From 3bc4863771e1ebf3420bc7c0948751233ff0c44b Mon Sep 17 00:00:00 2001
From: gav-hsu <gavhsu@gmail.com>
Date: Thu, 16 May 2024 18:39:41 -0400
Subject: [PATCH 1/4] updated sliceshow

---
 .gitignore       |  28 ++++++
 brainCrop.m      |  15 +++
 meshByIso2mesh.m |   2 +-
 reviewRes.m      |  15 +--
 sliceshow.m      | 243 ++++++++++++++++++++++++++++++++++++-----------
 start_seg.m      |   4 +-
 visualizeRes.m   |  15 +--
 7 files changed, 251 insertions(+), 71 deletions(-)
 create mode 100644 .gitignore
 create mode 100644 brainCrop.m

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..ca37d1e
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,28 @@
+example/c1MNI152_T1_1mm_ras_T1orT2.nii
+example/c2MNI152_T1_1mm_ras_T1orT2.nii
+example/c3MNI152_T1_1mm_ras_T1orT2.nii
+example/c4MNI152_T1_1mm_ras_T1orT2.nii
+example/c5MNI152_T1_1mm_ras_T1orT2.nii
+example/c6MNI152_T1_1mm_ras_T1orT2.nii
+example/MNI152_T1_1mm_20240516T173547_e.nii
+example/MNI152_T1_1mm_20240516T173547_e.pos
+example/MNI152_T1_1mm_20240516T173547_emag.nii
+example/MNI152_T1_1mm_20240516T173547_mask_elec.nii
+example/MNI152_T1_1mm_20240516T173547_mask_gel.nii
+example/MNI152_T1_1mm_20240516T173547_ready.msh
+example/MNI152_T1_1mm_20240516T173547_roastOptions.mat
+example/MNI152_T1_1mm_20240516T173547_roastResult.mat
+example/MNI152_T1_1mm_20240516T173547_usedElecArea.mat
+example/MNI152_T1_1mm_20240516T173547_v.nii
+example/MNI152_T1_1mm_20240516T173547_v.pos
+example/MNI152_T1_1mm_20240516T173547.mat
+example/MNI152_T1_1mm_20240516T173547.msh
+example/MNI152_T1_1mm_20240516T173547.pro
+example/MNI152_T1_1mm_ras_header.mat
+example/MNI152_T1_1mm_ras_MNI.nii
+example/MNI152_T1_1mm_ras_T1orT2_rmask.mat
+example/MNI152_T1_1mm_ras_T1orT2_seg8.mat
+example/MNI152_T1_1mm_ras_T1orT2_SPM_masks_MNI.nii
+example/MNI152_T1_1mm_ras_T1orT2_SPM_masks.nii
+example/MNI152_T1_1mm_ras.nii
+example/MNI152_T1_1mm_roastLog
diff --git a/brainCrop.m b/brainCrop.m
new file mode 100644
index 0000000..4a856bd
--- /dev/null
+++ b/brainCrop.m
@@ -0,0 +1,15 @@
+% Crops the image to the brain using segmentation
+% Returns the upper and lower bounds of the brain in each direction
+% column 1 = R/L, column 2 = A/P, column 3 = S/I
+% (c) 2024 Gavin Hsu and Andrew Birnbaum
+
+function bbox = brainCrop(subj)       
+    [dirname,baseFilename,ext] = fileparts(subj);
+    seg = [dirname,'\',baseFilename,'_masks',ext];
+    data = load_untouch_nii(seg);
+    wm = data.img == 1;
+    thresh = [0,0,100];
+    [bbox(1,1),bbox(2,1)]=bounds(find(sum(sum(wm,2),3)>thresh(1)));
+    [bbox(1,2),bbox(2,2)]=bounds(find(sum(sum(wm,1),3)>thresh(2)));
+    [bbox(1,3),bbox(2,3)]=bounds(find(sum(sum(wm,1),2)>thresh(3)));
+end
\ No newline at end of file
diff --git a/meshByIso2mesh.m b/meshByIso2mesh.m
index 614c50e..83feb0a 100644
--- a/meshByIso2mesh.m
+++ b/meshByIso2mesh.m
@@ -45,7 +45,7 @@
 allMaskShow(data.img>0) = numOfTissue + 2;
 
 % sliceshow(allMask,[],[],[],'Tissue index','Segmentation. Click anywhere to navigate.')
-sliceshow(allMaskShow,[],[],[],'Tissue index','Segmentation. Click anywhere to navigate.',[],mri2mni)
+sliceshow(allMaskShow,[],[],[],'Tissue index','Segmentation. Click anywhere to navigate.',[],mri2mni,[])
 drawnow
 
 % allMask = uint8(allMask);
diff --git a/reviewRes.m b/reviewRes.m
index d37d36e..b7077fc 100644
--- a/reviewRes.m
+++ b/reviewRes.m
@@ -70,6 +70,8 @@ function reviewRes(subj,simTag,tissue,fastRender,tarTag)
 % (c) MultiPriors segmentation developed by Lukas Hirsch, and integrated into
 % ROAST by Andrew Birnbaum
 % April 2024
+%
+% (c) May 2024 Gavin Hsu
 
 fprintf('\n\n');
 disp('=============================================================')
@@ -243,7 +245,7 @@ function reviewRes(subj,simTag,tissue,fastRender,tarTag)
         if ~exist(subjRasRSPD,'file')
             error(['The subject MRI you provided ' subjRasRSPD ' does not exist. Check if you run through resampling or zero-padding if you tried to do that.']);
         else
-            data = load_untouch_nii(subjRasRSPD); sliceshow(data.img,[],'gray',[],[],'MRI: Click anywhere to navigate.',[],mri2mni); drawnow
+            data = load_untouch_nii(subjRasRSPD); sliceshow(data.img,[],'gray',[],[],'MRI: Click anywhere to navigate.',[],mri2mni,[]); drawnow
         end
         
         if ~isempty(optRoast.T2) %T2 specified
@@ -251,7 +253,7 @@ function reviewRes(subj,simTag,tissue,fastRender,tarTag)
                 error(['T2 file ' optRoast.T2 ' does not exist. You used that to run ROAST but maybe later deleted it.']);
             else
                 data = load_untouch_nii(optRoast.T2);
-                sliceshow(data.img,[],'gray',[],[],'MRI: T2. Click anywhere to navigate.',[],mri2mni); drawnow
+                sliceshow(data.img,[],'gray',[],[],'MRI: T2. Click anywhere to navigate.',[],mri2mni,[]); drawnow
             end
         end
     else
@@ -298,7 +300,7 @@ function reviewRes(subj,simTag,tissue,fastRender,tarTag)
     allMaskShow = masks.img;
     allMaskShow(gel.img>0) = numOfTissue + 1;
     allMaskShow(elec.img>0) = numOfTissue + 2;
-    sliceshow(allMaskShow,[],[],[],'Tissue index','Segmentation. Click anywhere to navigate.',[],mri2mni)
+    sliceshow(allMaskShow,[],[],[],'Tissue index','Segmentation. Click anywhere to navigate.',[],mri2mni,[])
     drawnow
     
 else
@@ -517,6 +519,7 @@ function reviewRes(subj,simTag,tissue,fastRender,tarTag)
 nan_mask(find(mask)) = 1;
 
 cm = colormap(jet(2^11)); cm = [1 1 1;cm];
+bbox = brainCrop(subjRasRSPD);
 
 if isRoast
     
@@ -528,13 +531,13 @@ function reviewRes(subj,simTag,tissue,fastRender,tarTag)
     end
     
