On 2/26/19 7:58 PM, Alon Baram wrote:
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Hello,
I have subject's surfaces where I first register the rh to the lh using xhemireg, then register both hemispheres to fsaverage_sym using surfreg, and then resample the registered surface to the isocahedron using mris_surf2surf (see code below if that's helpful, part of the RSA toolbox, written by Joern Diedrichsen). This means that for the two hemispheres of these surfaces, each vertex number corresponds to an exact anatomical location (vertex i in rh will be in the exact mirroring location of vertex i).
(I then also move the coordinates of the surface to correspond to world, rather than RAS_tkreg coords, but I think that is irrelevant to my question. This is used to create searchlights ).
I then compute curvature maps on these surfaces, and would like to view them in Freeview overlaid on a common surface. As the remapped surfaces were registered to fsaverage_sym, I thought it would make sense to load them as overlays on the fsaverage_sym surfaces. However I'm not sure on which hemisphere of fsaverage_sym should the curv of the rh be overlaid on. I originally thought it shouldn't matter - that the rh of fsaverage_sym was an exact mirror of the lh, so it shouldn't matter if I load the curv as overlay on the lh or rh. But for a reason I don't understand, that is not true, and it really changes how the curvature looks on the surface.
I can't tell from your code, but you probably registered both lh and rh to the lh of fsaveage_sym, so you should only view the results on that. If you want us to look at your code, you must give us simple command lines.
Moreover, it looks exactly the same if I load the curvature as overlay on the rh of fsaverage or fsaverage_sym - I thought these two should be different.
The overlay will be the same since it is the same overlay. If you look carefully, you will see that there are some small differences in the curvature patterns. fsaverage_sym was created from the same subjects as fsaverage, so it is not surprising that they are similar.
What am I getting wrong? which is the correct way of viewing the curvature? Thanks very much for the help.
function S=freesurfer_mapicosahedron_xhem(subj,subject_dir,varargin);
% function S=freesurfer_mapicosahedron(subj,subject_dir,varargin);
% Resampels a registered subject surface to a regular isocahedron
% This allows things to happen exactly in atlas space - each vertex number
% corresponds exactly to a anatomical location
% Makes a new folder, called ['x' subj] that contains the remapped subject
% Uses function mri_surf2surf
% INPUT:
% subj: subject name
% subjects_dir: freesurfer's SUBJECT_DIR
% VARARGIN:
% 'hemisphere',[1 2]: left / right or both hemispheres
% 'surf_files',{'',''}: Surface files to be resampled
% {'.white','.pial','.inflated','.sphere.reg','.sphere'};
% 'curv_files',{'',''}: Curvature files to be resampled
% {'.curv','.sulc','.area'};
% 'smoothing',1:Smoothing iterations applied (otherwise nearest neighbour)
% ---------------------------
% v1.0 Joern Diedrichsen (j.diedrichsen@ucl.ac.uk mailto:j.diedrichsen@ucl.ac.uk
%
current_dir=pwd;
direct=[getenv('FREESURFER_HOME') filesep 'average' filesep 'surf' ];
old_dir=getenv('SUBJECTS_DIR');
% if (isempty(subject_dir))
%subject_dir=getenv('SUBJECTS_DIR');
% else
%setenv('SUBJECTS_DIR',subject_dir);
% end;
subject_dir=getenv('SUBJECTS_DIR');
