvol_thresh = airvol_tmp .* T1_tmp;
116-
airvol_thresh = airvol_thresh(:);
117-
118-
MRS_struct.out.QA.CV_WM(ii) = std(WMvol_thresh, 'omitnan') / mean(WMvol_thresh, 'omitnan');
119-
MRS_struct.out.QA.CV_GM(ii) = std(GMvol_thresh, 'omitnan') / mean(GMvol_thresh, 'omitnan');
120-
MRS_struct.out.QA.CJV(ii) = (std(WMvol_thresh, 'omitnan') + std(GMvol_thresh, 'omitnan')) ...
121-
/ abs(mean(WMvol_thresh, 'omitnan') - mean(GMvol_thresh, 'omitnan'));
122-
MRS_struct.out.QA.CNR(ii) = abs(mean(WMvol_thresh, 'omitnan') - mean(GMvol_thresh, 'omitnan')) / ...
123-
sqrt(var(airvol_thresh, 'omitnan') + var(WMvol_thresh, 'omitnan') + var(GMvol_thresh, 'omitnan'));
124-
105+
106+
WM_vol_tmp = WM_vol.private.dat(:,:,:);
107+
WM_vol_tmp(WM_vol_tmp < prob_threshold) = 0;
108+
T1_WM = WM_vol_tmp .* T1_tmp;
109+
T1_WM = T1_WM(:);
110+
T1_WM = T1_WM(T1_WM > 0); % include only nonzero voxels
111+
112+
GM_vol_tmp = GM_vol.private.dat(:,:,:);
113+
GM_vol_tmp(GM_vol_tmp < prob_threshold) = 0;
114+
T1_GM = GM_vol_tmp .* T1_tmp;
115+
T1_GM = T1_GM(:);
116+
T1_GM = T1_GM(T1_GM > 0);
117+
118+
CSF_vol_tmp = CSF_vol.private.dat(:,:,:);
119+
CSF_vol_tmp(CSF_vol_tmp < prob_threshold) = 0;
120+
T1_CSF = CSF_vol_tmp .* T1_tmp;
121+
T1_CSF = T1_CSF(:);
122+
T1_CSF = T1_CSF(T1_CSF > 0);
123+
124+
BG_vol_tmp = BG_vol.private.dat(:,:,:);
125+
BG_vol_tmp(BG_vol_tmp < prob_threshold) = 0;
126+
T1_BG = BG_vol_tmp .* T1_tmp;
127+
T1_BG = T1_BG(:);
128+
T1_BG = T1_BG(T1_BG > 0);
129+
130+
head_vol_tmp = 1 - BG_vol.private.dat(:,:,:);
131+
head_vol_tmp(head_vol_tmp < prob_threshold) = 0;
132+
T1_head = head_vol_tmp .* T1_tmp;
133+
T1_head = T1_head(:);
134+
T1_head = T1_head(T1_head > 0);
135+
136+
MRS_struct.out.QA.CV.WM(ii) = mad(T1_WM,1) / median(T1_WM);
137+
MRS_struct.out.QA.CV.GM(ii) = mad(T1_GM,1) / median(T1_GM);
138+
MRS_struct.out.QA.CV.CSF(ii) = mad(T1_CSF,1) / median(T1_CSF);
139+
MRS_struct.out.QA.CJV(ii) = (mad(T1_WM,1) + mad(T1_GM,1)) / abs(median(T1_WM) - median(T1_GM));
140+
MRS_struct.out.QA.CNR(ii) = abs(median(T1_WM) - median(T1_GM)) / sqrt(std(T1_WM).^2 + std(T1_GM).^2 + std(T1_BG).^2);
141+
125142
T1_tmp = T1_tmp(:);
126143
n_vox = numel(T1_tmp);
127144
efc_max = n_vox * (1/sqrt(n_vox)) * log(1/sqrt(n_vox));
128145
b_max = sqrt(sum(T1_tmp.^2));
129-