     figName = ['Voltage in Simulation: ' simTag];
-    sliceshow(vol_all.*nan_mask,[],cm,[],'Voltage (mV)',[figName '. Click anywhere to navigate.'],[],mri2mni); drawnow
+    sliceshow(vol_all.*nan_mask,[],cm,[],'Voltage (mV)',[figName '. Click anywhere to navigate.'],[],mri2mni,bbox); drawnow
     
     figName = ['Electric field in Simulation: ' simTag];
     for i=1:size(ef_all,4), ef_all(:,:,:,i) = ef_all(:,:,:,i).*nan_mask; end
     ef_mag = ef_mag.*nan_mask;
     dataShowVal = ef_mag(~isnan(ef_mag(:)));
-    sliceshow(ef_mag,[],cm,[min(dataShowVal) prctile(dataShowVal,95)],'Electric field (V/m)',[figName '. Click anywhere to navigate.'],ef_all,mri2mni); drawnow
+    sliceshow(ef_mag,[],cm,[min(dataShowVal) prctile(dataShowVal,95)],'Electric field (V/m)',[figName '. Click anywhere to navigate.'],ef_all,mri2mni,bbox); drawnow
     
 else
     
@@ -543,6 +546,6 @@ function reviewRes(subj,simTag,tissue,fastRender,tarTag)
     dataShowVal = r.ef_mag(~isnan(r.ef_mag(:)));
     for i=1:size(r.targetCoord,1)
         figName = ['Electric field at Target ' num2str(i) ' in Targeting: ' tarTag];
-        sliceshow(r.ef_mag,r.targetCoord(i,:),cm,[min(dataShowVal) prctile(dataShowVal,95)],'Electric field (V/m)',[figName '. Click anywhere to navigate.'],r.ef_all,mri2mni); drawnow
+        sliceshow(r.ef_mag,r.targetCoord(i,:),cm,[min(dataShowVal) prctile(dataShowVal,95)],'Electric field (V/m)',[figName '. Click anywhere to navigate.'],r.ef_all,mri2mni,bbox); drawnow
     end
 end
\ No newline at end of file
diff --git a/sliceshow.m b/sliceshow.m
index f184bfd..5749c84 100644
--- a/sliceshow.m
+++ b/sliceshow.m
@@ -1,6 +1,4 @@
-function sliceshow(img,pos,color,clim,label,figName,vecImg,mri2mni)
-% sliceshow(img,pos,color,clim,label,figName,vecImg,mri2mni)
-%
+function sliceshow(img,pos,color,clim,label,figName,vecImg,mri2mni,bbox)
 % sliceshow displays a 3D volume allowing the user to click on different
 % slices. If the variable "vecImg" is specified, sliceshow will also
 % overlay a 3D vectorial field represented by arrows on the slices.
@@ -8,6 +6,9 @@ function sliceshow(img,pos,color,clim,label,figName,vecImg,mri2mni)
 % If pos is given as input, then the function will start the display with
 % the slices intersecting this position. Defaults to the middle of the
 % volume.
+% 
+% Coordinates are editable. Enter the desired voxel or MNI coordinates to
+% navigate to the desired position.
 %
 % color is the colormap the display will use. Defaults to 'jet'.
 %
@@ -20,11 +21,29 @@ function sliceshow(img,pos,color,clim,label,figName,vecImg,mri2mni)
 % vecImg is the 3D vectorial field, e.g. an electric field.
 % 
 % mri2mni is the mapping from MRI voxel space to the MNI space, so
+%
+% bbox is the output of brainCrop(). Use this to display only the brain.
+%
 % sliceshow can display both the voxel and MNI coordinates.
 %
 % (c) Nov 02, 2017, Lucas C Parra
 % (c) June 29, 2018, Yu (Andy) Huang
 % (c) August 2019, Yu (Andy) Huang
+% (c) 2024, Gavin Hsu and Andrew Birnbaum
+
+if nargin >= 2 && ~isempty(bbox)
+    minR = bbox(1,1);
+    maxR = bbox(2,1);
+    minA = bbox(1,2);
+    maxA = bbox(2,2);
+    minS = bbox(1,3);
+    maxS = bbox(2,3);    
+    img = img(minR:maxR, minA:maxA, minS:maxS);
+else
+    minR = 0;
+    minA = 0;
+    minS = 0;
+end
 
 if nargin<1 || isempty(img)
     error('At least give us a volume to display')
@@ -35,8 +54,10 @@ function sliceshow(img,pos,color,clim,label,figName,vecImg,mri2mni)
 
 if nargin<2 || isempty(pos)
     mydata.pos = round(size(img)/2);
+    mydata.pos_crop = mydata.pos + [minR,minA,minS];
 else
-    mydata.pos=pos;
+     mydata.pos=pos-[minR,minA,minS];
+     mydata.pos_crop = mydata.pos + [minR,minA,minS];
 end
 
 if nargin<3 || isempty(color)
@@ -70,6 +91,9 @@ function sliceshow(img,pos,color,clim,label,figName,vecImg,mri2mni)
 if nargin<7 || isempty(vecImg)
     mydata.vecImg = [];
 else
+    if nargin >= 2 && ~isempty(bbox)
+        vecImg = vecImg(minR:maxR, minA:maxA, minS:maxS,:);
+    end
     temp = size(vecImg);
     if any(temp(1:3)~=[Nx,Ny,Nz]) || temp(4)~=3
         error('Vector field does not have correct size.');
@@ -86,22 +110,24 @@ function sliceshow(img,pos,color,clim,label,figName,vecImg,mri2mni)
         error('Unrecognized format of the voxel-to-MNI mapping.');
     end
     mydata.mri2mni = mri2mni;
+    mydata.mnipos = round(mydata.mri2mni*[mydata.pos_crop 1]');
 end
 
-% link the calback function to new figure
-fh = figure('WindowButtonDownFcn',@myCallback,'Name',figName,'NumberTitle','off');
-
+whratio = 1.0187; %Width-to-height ratio
+w = 8.5; %Width in inches
+% link the callback function to new figure
+fh = uifigure('WindowButtonDownFcn',@(src, event) myCallback(src, event, minR, minA, minS),'Name',figName,'NumberTitle','off','Units','inches','Position',[0,0,w,w/whratio],'AutoResizeChildren','off','SizeChangedFcn',@(src,event) figResize(src,event,minR,minA,minS));
+movegui(fh,'center')
 % store data as figure property
 set(fh,'UserData',mydata);
+set(fh,'HandleVisibility','on')
 
-% first display
-showimages
-
-
+% initial display
+showimages(minR,minA,minS,fh)
 end
 
-function myCallback(fh,~)
-% This selects new position depending on which subplot a button is clicked.
+function myCallback(fh,~,minR, minA, minS)
+% Selects new position depending on which subplot is clicked on.
 % Updates display information in mydata.
 
 mydata = get(fh,'UserData');
@@ -112,78 +138,183 @@ function myCallback(fh,~)
     case mydata.h(2); mydata.pos([2 3]) = pos;
     case mydata.h(3); mydata.pos([1 2]) = pos;
 end
+mydata.pos_crop = mydata.pos + [minR,minA,minS];
+mydata.mnipos = round(mydata.mri2mni*[mydata.pos_crop 1]');
 
 % if new position is valid, update mydata as figure property and display
 % otherwise do nothing
 if ~sum( mydata.pos<1 | mydata.pos>size(mydata.img) )
     set(fh,'UserData',mydata);
-    showimages
+    showimages(minR,minA,minS,fh)
 end
-
 end
 
-function showimages
-% Displays the image based on current mydata.
+function showimages(minR,minA,minS,fh)
+% Displays the image based on current UserData.
 
