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morph_wb_sensitivity_072521.m
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morph_wb_sensitivity_072521.m
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close all; clear all;
clear global etc_render_fsbrain;
setenv('SUBJECTS_DIR','/Users/fhlin/workspace/seeg/subjects/');
%setenv('SUBJECTS_DIR','/space_lin2/fhlin/seeg/subjects');
subject='s027';
surf='orig';
file_forward_mat='seeg_fwd_wb_dec_072521.mat';
%mri=MRIread('/Users/fhlin_admin/workspace/seeg/subjects/s027/mri/orig.mgz'); %for MAC/Linux
mri=MRIread(sprintf('%s/%s/mri/orig.mgz',getenv('SUBJECTS_DIR'),subject));
file_stc={
'seeg_wb_sensitivity_072521_snr-vol.stc';
'seeg_wb_sensitivity_072521_s-vol.stc';
};
output_stem='';
timeVec=[]; %empty for all time points
target_subject='fsaverage';
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%load the Talairach transformation matrix from the "pre-OP" data
%talxfm=etc_read_xfm('file_xfm','/Users/fhlin_admin/workspace/seeg/subjects/s027/mri/transforms/talairach.xfm'); %for MAC/Linux
load(file_forward_mat);
%append the forward matrix object 'A' surface coordinates; used for
%interpolation
hemi={'lh','rh'};
for hemi_idx=1:2
file_surf=sprintf('%s/%s/surf/%s.%s',getenv('SUBJECTS_DIR'),subject,hemi{hemi_idx},surf);
[A(hemi_idx).vertex_coords, A(hemi_idx).faces] = read_surf(file_surf);
end;
for f_idx=1:length(file_stc)
[dummy, fstem]=fileparts(file_stc{f_idx});
fn_output=sprintf('%s%s.mgz',output_stem,fstem);
fn_under_output=sprintf('%s%s_under.mgz',output_stem,fstem);
%volume stc
[vol_stc,d0,d1]=inverse_read_stc(file_stc{f_idx});
overlay_D{1}=[];
overlay_D{2}=[];
loc_vol_idx{1}=[];
loc_vol_idx{2}=[];
mri_overlay=mri;
if(isempty(timeVec))
timeVec=[1:size(vol_stc,2)];
end;
for t_idx=1:length(timeVec)
fprintf('time point [%04d]...',timeVec(t_idx));
try
%initialize
loc_vol=[];
for hemi_idx=1:2
n_dip(hemi_idx)=size(A(hemi_idx).A,2);
n_source(hemi_idx)=n_dip(hemi_idx)/3;
switch hemi_idx
case 1
offset=0;
hemi_str='lh';
case 2
offset=n_source(1);
hemi_str='rh';
end;
%get source estimates at cortical and sub-cortical locations
X_hemi_cort=vol_stc(offset+1:offset+length(A(hemi_idx).v_idx),t_idx);
X_hemi_subcort=vol_stc(offset+length(A(hemi_idx).v_idx)+1:offset+n_source(hemi_idx),t_idx);
%smooth source estimates at cortical locations
ov=zeros(size(A(hemi_idx).vertex_coords,1),1);
ov(A(hemi_idx).v_idx+1)=X_hemi_cort;
flag_overlay_D_init=1;
%if(isfield(etc_render_fsbrain,'overlay_D'))
% if(length(etc_render_fsbrain.overlay_D)==2)
% if(~isempty(etc_render_fsbrain.overlay_D{hemi_idx}))
if(~isempty(overlay_D{hemi_idx}))
flag_overlay_D_init=0;
end;
% end;
% end;
%end;
%if(flag_overlay_D_init) etc_render_fsbrain.overlay_D{hemi_idx}=[];end;
overlay_smooth=5;
fprintf('smoothing <%s>...',hemi_str);
[ovs,dd0,dd1,overlay_Ds,overlay_D{hemi_idx}]=inverse_smooth('','vertex',A(hemi_idx).vertex_coords','face',A(hemi_idx).faces','value',ov,'value_idx',A(hemi_idx).v_idx+1,'step',overlay_smooth,'n_ratio',length(ov)/size(X_hemi_cort,1),'flag_display',0,'flag_regrid',0,'flag_fixval',0,'D',overlay_D{hemi_idx});