MRS_struct.out.QA.EFC(ii) = (1/efc_max) .* sum((T1_tmp ./ b_max) .* log((T1_tmp + eps) ./ b_max));
130-
146+
MRS_struct.out.QA.EFC(ii) = (1/efc_max) .* sum((T1_tmp / b_max) .* log((T1_tmp + eps) / b_max));
147+
148+
MRS_struct.out.QA.FBER(ii) = median(abs(T1_head).^2) / median(abs(T1_BG).^2);
149+
MRS_struct.out.QA.WM2MAX(ii) = median(T1_WM) / prctile(T1_tmp, 99.95);
150+
151+
MRS_struct.out.QA.SNR.WM(ii) = median(T1_WM) / (std(T1_WM) * sqrt(numel(T1_WM) / (numel(T1_WM) - 1)));
152+
MRS_struct.out.QA.SNR.GM(ii) = median(T1_GM) / (std(T1_GM) * sqrt(numel(T1_GM) / (numel(T1_GM) - 1)));
153+
MRS_struct.out.QA.SNR.CSF(ii) = median(T1_CSF) / (std(T1_CSF) * sqrt(numel(T1_CSF) / (numel(T1_CSF) - 1)));
154+
MRS_struct.out.QA.SNR.total(ii) = mean([MRS_struct.out.QA.SNR.WM(ii) MRS_struct.out.QA.SNR.GM(ii) MRS_struct.out.QA.SNR.CSF(ii)]);
155+
156+
MRS_struct.out.QA.SNR_D.WM(ii) = median(T1_WM) / (sqrt(2 / (4 - pi)) * mad(T1_BG,1));
157+
MRS_struct.out.QA.SNR_D.GM(ii) = median(T1_GM) / (sqrt(2 / (4 - pi)) * mad(T1_BG,1));
158+
MRS_struct.out.QA.SNR_D.CSF(ii) = median(T1_CSF) / (sqrt(2 / (4 - pi)) * mad(T1_BG,1));
159+
MRS_struct.out.QA.SNR_D.total(ii) = mean([MRS_struct.out.QA.SNR_D.WM(ii) MRS_struct.out.QA.SNR_D.GM(ii) MRS_struct.out.QA.SNR_D.CSF(ii)]);
160+
131161
% Loop over voxels if PRIAM
132162
for kk = 1:length(vox)
133-
134-
voxmaskvol = spm_vol(cell2mat(MRS_struct.mask.(vox{kk}).fname(ii)));
135-
[a,b,c] = fileparts(voxmaskvol.fname);
136-
163+
164+
vox_mask_vol = spm_vol(cell2mat(MRS_struct.mask.(vox{kk}).fname(ii)));
165+
[a,b,c] = fileparts(vox_mask_vol.fname);
166+
137167
% GM
138-
O_GMvox.fname = fullfile(a, [b '_GM' c]);
139-
O_GMvox.descrip = 'MRS_voxel_mask_GM';
140-
O_GMvox.dim = voxmaskvol.dim;
141-
O_GMvox.dt = voxmaskvol.dt;
142-
O_GMvox.mat = voxmaskvol.mat;
143-
GM_voxmask_vol = GMvol.private.dat(:,:,:) .* voxmaskvol.private.dat(:,:,:);
144-
O_GMvox = spm_write_vol(O_GMvox, GM_voxmask_vol);
168+
GM_vox.fname = fullfile(a, [b '_GM' c]);
169+
GM_vox.descrip = 'MRS_voxel_mask_GM';
170+
GM_vox.dim = vox_mask_vol.dim;
171+
GM_vox.dt = vox_mask_vol.dt;
172+
GM_vox.mat = vox_mask_vol.mat;
173+
GM_vox_mask_vol = GM_vol.private.dat(:,:,:) .* vox_mask_vol.private.dat(:,:,:);
174+
GM_vox = spm_write_vol(GM_vox, GM_vox_mask_vol);
145175