 % grab the stuff to display from figure
-mydata  = get(gcf,'UserData');
+mydata  = get(fh,'UserData');
+
+% Show the images and keep track of the axes that are generated
+mytile = tiledlayout(fh,2,2,'Padding','tight','TileSpacing','none');
 
-% show the images and keep track of the axes that are generated
-h(1)=subplot(2,2,1);
-imagesc(squeeze(mydata.img(:,mydata.pos(2),:))'); d(1,:)=[1 3];
+h(1) = nexttile(mytile,1); 
+imagesc(h(1),squeeze(mydata.img(:,mydata.pos(2),:))'); d(1,:)=[1 3];
 if ~isempty(mydata.vecImg)
-    hold on;
+    hold(h(1),'on');
     rngx=1:5:size(mydata.xi,1); rngy=mydata.pos(2); rngz=1:5:size(mydata.xi,3);
-    quiver3(mydata.xi(rngx,rngy,rngz),mydata.zi(rngx,rngy,rngz),mydata.yi(rngx,rngy,rngz),...
-        mydata.vecImg(rngx,rngy,rngz,1),mydata.vecImg(rngx,rngy,rngz,3),mydata.vecImg(rngx,rngy,rngz,2),2,'color','k'); %,0.08,'nointerp');
-    hold off;
+    quiver3(h(1),mydata.xi(rngx,rngy,rngz),mydata.zi(rngx,rngy,rngz),mydata.yi(rngx,rngy,rngz),...
+        mydata.vecImg(rngx,rngy,rngz,1),mydata.vecImg(rngx,rngy,rngz,3),mydata.vecImg(rngx,rngy,rngz,2),2,'color','k');
+    hold(h(1),'off');
 end
-h(2)=subplot(2,2,2);
-imagesc(squeeze(mydata.img(mydata.pos(1),:,:))'); d(2,:)=[2 3];
+axtoolbar(h(1),{});
+
+h(2) = nexttile(mytile,2); 
+imagesc(h(2),squeeze(mydata.img(mydata.pos(1),:,:))'); d(2,:)=[2 3];
 if ~isempty(mydata.vecImg)
-    hold on;
+    hold(h(2),'on');
     rngx=mydata.pos(1); rngy=1:5:size(mydata.xi,2); rngz=1:5:size(mydata.xi,3);
-    quiver3(mydata.yi(rngx,rngy,rngz),mydata.zi(rngx,rngy,rngz),mydata.xi(rngx,rngy,rngz),...
-        mydata.vecImg(rngx,rngy,rngz,2),mydata.vecImg(rngx,rngy,rngz,3),mydata.vecImg(rngx,rngy,rngz,1),2,'color','k'); %,0.08,'nointerp');
-    hold off;
+    quiver3(h(2),mydata.yi(rngx,rngy,rngz),mydata.zi(rngx,rngy,rngz),mydata.xi(rngx,rngy,rngz),...
+        mydata.vecImg(rngx,rngy,rngz,2),mydata.vecImg(rngx,rngy,rngz,3),mydata.vecImg(rngx,rngy,rngz,1),2,'color','k');
+    hold(h(2),'off');
 end
-h(3)=subplot(2,2,3);
-imagesc(squeeze(mydata.img(:,:,mydata.pos(3)))'); d(3,:)=[1 2];
+axtoolbar(h(2),{});
+
+h(3) = nexttile(mytile,3); 
+imagesc(h(3),squeeze(mydata.img(:,:,mydata.pos(3)))'); d(3,:)=[1 2];
 if ~isempty(mydata.vecImg)
-    hold on;
+    hold(h(3),'on');
     rngx=1:5:size(mydata.xi,1); rngy=1:5:size(mydata.xi,2); rngz=mydata.pos(3);
-    quiver3(mydata.xi(rngx,rngy,rngz),mydata.yi(rngx,rngy,rngz),mydata.zi(rngx,rngy,rngz),...
-        mydata.vecImg(rngx,rngy,rngz,1),mydata.vecImg(rngx,rngy,rngz,2),mydata.vecImg(rngx,rngy,rngz,3),2,'color','k'); %,0.08,'nointerp');
-    hold off;
+    quiver3(h(3),mydata.xi(rngx,rngy,rngz),mydata.yi(rngx,rngy,rngz),mydata.zi(rngx,rngy,rngz),...
+        mydata.vecImg(rngx,rngy,rngz,1),mydata.vecImg(rngx,rngy,rngz,2),mydata.vecImg(rngx,rngy,rngz,3),2,'color','k');
+    hold(h(3),'off');
 end
+axtoolbar(h(3),{});
 
-% some aesthetics
-val = mydata.img(mydata.pos(1),mydata.pos(2),mydata.pos(3));
+% Aesthetics
+val = mydata.img(mydata.pos(1),mydata.pos(2),mydata.pos(3)); %EF value
 for i=1:3
-    subplot(2,2,i);
-    hold on; plot(mydata.pos(d(i,1)),mydata.pos(d(i,2)),'o','color',ones(1,3)*0.4,'linewidth',3,'markersize',12); hold off;
-    axis xy; axis equal; axis tight; axis off; caxis(mydata.clim);
-    title([num2str(mydata.pos(d(i,:))) ': ' num2str(val,'%.2f')])
+    han = nexttile(mytile,i);
+    % Place position marker
+    hold(han,'on'); plot(han,mydata.pos(d(i,1)),mydata.pos(d(i,2)),'o','color','m','linewidth',3,'markersize',12); hold(han,'off');
+    axis(han,'xy'); axis(han,'equal'); axis(han,'tight'); axis(han,'off'); clim(han,mydata.clim);
+    stackorder = get(h(i),'Children');
+    if size(stackorder,1)>2
+        set(h(i),'Children',[stackorder(1),stackorder(2),stackorder(3)]);
+    end
+    % Show crosshairs
+    xline(han,mydata.pos(d(i,1))); yline(han,mydata.pos(d(i,2)));
 end
 
