Update Transformation matrix mcspace to mni space after importing a new MRI anatomy

AtlasViewerGUI.m

@@ -57,8 +57,10 @@ function ParseArgs(args)
     atlasViewer.dirnameAtlas = getAtlasDir(args);
 end
 if length(args)>3
-    atlasViewer.handles.dataTree = args{4};
-    atlasViewer.dataTree = get(atlasViewer.handles.dataTree, 'userdata');
+    if sum(isgraphics(args{4}))
+        atlasViewer.handles.dataTree = args{4};
+        atlasViewer.dataTree = get(atlasViewer.handles.dataTree, 'userdata');
+    end
 end
 
 % Change current folder to dirnameSubj and load data
@@ -651,7 +653,7 @@ function pushbuttonRegisterProbeToSurface_Callback(hObject, eventdata, handles)
 refpts = set_eeg_active_pts(refpts, [], false);
 
 % Finish registration
-if isPreRegisteredProbe(probe, refpts)
+if 0 %isPreRegisteredProbe(probe, refpts)
 
     % Register probe by simply pulling (or pushing) optodes toward surface
     % toward (or away from) center of head.

Labelssurf/getLabelssurf.m

@@ -19,6 +19,12 @@
 end
 dirname = [dirname0 'anatomical/'];
 
+if exist([dirname 'labelssurf2vol.txt'],'file')
+    T_2vol = load([dirname 'labelssurf2vol.txt'],'ascii');
+    labelssurf.T_2vol = T_2vol;
+end
+
+
 if exist([dirname 'labelssurf.mat'],'file')
     load([dirname 'labelssurf.mat'],'-mat');
 else
@@ -33,9 +39,9 @@
 end
 
 load([dirname 'labelssurf.mat']);
-if exist([dirname 'labelssurf2vol.txt'],'file')
-    T_2vol = load([dirname 'labelssurf2vol.txt'],'ascii');
-end
+% if exist([dirname 'labelssurf2vol.txt'],'file')
+%     T_2vol = load([dirname 'labelssurf2vol.txt'],'ascii');
+% end
 
 fv = struct('vertices',[],'faces',[]);
 idxL = [];
@@ -65,7 +71,7 @@
 labelssurf.colormaps = cm;
 labelssurf.colormapsIdx = 4;
 labelssurf.idxL = idxL;
-labelssurf.T_2vol = T_2vol;
+% labelssurf.T_2vol = T_2vol;
 
 
 if ~labelssurf.isempty(labelssurf)

Labelssurf/saveLabelSurf2Vol.m

@@ -0,0 +1,20 @@
+function saveLabelSurf2Vol(headvol)
+% Author:Sreekanth Kura ([email protected])
+
+% I am assuming imported anatomy will be saved in RAS orientation. 
+S = size(headvol.img);
+T = headvol.T_2ras;
+Tras_2vol = T;
+for u = 1:3
+    if sum(Tras_2vol(u,1:3)) == -1
+        Tras_2vol(u,4) = S(u);
+    else
+        Tras_2vol(u,4) = 0;
+    end
+end
+
+Tras_mni = (Tras_2vol'*T')';
+Tmni_ras = inv(Tras_mni);
+dirname = [headvol.pathname, '/anatomical/'];
+filename = [dirname 'labelssurf2vol.txt'];
+writematrix(Tmni_ras,filename,'Delimiter',' ')

Probe/isPreRegisteredProbe.m

@@ -80,7 +80,10 @@
 end
 if probeHasSpringRegistration(probe)
     refpts1.labels  = probe.registration.al(:,2);
-    refpts1.pos     = probe.optpos(cell2array(probe.registration.al(:,1)), :);
+    refpts1.pos     = probe.optpos_reg(cell2array(probe.registration.al(:,1)), :);
+    catch
+        d = 1;
+    end
 else
     refpts1         = probe.registration.refpts;
 end

Utils/fs2viewer/ImportMriAnatomy.m

@@ -356,6 +356,7 @@ function ImportMriAnatomy_CloseRequestFcn(~, ~, handles)
     saveHeadvol(headvol);
     saveHeadsurf(headsurf);
     savePialsurf(pialsurf);
+    saveLabelSurf2Vol(headvol);
 
 catch ME
 

Utils/fs2viewer/segment_head_vols.m

@@ -116,12 +116,27 @@
 end
 
 % Align layer volume with head volume
-X = inv(layer.vox2ras) * head.vox2ras;
-layer.vol = xform_apply_vol_smooth(layer.vol, X);
+X = inv(inv(layer.vox2ras) * head.vox2ras);
+% layer.vol = xform_apply_vol_smooth(layer.vol, X);
+
+tform = affinetform3d(X);
+% layer.vol = imwarp(layer.vol,tform,'OutputView',imref3d(size(head.vol)));
 
 % Assign layer segmentation number
 s = max(hseg(:))+1;
-layer_i = find(layer.vol ~= 0);
+% layer_i = find(layer.vol ~= 0);
+
+ind = find(layer.vol ~=0);
+[I1,I2,I3] = ind2sub(size(layer.vol),ind);
+t_ind = round([I1 I2 I3 ones(size(I1))]*X');
+idx = find(t_ind(:,1) < 1 | t_ind(:,1) > size(head.vol,1));
+t_ind(idx,:) = [];
+idx = find(t_ind(:,2) < 1 | t_ind(:,2) > size(head.vol,2));
+t_ind(idx,:) = [];
+idx = find(t_ind(:,3) < 1 | t_ind(:,3) > size(head.vol,3));
+t_ind(idx,:) = [];
+layer_i = sub2ind(size(head.vol),t_ind(:,1),t_ind(:,2),t_ind(:,3));
+
 hseg(layer_i) = s;
 tiss_type{s}=name;