structname={'left','right'};
dirname={'LeftHem','RightHem'};
hem={'lh','rh'};
surf_files={'.white','.pial','.inflated'};
curv_files={'.curv','.sulc','.area'};
smoothing=1;
hemisphere=[1:2]; % Do both hemispheres
vararginoptions(varargin,{'smoothing','surf_files','curv_files','hemisphere'});
% read freesurfer version
ver_file = fullfile(getenv('FREESURFER_HOME'),'build-stamp.txt');
if exist(ver_file)
fid = fopen(ver_file);
verStr= fgetl(fid);
fclose(fid);
verStr= strrep(verStr,'-v',' ');
verStr= textscan(verStr,'%s%f');
fsl_ver = verStr{2};
end
new_dir = [subject_dir filesep 'x' subj filesep 'surf'];
if (~exist(new_dir))
mkdir(new_dir);
end;
num_surf=length(surf_files);
files={surf_files{:},curv_files{:}};
for h=hemisphere
% Original subjects dir
if (h==1)
orig_dir =fullfile(subject_dir,subj,'surf');
else
orig_dir =fullfile(subject_dir,subj,'xhemi','surf');
end;
cd(orig_dir);
% [vertex_coords, faces]
[Vico,F]=read_surf([direct filesep 'lh.sphere.reg']); % /opt/fmrib/FreeSurfer_releases/6.0/average/surf/lh.sphere.reg
% Topology file
for i=1:length(files)
if i<=num_surf
% e.g /home/fs0/abaram/scratch/freesurfer-subjects/s99/surf/lh.white
[V]=read_surf([orig_dir filesep 'lh' files{i}]);
else
[V]=read_curv([orig_dir filesep 'lh' files{i}]);
end;
B=[];
forj=1:size(V,2) % Alon: number of coords - usually 3
% Alon's comment: write the coords of the vertices (one dimension at a
% time) as curv files
write_curv([orig_dir filesep 'lh.temp.curv'],V(:,j),10000); % e.g [$SUBJECTS_DIR/s99/surf/lh.temp.curv, only x coords of V, number of faces (why only 10000?! I think it's just not used)]
if (h==1)
system(['DYLD_LIBRARY_PATH=/opt/fmrib/FreeSurfer_releases/6.0/lib/gcc/lib '...
'mri_surf2surf --srcsubject 'subj ' --hemi lh'...
' --trgsubject ico--trgicoorder 7'...
' --surfreg fsaverage_sym.sphere.reg'...
' --srcsurfval temp.curv --src_type curv'...
' --trgsurfval tempN.curv --trg_type curv --mapmethod nnf --nsmooth-out 'num2str(smoothing)]);
else
% Reslice the left hemisphere of the xhemi subject - this
% is originally the right hemisphere
system(['DYLD_LIBRARY_PATH=/opt/fmrib/FreeSurfer_releases/6.0/lib/gcc/lib '...
'mri_surf2surf --srcsubject 'subj '/xhemi --hemi lh'...
' --trgsubject ico--trgicoorder 7'...
' --surfreg fsaverage_sym.sphere.reg'...
' --srcsurfval temp.curv --src_type curv'...
' --trgsurfval tempN.curv --trg_type curv --mapmethod nnf --nsmooth-out 'num2str(smoothing)]);
end;
%B(:,i)=read_curv([orig_dir filesep hem{h} '.tempN.curv']);
%For different alignment, I would have to use -surf_reg option
%here
% Alon's comment: read in the resampled curv file of a single dim of the
% coordinates per vertex. At the end of the j loop, B will have
% the all 3 resamped dims of the coordinates.
if fsl_ver <= 5.1
B(:,j)=read_curv(fullfile(orig_dir,'tempN.curv'));
else
B(:,j)=read_curv(fullfile([orig_dir filesep 'lh.tempN.curv']));
end;
end;
% write the surfaces (3 col) and curvs (1 col).
if i<=num_surf
freesurfer_write_surf([new_dir filesep hem{h} files{i}],B(:,1:3),F);
else
write_curv([new_dir filesep hem{h} files{i}],B(:,1),size(F,1));
end;
end;
% deleting temporary files
try
delete(fullfile(orig_dir,['lh.temp.curv']));
if fsl_ver <= 5.1
delete(fullfile(orig_dir,['tempN.curv']));
else
delete(fullfile(orig_dir,['lh.tempN.curv']));
end
catch err
disp(getReport(err));
end;
end;
setenv('SUBJECTS_DIR',old_dir);
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