+% Set x- and y-lims equal in all views (for uniform scaling)
+xlim(h,[0,max(size(mydata.img))])
+ylim(h,[0,max(size(mydata.img))])
+
+h(4) = nexttile(mytile,4); axis(h(4),'off'); box(h(4),'off'); clim(h(4),mydata.clim); axtoolbar(h(4),{});
+mydata.pos_crop = mydata.pos + [minR,minA,minS];
+
+% Arrange user input and coordinates in a UI Panel
+ip = uipanel(fh,'BackgroundColor','white','AutoResizeChildren','off');
+ip.Units = 'normalized';
+ip.Position = [0.5,0,0.5,0.3];
+ip.BorderType = 'none';
+ip.Units = 'pixels';
+panelsize = ip.Position;
+ip.Units = 'normalized';
+l = 0.28*panelsize(3); %left reference point
+b = 0.59*panelsize(4); %bottom reference point
+FSEF = 24; %Font size for displaying EF
+FSc = 20; %Font size for coordinates
+padding = 10;
+%Display value:
+uilabel(ip,'Position',[l-3.4*FSc,b-3*FSc,FSEF*12,FSEF+padding],'Text',strcat(mydata.label),'FontSize',FSEF,'FontWeight','bold','HorizontalAlignment','center');
+uilabel(ip,'Position',[l-3.4*FSc,b-4.5*FSc,FSEF*12,FSEF+padding],'Text',num2str(val,'%.2f'),'FontSize',FSEF,'FontWeight','bold','HorizontalAlignment','center');
+%Display voxel coordinates (callback below):
+uilabel(ip,'Position',[l-3.4*FSc,b+2*FSc,3.1*FSc,FSc+padding],'Text','Voxel','FontSize',FSc,'FontWeight','bold');
+efx = uieditfield(ip,'Position',[l+FSc,b+2*FSc,2.5*FSc,FSc+padding],'Tag','x','FontSize',FSc,'ValueChangedFcn',@(src,event) updateX(src,event,minR,minA,minS,fh),'HorizontalAlignment','right','FontWeight','bold');
+efx.Value = num2str(mydata.pos_crop(1));
+uilabel(ip,'Position',[l,b+2*FSc,1.25*FSc,FSc+padding],'Text','X','FontSize',FSc);
+efy = uieditfield(ip,'Position',[l+5.25*FSc,b+2*FSc,2.5*FSc,FSc+padding],'Tag','y','FontSize',FSc,'ValueChangedFcn',@(src,event) updateX(src,event,minR,minA,minS,fh),'HorizontalAlignment','right','FontWeight','bold');
+efy.Value = num2str(mydata.pos_crop(2));
+uilabel(ip,'Position',[l+4.25*FSc,b+2*FSc,1.25*FSc,FSc+padding],'Text','Y','FontSize',FSc);
+efz = uieditfield(ip,'Position',[l+9.5*FSc,b+2*FSc,2.5*FSc,FSc+padding],'Tag','z','FontSize',FSc,'ValueChangedFcn',@(src,event) updateX(src,event,minR,minA,minS,fh),'HorizontalAlignment','right','FontWeight','bold');
+efz.Value = num2str(mydata.pos_crop(3));
+uilabel(ip,'Position',[l+8.5*FSc,b+2*FSc,1.25*FSc,FSc+padding],'Text','Z','FontSize',FSc);
+
+%Display MNI coordinates (callback below):
 if ~isempty(mydata.mri2mni)
-    h(4) = subplot(2,2,4); axis off; caxis(mydata.clim);
-    mniCoord = round(mydata.mri2mni*[mydata.pos 1]');
-    coordInfo = {['Voxel: ' num2str(mydata.pos(1)) ',' num2str(mydata.pos(2)) ',' num2str(mydata.pos(3))],...
-        ['MNI: ' num2str(mniCoord(1)) ',' num2str(mniCoord(2)) ',' num2str(mniCoord(3))]};
-    title(h(4), coordInfo,'FontSize',16);
+    uilabel(ip,'Position',[l-3.4*FSc,b,3.1*FSc,FSc+padding],'Text','MNI','FontSize',FSc,'FontWeight','bold');
+    efxm = uieditfield(ip,'Position',[l+FSc,b,2.5*FSc,FSc+padding],'Tag','x','FontSize',FSc,'ValueChangedFcn',@(src,event) updateXMNI(src,event,minR,minA,minS,fh),'HorizontalAlignment','right','FontWeight','bold');
+    efxm.Value = num2str(mydata.mnipos(1));
+    uilabel(ip,'Position',[l,b,1.25*FSc,FSc+padding],'Text','X','FontSize',FSc);
+    efym = uieditfield(ip,'Position',[l+5.25*FSc,b,2.5*FSc,FSc+padding],'Tag','y','FontSize',FSc,'ValueChangedFcn',@(src,event) updateXMNI(src,event,minR,minA,minS,fh),'HorizontalAlignment','right','FontWeight','bold');
+    efym.Value = num2str(mydata.mnipos(2));
+    uilabel(ip,'Position',[l+4.25*FSc,b,1.25*FSc,FSc+padding],'Text','Y','FontSize',FSc);
+    efzm = uieditfield(ip,'Position',[l+9.5*FSc,b,2.5*FSc,FSc+padding],'Tag','z','FontSize',FSc,'ValueChangedFcn',@(src,event) updateXMNI(src,event,minR,minA,minS,fh),'HorizontalAlignment','right','FontWeight','bold');
+    efzm.Value = num2str(mydata.mnipos(3));
+    uilabel(ip,'Position',[l+8.5*FSc,b,1.25*FSc,FSc+padding],'Text','Z','FontSize',FSc);
 end
 
-if ~isempty(mydata.label)
-    h(4) = subplot(2,2,4); axis off; caxis(mydata.clim);
-    h(5) = colorbar('west');
-    set(h(5),'YAxisLocation','right','FontSize',18);
-    title(h(5), mydata.label,'FontSize',18);
-end
+% Display colorbar
+h(5) = colorbar(nexttile(mytile,2),'southoutside');
+set(h(5),'YAxisLocation','bottom','FontSize',16);
+h(5).Label.String = mydata.label;
 
-colormap(mydata.color);
+colormap(fh,mydata.color);
+set(fh,'color','w')
 
 mydata.h=h;
-set(gcf,'UserData',mydata);
+set(fh,'UserData',mydata);
+end
+
+function updateX(src,event,minR, minA, minS,fh)
+% Update figure to display location specified by voxel coordinate input
+mydata = get(fh,'UserData');
+if ~isempty(str2double(event.Value))
+    switch src.Tag
+        case 'x'
+            mydata.pos(1) = round(str2double(event.Value))-minR;
+            mydata.pos_crop(1) = str2double(event.Value);
+        case 'y'
+            mydata.pos(2) = round(str2double(event.Value))-minA;
+            mydata.pos_crop(2) = str2double(event.Value);
+        case 'z'
+            mydata.pos(3) = round(str2double(event.Value))-minS;
+            mydata.pos_crop(3) = str2double(event.Value);
+    end
+    mydata.mnipos = round(mydata.mri2mni*[mydata.pos_crop 1]');
+end
+if ~sum( mydata.pos<1 | mydata.pos>size(mydata.img) )
+    set(fh,'UserData',mydata);
+    showimages(minR,minA,minS,fh)
+end
+end
 
+function updateXMNI(src,event,minR, minA, minS,fh)
+% Update figure to display location specified by MNI coordinate input
+mydata = get(fh,'UserData');
+if ~isempty(str2double(event.Value))
+    switch src.Tag
+        case 'x'
+            mydata.mnipos(1) = round(str2double(event.Value));
+        case 'y'
+            mydata.mnipos(2) = round(str2double(event.Value));
+        case 'z'
+            mydata.mnipos(3) = round(str2double(event.Value));
+    end
+    mydata.pos_crop = round(mydata.mri2mni\mydata.mnipos);
+    mydata.pos(1) = mydata.pos_crop(1)-minR;
+    mydata.pos(2) = mydata.pos_crop(2)-minA;
+    mydata.pos(3) = mydata.pos_crop(3)-minS;
+end
+if ~sum( mydata.pos<1 | mydata.pos>size(mydata.img) )
+    set(fh,'UserData',mydata);
+    showimages(minR,minA,minS,fh)
+end
+end
+
+function figResize(fh,~,minR,minA,minS)
+    if ~isempty(fh.Children)
+        showimages(minR,minA,minS,fh)
+    end
 end
\ No newline at end of file
diff --git a/start_seg.m b/start_seg.m
index cec66ab..1857fb2 100644
--- a/start_seg.m
+++ b/start_seg.m
@@ -62,7 +62,7 @@ function start_seg(T1,T2,Template,norm)
     if strcmp(ext,'.hdr'), ref = [dirname filesep t1name '.img']; end
     
