From a572858cf55667912d50b894ae1b6098faa68e49 Mon Sep 17 00:00:00 2001
From: Ningfei Li <ningfei.li@gmail.com>
Date: Sat, 5 Dec 2020 00:28:24 +0100
Subject: [PATCH] BUG: Adapt new atlas roi structures.

---
 ea_checkstructures.m             | 16 ++++++++--------
 ea_genvat_horn.m                 |  6 +++---
 helpers/ea_atlasmajorcomponent.m | 16 ++++++++--------
 helpers/ea_atlasreducepatch.m    |  4 ++--
 4 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/ea_checkstructures.m b/ea_checkstructures.m
index 2d5f40979..8eec47d7d 100644
--- a/ea_checkstructures.m
+++ b/ea_checkstructures.m
@@ -240,29 +240,29 @@ function ea_setnewatlas(h,gf,options,handles,dontupdate)
 options.atlasset=h.Parent.Label;
 load([ea_space(options,'atlases'),options.atlasset,filesep,'atlas_index.mat']);
 if strcmp(h.Label,'ALL')
-    fv=atlases.fv;
+    roi=atlases.roi;
     pixdim=atlases.pixdim;
     xyz=[];
-    for i=1:numel(fv)
+    for i=1:numel(roi)
         try % some are empty in case of midline/mixed structures
-            xyz=[xyz;fv{i}.vertices];
+            xyz=[xyz;roi{i}.fv.vertices];
         end
     end
     pixdim=pixdim{1};
 else
     [~,six]=ismember(h.Label,ea_rmext(atlases.names));
-    fv=atlases.fv(six,:);
+    roi=atlases.roi(six,:);
     pixdim=atlases.pixdim(six,:);
-    if length(fv)>1
+    if length(roi)>1
         xyz=[];
-        for i=1:numel(fv)
+        for i=1:numel(roi)
             try % some are empty in case of midline/mixed structures
-                xyz=[xyz;fv{i}.vertices];
+                xyz=[xyz;roi{i}.fv.vertices];
             end
         end
         pixdim=mean([pixdim{1};pixdim{2}]);
     else
-        xyz=fv{1}.vertices;
+        xyz=roi{1}.fv.vertices;
         pixdim=pixdim{1};
     end
 end
diff --git a/ea_genvat_horn.m b/ea_genvat_horn.m
index a8025780f..2605332c0 100644
--- a/ea_genvat_horn.m
+++ b/ea_genvat_horn.m
@@ -88,11 +88,11 @@
                 if ~isfield(atlases,'tissuetypes')
                     atlases.tissuetypes=ones(length(atlases.names),1);
                 end
-                for atlas=1:numel(atlases.fv)
-                    if isempty(atlases.fv{atlas}) || (atlases.tissuetypes~=1)
+                for atlas=1:numel(atlases.roi)
+                    if isempty(atlases.roi{atlas}.fv) || (atlases.tissuetypes~=1)
                         continue
                     end
-                    fv(cnt)=atlases.fv{atlas};
+                    fv(cnt)=atlases.roi{atlas}.fv;
 
                     ins=surfinterior(fv(cnt).vertices,fv(cnt).faces);
                     %tissuetype(cnt)=1;
diff --git a/helpers/ea_atlasmajorcomponent.m b/helpers/ea_atlasmajorcomponent.m
index 8f5120fe5..9732277cd 100644
--- a/helpers/ea_atlasmajorcomponent.m
+++ b/helpers/ea_atlasmajorcomponent.m
@@ -1,17 +1,17 @@
 function atlases=ea_atlasmajorcomponent(atlases,toclean)
 % from specified component, only preserve largest component
 
-for c=toclean 
+for c=toclean
    for side=1:2
-       % figure, patch(atlases.fv{c,side},'FaceColor','none')
-       
-       fvsplit=splitFV(atlases.fv{c,side}.faces,atlases.fv{c,side}.vertices);
+       % figure, patch(atlases.roi{c,side}.fv,'FaceColor','none')
+
+       fvsplit=splitFV(atlases.roi{c,side}.fv.faces,atlases.roi{c,side}.fv.vertices);
        for comp=1:length(fvsplit)
            lengths(comp)=length(fvsplit(comp).faces);
        end
        [~,ix]=max(lengths);
-       atlases.fv{c,side}.faces=fvsplit(ix).faces;
-       atlases.fv{c,side}.vertices=fvsplit(ix).vertices;
+       atlases.roi{c,side}.fv.faces=fvsplit(ix).faces;
+       atlases.roi{c,side}.fv.vertices=fvsplit(ix).vertices;
    end
 end
 
@@ -69,7 +69,7 @@
     openVertices = f(nextAvailFace,:);
     while ~isempty(openVertices)
         availFaceInds = find(fSets==0);
-        [availFaceSub, ~] = find(ismember(f(availFaceInds,:), openVertices)); 
+        [availFaceSub, ~] = find(ismember(f(availFaceInds,:), openVertices));
         fSets(availFaceInds(availFaceSub)) = currentSet;
         openVertices = f(availFaceInds(availFaceSub),:);
     end
@@ -85,4 +85,4 @@
     [unqVertIds, ~, newVertIndices] = unique(setF);
     fvOut(currentSet).faces = reshape(newVertIndices,size(setF));
     fvOut(currentSet).vertices = v(unqVertIds,:);
-end
\ No newline at end of file
+end
diff --git a/helpers/ea_atlasreducepatch.m b/helpers/ea_atlasreducepatch.m
index 288e2e163..f07704ca0 100644
--- a/helpers/ea_atlasreducepatch.m
+++ b/helpers/ea_atlasreducepatch.m
@@ -2,8 +2,8 @@
 
 for atl=1:length(atlases.names)
     for side=1:2
-        atlases.fv{atl,side}=reducepatch(atlases.fv{atl,side},red);
-        
+        atlases.roi{atl,side}.fv=reducepatch(atlases.roi{atl,side}.fv,red);
+
     end
 end