%assemble smoothed source at cortical locations and sources at sub-cortical locations
X_wb{hemi_idx}=cat(1,ovs(:),X_hemi_subcort(:));
flag_cal_loc_vol_idx=1;
%if(isfield(etc_render_fsbrain,'loc_vol_idx'))
% if(length(etc_render_fsbrain.loc_vol_idx)==2)
% if(~isempty(etc_render_fsbrain.loc_vol_idx{hemi_idx}))
if(~isempty(loc_vol_idx{hemi_idx}))
flag_cal_loc_vol_idx=0;
end;
% end;
% end;
%end;
fprintf('creating indices <%s>...',hemi_str);
if(flag_cal_loc_vol_idx==1)
etc_render_fsbrain.loc_vol_idx{hemi_idx}=[];
%get coordinates from surface to volume
loc=cat(1,A(hemi_idx).vertex_coords./1e3,A(hemi_idx).wb_loc);
loc_surf=[loc.*1e3 ones(size(loc,1),1)]';
tmp=inv(mri.tkrvox2ras)*loc_surf;
loc_vol{hemi_idx}=round(tmp(1:3,:))';
loc_vol{hemi_idx}=round(tmp(1:3,:))';
loc_vol_idx{hemi_idx}=sub2ind(size(mri.vol),loc_vol{hemi_idx}(:,2),loc_vol{hemi_idx}(:,1),loc_vol{hemi_idx}(:,3));
end;
end;
fprintf('saving data ...');
tmp=zeros(size(mri.vol));
for hemi_idx=1:2
tmp(loc_vol_idx{hemi_idx})=X_wb{hemi_idx};
end;
mri_overlay.vol=tmp;
if(t_idx==1)
if(strcmp(target_subject,'fsaverage'))
%targ=MRIread('/Applications/freesurfer/average/mni305.cor.subfov2.mgz'); %MNI-Talairach space with 2mm resolution (for MAC)
targ0=MRIread(sprintf('%s/%s/mri/orig.mgz',getenv('SUBJECTS_DIR'),'fsaverage'));
targ1=MRIread(sprintf('%s/average/mni305.cor.subfov2.mgz',getenv('FREESURFER_HOME'))); %MNI-Talairach space with 2mm resolution (for server)
fprintf('loading transformation for subject [%s]...\n',subject);
mov_xfm0=etc_read_xfm('subject',subject);
mov_xfm1=etc_read_xfm('file_xfm','/Applications/freesurfer/average/mni305.cor.subfov2.reg');
end;
%subject to Talairach 256x256x256
R0=mri.tkrvox2ras*inv(mri.vox2ras)*inv(mov_xfm0)*(targ0.vox2ras)*inv(targ0.tkrvox2ras);
MRI_underlay_tal0=etc_MRIvol2vol(mri,targ0,R0);
%figure; imagesc(targ0.vol(:,:,100))
%figure; imagesc(MRI_underlay_tal0.vol(:,:,100))
%Talairach 256x256x256 oto Talairach 76x76x93 (2-mm iso.)
R1=MRI_underlay_tal0.tkrvox2ras*inv(MRI_underlay_tal0.vox2ras)*inv(mov_xfm1)*(targ1.vox2ras)*inv(targ1.tkrvox2ras);
MRI_underlay_tal=etc_MRIvol2vol(MRI_underlay_tal0,targ1,R1);
%figure; imagesc(targ1.vol(:,:,60))
%figure; imagesc(MRI_underlay_tal.vol(:,:,60))
MRIwrite(MRI_underlay_tal,sprintf('%s%s_under-tal.2mm.mgh',output_stem,fstem));
mri_overlay_tal=MRI_underlay_tal;
mri_overlay_tal.nframes=length(timeVec);
mri_overlay_tal.vol=zeros(mri_overlay_tal.volsize(1),mri_overlay_tal.volsize(2),mri_overlay_tal.volsize(3),length(timeVec));
end;
%subject to Talairach 256x256x256
R0=mri.tkrvox2ras*inv(mri.vox2ras)*inv(mov_xfm0)*(targ0.vox2ras)*inv(targ0.tkrvox2ras);
tmp=etc_MRIvol2vol(mri_overlay,targ0,R0);
%Talairach 256x256x256 oto Talairach 76x76x93 (2-mm iso.)
R1=tmp.tkrvox2ras*inv(tmp.vox2ras)*inv(mov_xfm1)*(targ1.vox2ras)*inv(targ1.tkrvox2ras);
tmp=etc_MRIvol2vol(tmp,targ1,R1);
mri_overlay_tal.vol(:,:,:,t_idx)=tmp.vol;
catch ME
end;
fprintf('\n');
end;
MRIwrite(mri_overlay_tal,sprintf('%s%s-tal.2mm.mgh',output_stem,fstem));
end;