     t1Data = load_untouch_nii(ref);
-    sliceshow(t1Data.img,[],'gray',[],[],'MRI: Click anywhere to navigate.'); drawnow
+    sliceshow(t1Data.img,[],'gray',[],[],'MRI: Click anywhere to navigate.',[],[],[]); drawnow
         
     matlabbatch{1}.spm.spatial.preproc.channel.vols = {ref};  % image to be segmented
     matlabbatch{1}.spm.spatial.preproc.channel.biasreg = 0.001; % P(beta) % 0.0001;
@@ -81,7 +81,7 @@ function start_seg(T1,T2,Template,norm)
 %         fprintf('Using %s to segment T1 and T2 images: %s %s\n', Template, ref, ref2);
 
         t2Data = load_untouch_nii(ref2);
-        sliceshow(t2Data.img,[],'gray',[],[],'MRI: T2. Click anywhere to navigate.'); drawnow
+        sliceshow(t2Data.img,[],'gray',[],[],'MRI: T2. Click anywhere to navigate.',[],[],[]); drawnow
         
         matlabbatch{1}.spm.spatial.preproc.channel(2).vols = {ref2}; % the 2nd image aiding segmentation
         matlabbatch{1}.spm.spatial.preproc.channel(2).biasreg = 0.001; % 0.0001;
diff --git a/visualizeRes.m b/visualizeRes.m
index 9859ba2..5b4ec12 100644
--- a/visualizeRes.m
+++ b/visualizeRes.m
@@ -8,6 +8,8 @@ function visualizeRes(subj,subjRasRSPD,spmOut,segOut,T2,node,elem,face,inCurrent
 % yhuang16@citymail.cuny.edu
 % April 2018
 % August 2019 callable by roast_target()
+%
+% (c) May 2024 Gavin Hsu and Andrew Birnbaum
 
 if ndims(varargin{1})==3
     isRoast = 1;
@@ -33,11 +35,11 @@ function visualizeRes(subj,subjRasRSPD,spmOut,segOut,T2,node,elem,face,inCurrent
 if showAll    
     if ~strcmp(subjName,'nyhead')
         disp('showing MRI and segmentations...');
-        data = load_untouch_nii(subjRasRSPD); sliceshow(data.img,[],'gray',[],[],'MRI: Click anywhere to navigate.',[],mri2mni); drawnow
+        data = load_untouch_nii(subjRasRSPD); sliceshow(data.img,[],'gray',[],[],'MRI: Click anywhere to navigate.',[],mri2mni,[]); drawnow
         
         if ~isempty(T2) %T2 specified
             data = load_untouch_nii(T2);
-            sliceshow(data.img,[],'gray',[],[],'MRI: T2. Click anywhere to navigate.',[],mri2mni); drawnow
+            sliceshow(data.img,[],'gray',[],[],'MRI: T2. Click anywhere to navigate.',[],mri2mni,[]); drawnow
         end
     else
         disp('NEW YORK HEAD selected, there is NO MRI for it to show.')
@@ -62,7 +64,7 @@ function visualizeRes(subj,subjRasRSPD,spmOut,segOut,T2,node,elem,face,inCurrent
     allMaskShow = masks.img;
     allMaskShow(gel.img>0) = numOfTissue + 1;
     allMaskShow(elec.img>0) = numOfTissue + 2;
-    sliceshow(allMaskShow,[],[],[],'Tissue index','Segmentation. Click anywhere to navigate.',[],mri2mni)
+    sliceshow(allMaskShow,[],[],[],'Tissue index','Segmentation. Click anywhere to navigate.',[],mri2mni,[])
     drawnow
 end
 
@@ -232,10 +234,11 @@ function visualizeRes(subj,subjRasRSPD,spmOut,segOut,T2,node,elem,face,inCurrent
 nan_mask_brain(find(brain)) = 1;
 
 cm = colormap(jet(2^11)); cm = [1 1 1;cm];
+bbox = brainCrop(segOut);
 
 if isRoast
     figName = ['Voltage in Simulation: ' uniTag];
-    sliceshow(vol_all.*nan_mask_brain,[],cm,[],'Voltage (mV)',[figName '. Click anywhere to navigate.'],[],mri2mni); drawnow
+    sliceshow(vol_all.*nan_mask_brain,[],cm,[],'Voltage (mV)',[figName '. Click anywhere to navigate.'],[],mri2mni,bbox); drawnow
 end
 
 for i=1:size(ef_all,4), ef_all(:,:,:,i) = ef_all(:,:,:,i).*nan_mask_brain; end
@@ -243,11 +246,11 @@ function visualizeRes(subj,subjRasRSPD,spmOut,segOut,T2,node,elem,face,inCurrent
 dataShowVal = ef_mag(~isnan(ef_mag(:)));
 if isRoast
     figName = ['Electric field in Simulation: ' uniTag];
-    sliceshow(ef_mag,[],cm,[min(dataShowVal) prctile(dataShowVal,95)],'Electric field (V/m)',[figName '. Click anywhere to navigate.'],ef_all,mri2mni); drawnow
+    sliceshow(ef_mag,[],cm,[min(dataShowVal) prctile(dataShowVal,95)],'Electric field (V/m)',[figName '. Click anywhere to navigate.'],ef_all,mri2mni,bbox); drawnow
 else
     
     for i=1:size(targetCoord,1)
         figName = ['Electric field at Target ' num2str(i) ' in Targeting: ' uniTag];
-        sliceshow(ef_mag,targetCoord(i,:),cm,[min(dataShowVal) prctile(dataShowVal,95)],'Electric field (V/m)',[figName '. Click anywhere to navigate.'],ef_all,mri2mni); drawnow
+        sliceshow(ef_mag,targetCoord(i,:),cm,[min(dataShowVal) prctile(dataShowVal,95)],'Electric field (V/m)',[figName '. Click anywhere to navigate.'],ef_all,mri2mni,bbox); drawnow
     end
 end
\ No newline at end of file

From 4fe252f429eaf9f9d0b2ed7f154545e1471a0201 Mon Sep 17 00:00:00 2001
From: Yu Andy Huang <andypotatohy@gmail.com>
Date: Tue, 21 May 2024 15:56:06 -0400
Subject: [PATCH 2/4] fix some issues of the new sliceshow

---
 brainCrop.m        |  4 +--
 meshByIso2mesh.m   |  2 +-
 releasingNotes.txt |  2 ++
 reviewRes.m        | 20 ++++++++----
 sliceshow.m        | 79 +++++++++++++++++++++++-----------------------
 start_seg.m        |  4 +--
 visualizeRes.m     | 12 +++----
 7 files changed, 65 insertions(+), 58 deletions(-)

diff --git a/brainCrop.m b/brainCrop.m
index 4a856bd..24811c5 100644
--- a/brainCrop.m
+++ b/brainCrop.m
@@ -4,8 +4,8 @@
 % (c) 2024 Gavin Hsu and Andrew Birnbaum
 
 function bbox = brainCrop(subj)       
-    [dirname,baseFilename,ext] = fileparts(subj);
-    seg = [dirname,'\',baseFilename,'_masks',ext];
+    [dirname,baseFilename] = fileparts(subj);
+    seg = [dirname filesep baseFilename,'_masks.nii'];
     data = load_untouch_nii(seg);
     wm = data.img == 1;
     thresh = [0,0,100];
diff --git a/meshByIso2mesh.m b/meshByIso2mesh.m
index 83feb0a..614c50e 100644
--- a/meshByIso2mesh.m
+++ b/meshByIso2mesh.m
@@ -45,7 +45,7 @@
 allMaskShow(data.img>0) = numOfTissue + 2;
 
 % sliceshow(allMask,[],[],[],'Tissue index','Segmentation. Click anywhere to navigate.')
-sliceshow(allMaskShow,[],[],[],'Tissue index','Segmentation. Click anywhere to navigate.',[],mri2mni,[])
+sliceshow(allMaskShow,[],[],[],'Tissue index','Segmentation. Click anywhere to navigate.',[],mri2mni)
 drawnow
 
 % allMask = uint8(allMask);
diff --git a/releasingNotes.txt b/releasingNotes.txt
index 7b4cbe9..3a725b9 100644
--- a/releasingNotes.txt
+++ b/releasingNotes.txt
@@ -16,6 +16,8 @@ Added a function to set the headers of the MRI and segmentation masks so that th
 
 Added code to handle MRIs with nonzero qform in their header.
 