146176
% WM
147-
O_WMvox.fname = fullfile(a, [b '_WM' c]);
148-
O_WMvox.descrip = 'MRS_voxel_mask_WM';
149-
O_WMvox.dim = voxmaskvol.dim;
150-
O_WMvox.dt = voxmaskvol.dt;
151-
O_WMvox.mat = voxmaskvol.mat;
152-
WM_voxmask_vol = WMvol.private.dat(:,:,:) .* voxmaskvol.private.dat(:,:,:);
153-
O_WMvox = spm_write_vol(O_WMvox, WM_voxmask_vol);
177+
WM_vox.fname = fullfile(a, [b '_WM' c]);
178+
WM_vox.descrip = 'MRS_voxel_mask_WM';
179+
WM_vox.dim = vox_mask_vol.dim;
180+
WM_vox.dt = vox_mask_vol.dt;
181+
WM_vox.mat = vox_mask_vol.mat;
182+
WM_vox_mask_vol = WM_vol.private.dat(:,:,:) .* vox_mask_vol.private.dat(:,:,:);
183+
WM_vox = spm_write_vol(WM_vox, WM_vox_mask_vol);
154184

155185
% CSF
156-
O_CSFvox.fname = fullfile(a, [b '_CSF' c]);
157-
O_CSFvox.descrip = 'MRS_voxel_mask_CSF';
158-
O_CSFvox.dim = voxmaskvol.dim;
159-
O_CSFvox.dt = voxmaskvol.dt;
160-
O_CSFvox.mat = voxmaskvol.mat;
161-
CSF_voxmask_vol = CSFvol.private.dat(:,:,:) .* voxmaskvol.private.dat(:,:,:);
162-
O_CSFvox = spm_write_vol(O_CSFvox, CSF_voxmask_vol);
186+
CSF_vox.fname = fullfile(a, [b '_CSF' c]);
187+
CSF_vox.descrip = 'MRS_voxel_mask_CSF';
188+
CSF_vox.dim = vox_mask_vol.dim;
189+
CSF_vox.dt = vox_mask_vol.dt;
190+
CSF_vox.mat = vox_mask_vol.mat;
191+
CSF_vox_mask_vol = CSF_vol.private.dat(:,:,:) .* vox_mask_vol.private.dat(:,:,:);
192+
CSF_vox = spm_write_vol(CSF_vox, CSF_vox_mask_vol);
163193

164194
% 3. Calculate a CSF-corrected i.u. value and output it to the structure
165195

166-
GMsum = sum(sum(sum(O_GMvox.private.dat(:,:,:))));
167-
WMsum = sum(sum(sum(O_WMvox.private.dat(:,:,:))));
168-
CSFsum = sum(sum(sum(O_CSFvox.private.dat(:,:,:))));
169-
170-
fGM = GMsum / (GMsum + WMsum + CSFsum);
171-
fWM = WMsum / (GMsum + WMsum + CSFsum);
172-
fCSF = CSFsum / (GMsum + WMsum + CSFsum);
173-
196+
GM_vox_n = GM_vox.private.dat(:,:,:);
197+
GM_sum = sum(GM_vox_n(GM_vox_n > prob_threshold));
198+
WM_vox_n = WM_vox.private.dat(:,:,:);
199+
WM_sum = sum(WM_vox_n(WM_vox_n > prob_threshold));
200+
CSF_vox_n = CSF_vox.private.dat(:,:,:);
201+
CSF_sum = sum(CSF_vox_n(CSF_vox_n > prob_threshold));
202+
203+
fGM = GM_sum / (GM_sum + WM_sum + CSF_sum);
204+
fWM = WM_sum / (GM_sum + WM_sum + CSF_sum);
205+
fCSF = CSF_sum / (GM_sum + WM_sum + CSF_sum);
206+
174207
MRS_struct.out.(vox{kk}).tissue.fGM(ii) = fGM;
175208
MRS_struct.out.(vox{kk}).tissue.fWM(ii) = fWM;
176209
MRS_struct.out.(vox{kk}).tissue.fCSF(ii) = fCSF;
@@ -247,7 +280,7 @@
247280
end
248281