+Upgraded the sliceshow() function for better visualization of slices in a 3D volume.
+
 
 ROAST V3.0 (codename: Hell's Kitchen) -- 2019/09/02:
 
diff --git a/reviewRes.m b/reviewRes.m
index b7077fc..c6b67c0 100644
--- a/reviewRes.m
+++ b/reviewRes.m
@@ -71,7 +71,7 @@ function reviewRes(subj,simTag,tissue,fastRender,tarTag)
 % ROAST by Andrew Birnbaum
 % April 2024
 %
-% (c) May 2024 Gavin Hsu
+% (c) May 2024, sliceshow improved by Gavin Hsu and Andrew Birnbaum
 
 fprintf('\n\n');
 disp('=============================================================')
@@ -245,7 +245,7 @@ function reviewRes(subj,simTag,tissue,fastRender,tarTag)
         if ~exist(subjRasRSPD,'file')
             error(['The subject MRI you provided ' subjRasRSPD ' does not exist. Check if you run through resampling or zero-padding if you tried to do that.']);
         else
-            data = load_untouch_nii(subjRasRSPD); sliceshow(data.img,[],'gray',[],[],'MRI: Click anywhere to navigate.',[],mri2mni,[]); drawnow
+            data = load_untouch_nii(subjRasRSPD); sliceshow(data.img,[],'gray',[],[],'MRI: Click anywhere to navigate.',[],mri2mni); drawnow
         end
         
         if ~isempty(optRoast.T2) %T2 specified
@@ -253,7 +253,7 @@ function reviewRes(subj,simTag,tissue,fastRender,tarTag)
                 error(['T2 file ' optRoast.T2 ' does not exist. You used that to run ROAST but maybe later deleted it.']);
             else
                 data = load_untouch_nii(optRoast.T2);
-                sliceshow(data.img,[],'gray',[],[],'MRI: T2. Click anywhere to navigate.',[],mri2mni,[]); drawnow
+                sliceshow(data.img,[],'gray',[],[],'MRI: T2. Click anywhere to navigate.',[],mri2mni); drawnow
             end
         end
     else
@@ -300,7 +300,7 @@ function reviewRes(subj,simTag,tissue,fastRender,tarTag)
     allMaskShow = masks.img;
     allMaskShow(gel.img>0) = numOfTissue + 1;
     allMaskShow(elec.img>0) = numOfTissue + 2;
-    sliceshow(allMaskShow,[],[],[],'Tissue index','Segmentation. Click anywhere to navigate.',[],mri2mni,[])
+    sliceshow(allMaskShow,[],[],[],'Tissue index','Segmentation. Click anywhere to navigate.',[],mri2mni)
     drawnow
     
 else
@@ -519,7 +519,13 @@ function reviewRes(subj,simTag,tissue,fastRender,tarTag)
 nan_mask(find(mask)) = 1;
 
 cm = colormap(jet(2^11)); cm = [1 1 1;cm];
-bbox = brainCrop(subjRasRSPD);
+if strcmp(tissue,'white') | strcmp(tissue,'gray') | strcmp(tissue,'brain')
+    bbox = brainCrop(subjRasRSPDSeg);
+    pos = round(mean(bbox));
+else
+    bbox = [];
+    pos = [];
+end
 
 if isRoast
     
@@ -531,13 +537,13 @@ function reviewRes(subj,simTag,tissue,fastRender,tarTag)
     end
     
     figName = ['Voltage in Simulation: ' simTag];
-    sliceshow(vol_all.*nan_mask,[],cm,[],'Voltage (mV)',[figName '. Click anywhere to navigate.'],[],mri2mni,bbox); drawnow
+    sliceshow(vol_all.*nan_mask,pos,cm,[],'Voltage (mV)',[figName '. Click anywhere to navigate.'],[],mri2mni,bbox); drawnow
     
     figName = ['Electric field in Simulation: ' simTag];
     for i=1:size(ef_all,4), ef_all(:,:,:,i) = ef_all(:,:,:,i).*nan_mask; end
     ef_mag = ef_mag.*nan_mask;
     dataShowVal = ef_mag(~isnan(ef_mag(:)));
-    sliceshow(ef_mag,[],cm,[min(dataShowVal) prctile(dataShowVal,95)],'Electric field (V/m)',[figName '. Click anywhere to navigate.'],ef_all,mri2mni,bbox); drawnow
+    sliceshow(ef_mag,pos,cm,[min(dataShowVal) prctile(dataShowVal,95)],'Electric field (V/m)',[figName '. Click anywhere to navigate.'],ef_all,mri2mni,bbox); drawnow
     
 else
     
diff --git a/sliceshow.m b/sliceshow.m
index 5749c84..e9259ca 100644
--- a/sliceshow.m
+++ b/sliceshow.m
@@ -20,7 +20,7 @@ function sliceshow(img,pos,color,clim,label,figName,vecImg,mri2mni,bbox)
 % 
 % vecImg is the 3D vectorial field, e.g. an electric field.
 % 
-% mri2mni is the mapping from MRI voxel space to the MNI space, so
+% mri2mni is the mapping from MRI voxel space to the MNI space.
 %
 % bbox is the output of brainCrop(). Use this to display only the brain.
 %
@@ -31,33 +31,14 @@ function sliceshow(img,pos,color,clim,label,figName,vecImg,mri2mni,bbox)
 % (c) August 2019, Yu (Andy) Huang
 % (c) 2024, Gavin Hsu and Andrew Birnbaum
 
-if nargin >= 2 && ~isempty(bbox)
-    minR = bbox(1,1);
-    maxR = bbox(2,1);
-    minA = bbox(1,2);
-    maxA = bbox(2,2);
-    minS = bbox(1,3);
-    maxS = bbox(2,3);    
-    img = img(minR:maxR, minA:maxA, minS:maxS);
-else
-    minR = 0;
-    minA = 0;
-    minS = 0;
-end
-
 if nargin<1 || isempty(img)
-    error('At least give us a volume to display')
+    error('At least give us a volume to display');
 else
     [Nx,Ny,Nz] = size(img);
-    mydata.img = img;
 end
 
 if nargin<2 || isempty(pos)
-    mydata.pos = round(size(img)/2);
-    mydata.pos_crop = mydata.pos + [minR,minA,minS];
-else
-     mydata.pos=pos-[minR,minA,minS];
-     mydata.pos_crop = mydata.pos + [minR,minA,minS];
+    pos = round(size(img)/2);
 end
 
 if nargin<3 || isempty(color)
@@ -89,18 +70,12 @@ function sliceshow(img,pos,color,clim,label,figName,vecImg,mri2mni,bbox)
 end
 
 if nargin<7 || isempty(vecImg)
-    mydata.vecImg = [];
+    vecImg = [];
 else
-    if nargin >= 2 && ~isempty(bbox)
-        vecImg = vecImg(minR:maxR, minA:maxA, minS:maxS,:);
-    end
     temp = size(vecImg);
     if any(temp(1:3)~=[Nx,Ny,Nz]) || temp(4)~=3
         error('Vector field does not have correct size.');
     end
-    mydata.vecImg = vecImg;
-    [xi,yi,zi] = ndgrid(1:Nx,1:Ny,1:Nz);
-    mydata.xi = xi; mydata.yi = yi; mydata.zi = zi;
 end
 
 if nargin<8 || isempty(mri2mni)
@@ -110,9 +85,33 @@ function sliceshow(img,pos,color,clim,label,figName,vecImg,mri2mni,bbox)
         error('Unrecognized format of the voxel-to-MNI mapping.');
     end
     mydata.mri2mni = mri2mni;
-    mydata.mnipos = round(mydata.mri2mni*[mydata.pos_crop 1]');
 end
 
+if nargin<9 || isempty(bbox)
+    minR = 1; minA = 1; minS = 1;
+    maxR = Nx; maxA = Ny; maxS = Nz;
+else
+    minR = bbox(1,1);
+    maxR = bbox(2,1);
+    minA = bbox(1,2);
+    maxA = bbox(2,2);
+    minS = bbox(1,3);
+    maxS = bbox(2,3);    
+end
+
+% adjustment for bbox
+img = img(minR:maxR, minA:maxA, minS:maxS); mydata.img = img;
+temp = pos-[minR-1,minA-1,minS-1];
+if any(temp<=0), error('Voxel selected falls outside of the bounding box.'); end
+mydata.pos = temp;
+mydata.pos_crop = mydata.pos + [minR-1,minA-1,minS-1];
+if ~isempty(vecImg), vecImg = vecImg(minR:maxR, minA:maxA, minS:maxS,:); end 
+mydata.vecImg = vecImg;
+[Nx,Ny,Nz] = size(img);
+[xi,yi,zi] = ndgrid(1:Nx,1:Ny,1:Nz);
+mydata.xi = xi; mydata.yi = yi; mydata.zi = zi;
+if ~isempty(mydata.mri2mni), mydata.mnipos = round(mydata.mri2mni*[mydata.pos_crop 1]'); end
+
 whratio = 1.0187; %Width-to-height ratio
 w = 8.5; %Width in inches
 % link the callback function to new figure
@@ -138,8 +137,8 @@ function myCallback(fh,~,minR, minA, minS)
     case mydata.h(2); mydata.pos([2 3]) = pos;
     case mydata.h(3); mydata.pos([1 2]) = pos;
 end
-mydata.pos_crop = mydata.pos + [minR,minA,minS];
-mydata.mnipos = round(mydata.mri2mni*[mydata.pos_crop 1]');
+mydata.pos_crop = mydata.pos + [minR-1,minA-1,minS-1];
+if ~isempty(mydata.mri2mni), mydata.mnipos = round(mydata.mri2mni*[mydata.pos_crop 1]'); end
 
 % if new position is valid, update mydata as figure property and display
 % otherwise do nothing
@@ -211,7 +210,7 @@ function showimages(minR,minA,minS,fh)
 ylim(h,[0,max(size(mydata.img))])
 
 h(4) = nexttile(mytile,4); axis(h(4),'off'); box(h(4),'off'); clim(h(4),mydata.clim); axtoolbar(h(4),{});
-mydata.pos_crop = mydata.pos + [minR,minA,minS];
+mydata.pos_crop = mydata.pos + [minR-1,minA-1,minS-1];
 
 % Arrange user input and coordinates in a UI Panel
 ip = uipanel(fh,'BackgroundColor','white','AutoResizeChildren','off');
@@ -273,16 +272,16 @@ function updateX(src,event,minR, minA, minS,fh)
 if ~isempty(str2double(event.Value))
     switch src.Tag
         case 'x'
-            mydata.pos(1) = round(str2double(event.Value))-minR;
+            mydata.pos(1) = round(str2double(event.Value))-(minR-1);
             mydata.pos_crop(1) = str2double(event.Value);
         case 'y'
-            mydata.pos(2) = round(str2double(event.Value))-minA;
+            mydata.pos(2) = round(str2double(event.Value))-(minA-1);
             mydata.pos_crop(2) = str2double(event.Value);
         case 'z'
-            mydata.pos(3) = round(str2double(event.Value))-minS;
+            mydata.pos(3) = round(str2double(event.Value))-(minS-1);
             mydata.pos_crop(3) = str2double(event.Value);
     end
-    mydata.mnipos = round(mydata.mri2mni*[mydata.pos_crop 1]');
+    if ~isempty(mydata.mri2mni), mydata.mnipos = round(mydata.mri2mni*[mydata.pos_crop 1]'); end
 end
 if ~sum( mydata.pos<1 | mydata.pos>size(mydata.img) )
     set(fh,'UserData',mydata);
@@ -303,9 +302,9 @@ function updateXMNI(src,event,minR, minA, minS,fh)
             mydata.mnipos(3) = round(str2double(event.Value));
     end
     mydata.pos_crop = round(mydata.mri2mni\mydata.mnipos);
-    mydata.pos(1) = mydata.pos_crop(1)-minR;
-    mydata.pos(2) = mydata.pos_crop(2)-minA;
-    mydata.pos(3) = mydata.pos_crop(3)-minS;
+    mydata.pos(1) = mydata.pos_crop(1)-(minR-1);
+    mydata.pos(2) = mydata.pos_crop(2)-(minA-1);
+    mydata.pos(3) = mydata.pos_crop(3)-(minS-1);
 end
 if ~sum( mydata.pos<1 | mydata.pos>size(mydata.img) )
     set(fh,'UserData',mydata);
diff --git a/start_seg.m b/start_seg.m
index 1857fb2..cec66ab 100644
--- a/start_seg.m
+++ b/start_seg.m
@@ -62,7 +62,7 @@ function start_seg(T1,T2,Template,norm)
     if strcmp(ext,'.hdr'), ref = [dirname filesep t1name '.img']; end
     
     t1Data = load_untouch_nii(ref);
-    sliceshow(t1Data.img,[],'gray',[],[],'MRI: Click anywhere to navigate.',[],[],[]); drawnow
+    sliceshow(t1Data.img,[],'gray',[],[],'MRI: Click anywhere to navigate.'); drawnow
         
     matlabbatch{1}.spm.spatial.preproc.channel.vols = {ref};  % image to be segmented
     matlabbatch{1}.spm.spatial.preproc.channel.biasreg = 0.001; % P(beta) % 0.0001;
@@ -81,7 +81,7 @@ function start_seg(T1,T2,Template,norm)
 %         fprintf('Using %s to segment T1 and T2 images: %s %s\n', Template, ref, ref2);
 
         t2Data = load_untouch_nii(ref2);
-        sliceshow(t2Data.img,[],'gray',[],[],'MRI: T2. Click anywhere to navigate.',[],[],[]); drawnow
+        sliceshow(t2Data.img,[],'gray',[],[],'MRI: T2. Click anywhere to navigate.'); drawnow
         