249282
% Plot segmented voxel as a montage
250-
MRS_struct.mask.(vox{kk}).img_montage{ii} = PlotSegmentedVoxels(struc, voxoff, voxmaskvol, O_GMvox, O_WMvox, O_CSFvox);
283+
MRS_struct.mask.(vox{kk}).img_montage{ii} = PlotSegmentedVoxels(struc, voxoff, vox_mask_vol, GM_vox, WM_vox, CSF_vox);
251284

252285
if strcmp(MRS_struct.p.vendor,'Siemens_rda')
253286
[~,tmp,tmp2] = fileparts(MRS_struct.metabfile{ii*2-1});
@@ -348,13 +381,13 @@
348381
end
349382

350383

351-
function img_montage = PlotSegmentedVoxels(struc, voxoff, voxmaskvol, O_GMvox, O_WMvox, O_CSFvox)
384+
function img_montage = PlotSegmentedVoxels(struc, voxoff, vox_mask_vol, GM_vox, WM_vox, CSF_vox)
352385

353386
img_t = flipud(voxel2world_space(spm_vol(struc), voxoff));
354-
mask_t = flipud(voxel2world_space(voxmaskvol, voxoff));
355-
mask_t_GM = flipud(voxel2world_space(O_GMvox, voxoff));
356-
mask_t_WM = flipud(voxel2world_space(O_WMvox, voxoff));
357-
mask_t_CSF = flipud(voxel2world_space(O_CSFvox, voxoff));
387+
mask_t = flipud(voxel2world_space(vox_mask_vol, voxoff));
388+
mask_t_GM = flipud(voxel2world_space(GM_vox, voxoff));
389+
mask_t_WM = flipud(voxel2world_space(WM_vox, voxoff));
390+
mask_t_CSF = flipud(voxel2world_space(CSF_vox, voxoff));
358391

359392
w_t = zeros(size(img_t));
360393

‎GannetCoRegister.m‎

Lines changed: 28 additions & 22 deletions
Original file line numberDiff line numberDiff line change
@@ -23,7 +23,13 @@
2323
end
2424

2525
MRS_struct.info.datetime.coreg = datetime('now');
26-
MRS_struct.info.version.coreg = '250912';
26+
MRS_struct.info.version.coreg = '250914';
27+
28+
if ~isMATLABReleaseOlderThan("R2025a") && MRS_struct.p.append
29+
font_size_adj = 2.75;
30+
else
31+
font_size_adj = 0;
32+
end
2733

2834
warning('off'); % temporarily suppress warning messages
2935

@@ -188,34 +194,34 @@
188194
if length(fname) > 30
189195
fname = [fname(1:12) '...' fname(end-11:end)];
190196
end
191-
text(0.5, 0.75, 'Mask output: ', 'Units', 'normalized', 'HorizontalAlignment' , 'right', 'FontName', 'Arial', 'FontSize', 13);
192-
text(0.5, 0.75, [' ' fname], 'Units', 'normalized', 'FontName', 'Arial', 'FontSize', 13, 'Interpreter', 'none');
197+
text(0.5, 0.75, 'Mask output: ', 'Units', 'normalized', 'HorizontalAlignment' , 'right', 'FontName', 'Arial', 'FontSize', 13 - font_size_adj);
198+
text(0.5, 0.75, [' ' fname], 'Units', 'normalized', 'FontName', 'Arial', 'FontSize', 13 - font_size_adj, 'Interpreter', 'none');
193199

194-
text(0.5, 0.63, 'Spatial parameters: ', 'Units', 'normalized', 'HorizontalAlignment', 'right', 'FontName', 'Arial', 'FontSize', 13);
195-
text(0.5, 0.63, ' [LR, PA, SI]', 'Units', 'normalized', 'FontName', 'Arial', 'FontSize', 13);
200+
text(0.5, 0.63, 'Spatial parameters: ', 'Units', 'normalized', 'HorizontalAlignment', 'right', 'FontName', 'Arial', 'FontSize', 13 - font_size_adj);
201+
text(0.5, 0.63, ' [LR, PA, SI]', 'Units', 'normalized', 'FontName', 'Arial', 'FontSize', 13 - font_size_adj);
196202

197203
str = [' ' num2str(MRS_struct.p.voxdim(ii,1)) ' \times ' num2str(MRS_struct.p.voxdim(ii,2)) ' \times ' num2str(MRS_struct.p.voxdim(ii,3)) ' mm^{3}'];
198-
text(0.5, 0.51, 'Dimensions: ', 'Units', 'normalized', 'HorizontalAlignment', 'right', 'FontName', 'Arial', 'FontSize', 13);
199-
text(0.5, 0.51, str, 'Units', 'normalized', 'FontName', 'Arial', 'FontSize', 13, 'Interpreter', 'tex');
204+
text(0.5, 0.51, 'Dimensions: ', 'Units', 'normalized', 'HorizontalAlignment', 'right', 'FontName', 'Arial', 'FontSize', 13 - font_size_adj);
205+
text(0.5, 0.51, str, 'Units', 'normalized', 'FontName', 'Arial', 'FontSize', 13 - font_size_adj, 'Interpreter', 'tex');
200206

201207
str = [' ' num2str(prod(MRS_struct.p.voxdim(ii,:))/1e3) ' mL'];
202-
text(0.5, 0.39, 'Volume: ', 'Units', 'normalized', 'HorizontalAlignment', 'right', 'FontName', 'Arial', 'FontSize', 13);
203-
text(0.5, 0.39, str, 'Units', 'normalized', 'FontName', 'Arial', 'FontSize', 13);
208+
text(0.5, 0.39, 'Volume: ', 'Units', 'normalized', 'HorizontalAlignment', 'right', 'FontName', 'Arial', 'FontSize', 13 - font_size_adj);
209+
text(0.5, 0.39, str, 'Units', 'normalized', 'FontName', 'Arial', 'FontSize', 13 - font_size_adj);
204210

205211
str = [' [' num2str(MRS_struct.p.voxoff(ii,1), '%3.1f') ', ' num2str(MRS_struct.p.voxoff(ii,2), '%3.1f') ', ' num2str(MRS_struct.p.voxoff(ii,3), '%3.1f') '] mm'];
206-
text(0.5, 0.27, 'Position: ', 'Units', 'normalized', 'HorizontalAlignment', 'right', 'FontName', 'Arial', 'FontSize', 13);
207-
text(0.5, 0.27, str, 'Units', 'normalized', 'FontName', 'Arial', 'FontSize', 13);
212+
text(0.5, 0.27, 'Position: ', 'Units', 'normalized', 'HorizontalAlignment', 'right', 'FontName', 'Arial', 'FontSize', 13 - font_size_adj);
213+
text(0.5, 0.27, str, 'Units', 'normalized', 'FontName', 'Arial', 'FontSize', 13 - font_size_adj);
208214