         matlabbatch{1}.spm.spatial.preproc.channel(2).vols = {ref2}; % the 2nd image aiding segmentation
         matlabbatch{1}.spm.spatial.preproc.channel(2).biasreg = 0.001; % 0.0001;
diff --git a/visualizeRes.m b/visualizeRes.m
index 5b4ec12..f568996 100644
--- a/visualizeRes.m
+++ b/visualizeRes.m
@@ -9,7 +9,7 @@ function visualizeRes(subj,subjRasRSPD,spmOut,segOut,T2,node,elem,face,inCurrent
 % April 2018
 % August 2019 callable by roast_target()
 %
-% (c) May 2024 Gavin Hsu and Andrew Birnbaum
+% (c) May 2024, sliceshow improved by Gavin Hsu and Andrew Birnbaum
 
 if ndims(varargin{1})==3
     isRoast = 1;
@@ -35,11 +35,11 @@ function visualizeRes(subj,subjRasRSPD,spmOut,segOut,T2,node,elem,face,inCurrent
 if showAll    
     if ~strcmp(subjName,'nyhead')
         disp('showing MRI and segmentations...');
-        data = load_untouch_nii(subjRasRSPD); sliceshow(data.img,[],'gray',[],[],'MRI: Click anywhere to navigate.',[],mri2mni,[]); drawnow
+        data = load_untouch_nii(subjRasRSPD); sliceshow(data.img,[],'gray',[],[],'MRI: Click anywhere to navigate.',[],mri2mni); drawnow
         
         if ~isempty(T2) %T2 specified
             data = load_untouch_nii(T2);
-            sliceshow(data.img,[],'gray',[],[],'MRI: T2. Click anywhere to navigate.',[],mri2mni,[]); drawnow
+            sliceshow(data.img,[],'gray',[],[],'MRI: T2. Click anywhere to navigate.',[],mri2mni); drawnow
         end
     else
         disp('NEW YORK HEAD selected, there is NO MRI for it to show.')
@@ -64,7 +64,7 @@ function visualizeRes(subj,subjRasRSPD,spmOut,segOut,T2,node,elem,face,inCurrent
     allMaskShow = masks.img;
     allMaskShow(gel.img>0) = numOfTissue + 1;
     allMaskShow(elec.img>0) = numOfTissue + 2;
-    sliceshow(allMaskShow,[],[],[],'Tissue index','Segmentation. Click anywhere to navigate.',[],mri2mni,[])
+    sliceshow(allMaskShow,[],[],[],'Tissue index','Segmentation. Click anywhere to navigate.',[],mri2mni)
     drawnow
 end
 
@@ -238,7 +238,7 @@ function visualizeRes(subj,subjRasRSPD,spmOut,segOut,T2,node,elem,face,inCurrent
 
 if isRoast
     figName = ['Voltage in Simulation: ' uniTag];
-    sliceshow(vol_all.*nan_mask_brain,[],cm,[],'Voltage (mV)',[figName '. Click anywhere to navigate.'],[],mri2mni,bbox); drawnow
+    sliceshow(vol_all.*nan_mask_brain,round(mean(bbox)),cm,[],'Voltage (mV)',[figName '. Click anywhere to navigate.'],[],mri2mni,bbox); drawnow
 end
 
 for i=1:size(ef_all,4), ef_all(:,:,:,i) = ef_all(:,:,:,i).*nan_mask_brain; end
@@ -246,7 +246,7 @@ function visualizeRes(subj,subjRasRSPD,spmOut,segOut,T2,node,elem,face,inCurrent
 dataShowVal = ef_mag(~isnan(ef_mag(:)));
 if isRoast
     figName = ['Electric field in Simulation: ' uniTag];
-    sliceshow(ef_mag,[],cm,[min(dataShowVal) prctile(dataShowVal,95)],'Electric field (V/m)',[figName '. Click anywhere to navigate.'],ef_all,mri2mni,bbox); drawnow
+    sliceshow(ef_mag,round(mean(bbox)),cm,[min(dataShowVal) prctile(dataShowVal,95)],'Electric field (V/m)',[figName '. Click anywhere to navigate.'],ef_all,mri2mni,bbox); drawnow
 else
     
     for i=1:size(targetCoord,1)

From 165c21aa23a4697e4af2522e822df47198a5c6ac Mon Sep 17 00:00:00 2001
From: Yu Andy Huang <andypotatohy@gmail.com>
Date: Tue, 21 May 2024 17:29:09 -0400
Subject: [PATCH 3/4] a minor issue

---
 reviewRes.m | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/reviewRes.m b/reviewRes.m
index c6b67c0..70cf492 100644
--- a/reviewRes.m
+++ b/reviewRes.m
@@ -519,7 +519,7 @@ function reviewRes(subj,simTag,tissue,fastRender,tarTag)
 nan_mask(find(mask)) = 1;
 
 cm = colormap(jet(2^11)); cm = [1 1 1;cm];
-if strcmp(tissue,'white') | strcmp(tissue,'gray') | strcmp(tissue,'brain')
+if strcmp(tissue,'white') || strcmp(tissue,'gray') || strcmp(tissue,'brain')
     bbox = brainCrop(subjRasRSPDSeg);
     pos = round(mean(bbox));
 else

From 47efc9ca215360731d767237975a4790237b4b9c Mon Sep 17 00:00:00 2001
From: Yu Andy Huang <andypotatohy@gmail.com>
Date: Tue, 21 May 2024 17:35:17 -0400
Subject: [PATCH 4/4] Delete .gitignore

---
 .gitignore | 28 ----------------------------
 1 file changed, 28 deletions(-)
 delete mode 100644 .gitignore

diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index ca37d1e..0000000
--- a/.gitignore
+++ /dev/null
@@ -1,28 +0,0 @@
-example/c1MNI152_T1_1mm_ras_T1orT2.nii
-example/c2MNI152_T1_1mm_ras_T1orT2.nii
-example/c3MNI152_T1_1mm_ras_T1orT2.nii
-example/c4MNI152_T1_1mm_ras_T1orT2.nii
-example/c5MNI152_T1_1mm_ras_T1orT2.nii
-example/c6MNI152_T1_1mm_ras_T1orT2.nii
-example/MNI152_T1_1mm_20240516T173547_e.nii
-example/MNI152_T1_1mm_20240516T173547_e.pos
-example/MNI152_T1_1mm_20240516T173547_emag.nii
-example/MNI152_T1_1mm_20240516T173547_mask_elec.nii
-example/MNI152_T1_1mm_20240516T173547_mask_gel.nii
-example/MNI152_T1_1mm_20240516T173547_ready.msh
-example/MNI152_T1_1mm_20240516T173547_roastOptions.mat
-example/MNI152_T1_1mm_20240516T173547_roastResult.mat
-example/MNI152_T1_1mm_20240516T173547_usedElecArea.mat
-example/MNI152_T1_1mm_20240516T173547_v.nii
-example/MNI152_T1_1mm_20240516T173547_v.pos
-example/MNI152_T1_1mm_20240516T173547.mat
-example/MNI152_T1_1mm_20240516T173547.msh
-example/MNI152_T1_1mm_20240516T173547.pro
-example/MNI152_T1_1mm_ras_header.mat
-example/MNI152_T1_1mm_ras_MNI.nii
-example/MNI152_T1_1mm_ras_T1orT2_rmask.mat
-example/MNI152_T1_1mm_ras_T1orT2_seg8.mat
-example/MNI152_T1_1mm_ras_T1orT2_SPM_masks_MNI.nii
-example/MNI152_T1_1mm_ras_T1orT2_SPM_masks.nii
-example/MNI152_T1_1mm_ras.nii
-example/MNI152_T1_1mm_roastLog