209215
if any(strcmp(MRS_struct.p.vendor, {'Philips', 'Philips_data'}))
210216
str = [' [' num2str(MRS_struct.p.voxang(ii,2), '%3.1f') ', ' num2str(MRS_struct.p.voxang(ii,1), '%3.1f') ', ' num2str(MRS_struct.p.voxang(ii,3), '%3.1f') '] deg'];
211217
else
212218
str = [' [' num2str(MRS_struct.p.voxang(ii,1), '%3.1f') ', ' num2str(MRS_struct.p.voxang(ii,2), '%3.1f') ', ' num2str(MRS_struct.p.voxang(ii,3), '%3.1f') '] deg'];
213219
end
214-
text(0.5, 0.15, 'Angulation: ', 'Units', 'normalized', 'HorizontalAlignment', 'right', 'FontName', 'Arial', 'FontSize', 13);
215-
text(0.5, 0.15, str, 'Units', 'normalized', 'FontName', 'Arial', 'FontSize', 13);
220+
text(0.5, 0.15, 'Angulation: ', 'Units', 'normalized', 'HorizontalAlignment', 'right', 'FontName', 'Arial', 'FontSize', 13 - font_size_adj);
221+
text(0.5, 0.15, str, 'Units', 'normalized', 'FontName', 'Arial', 'FontSize', 13 - font_size_adj);
216222

217-
text(0.5, 0.03, 'CoRegVer: ', 'Units', 'normalized', 'HorizontalAlignment', 'right', 'FontName', 'Arial', 'FontSize', 13);
218-
text(0.5, 0.03, [' ' MRS_struct.info.version.coreg], 'Units', 'normalized', 'FontName', 'Arial', 'FontSize', 13);
223+
text(0.5, 0.03, 'CoRegVer: ', 'Units', 'normalized', 'HorizontalAlignment', 'right', 'FontName', 'Arial', 'FontSize', 13 - font_size_adj);
224+
text(0.5, 0.03, [' ' MRS_struct.info.version.coreg], 'Units', 'normalized', 'FontName', 'Arial', 'FontSize', 13 - font_size_adj);
219225

220226
hb = subplot(2,3,1:3);
221227

@@ -237,14 +243,14 @@
237243

238244
imagesc(MRS_struct.mask.(vox{kk}).img{ii});
239245
axis equal tight off;
240-
text(0.01, 0.5, 'L', 'Color', [1 1 1], 'FontSize', 20, 'Units', 'normalized');
241-
text(0.16, 0.95, 'A', 'Color', [1 1 1], 'FontSize', 20, 'Units', 'normalized');
242-
text(0.32, 0.5, 'A', 'Color', [1 1 1], 'FontSize', 20, 'Units', 'normalized');
243-
text(0.5, 0.95, 'S', 'Color', [1 1 1], 'FontSize', 20, 'Units', 'normalized');
244-
text(0.825, 0.95, 'S', 'Color', [1 1 1], 'FontSize', 20, 'Units', 'normalized');
245-
text(0.975, 0.5, 'R', 'Color', [1 1 1], 'FontSize', 20, 'Units', 'normalized');
246+
text(0.01, 0.5, 'L', 'Color', [1 1 1], 'FontSize', 20 - font_size_adj, 'Units', 'normalized');
247+
text(0.16, 0.95, 'A', 'Color', [1 1 1], 'FontSize', 20 - font_size_adj, 'Units', 'normalized');
248+
text(0.32, 0.5, 'A', 'Color', [1 1 1], 'FontSize', 20 - font_size_adj, 'Units', 'normalized');
249+
text(0.5, 0.95, 'S', 'Color', [1 1 1], 'FontSize', 20 - font_size_adj, 'Units', 'normalized');
250+
text(0.825, 0.95, 'S', 'Color', [1 1 1], 'FontSize', 20 - font_size_adj, 'Units', 'normalized');
251+
text(0.975, 0.5, 'R', 'Color', [1 1 1], 'FontSize', 20 - font_size_adj, 'Units', 'normalized');
246252
set(hb,'Position',[0 0.15 1 1]);
247-
title(t, 'FontName', 'Arial', 'FontSize', 15, 'Interpreter', 'none');
253+
title(t, 'FontName', 'Arial', 'FontSize', 15 - font_size_adj, 'Interpreter', 'none');
248254

249255
% Save output as PDF
250256
run_count = SavePDF(h, MRS_struct, ii, 1, kk, vox, mfilename, run_count);

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