/
s_fe_reject_ac_v1_unbelievable_conenction.m
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s_fe_reject_ac_v1_unbelievable_conenction.m
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function s_fe_reject_ac_v1_unbelievable_conenction()
%
% This script performs a test of conenctivity between diffrerent cortical
% ROIs that are not believable.
%
% Copyright by Franco Pestilli Stanford University, 2014
% Handle parallel computing
if matlabpool('size') == 0
c = parcluster;
c.NumWorkers = 12;
matlabpool(c);
end
% Get the base directory for the data
subjects = {...
'FP_96dirs_b2000_1p5iso', ...
'HT_96dirs_b2000_1p5iso', ...
'KW_96dirs_b2000_1p5iso', ...
'MP_96dirs_b2000_1p5iso', ...
'KK_96dirs_b2000_1p5iso', ...'JW_96dirs_b2000_1p5iso', ...
};
if notDefined('saveDir'), saveDir = fullfile('/marcovaldo/frk/Dropbox','pestilli_etal_revision',mfilename);end
anatomyPath = '/marcovaldo/frk/2t1/anatomy/';
datapath = '/marcovaldo/frk/2t1/predator/';
fibs = {'run01_fliprot_aligned_trilin_csd_lmax10_run01_fliprot_aligned_trilin_brainmask_run01_fliprot_aligned_trilin_wm_prob-500000_recomputed-rejected.mat', ...
'run01_fliprot_aligned_trilin_csd_lmax10_run01_fliprot_aligned_trilin_brainmask_run01_fliprot_aligned_trilin_wm_prob-500000_recomputed-optimized.mat'};
hemisphere = {'left','right'}; %left and right hemisphere
for iSbj = 1:length(subjects)
% Find all the ROI computed for each subject:
roiDir = fullfile(anatomyPath,matchSubject2FSSUBJ(subjects{iSbj}),'label');
% We will load three FreeSurfer ROIs (Pericalcarine, V1 and V2) We will
% combine them to obtain a full representation of early visual cortex
%pericalcarine = dir(fullfile(roiDir,'*pericalcarine*.mat'));
V1 = dir(fullfile(roiDir,'*V1_label*_smooth*.mat'));
%V2 = dir(fullfile(roiDir,'*V2*.mat'));
for ih = 1:length(hemisphere)
for ifb = 1:length(fibs)
tic, fprintf('\n[%s] Loading the fiber group... \n',mfilename)
fg = fgRead(fullfile(sprintf('%s',datapath),subjects{iSbj},'fibers',fibs{ifb}));toc
% Load the FreeSurfer V1
tic, fprintf('\n[%s] Building a combined V1 (%s) | Anterior Commissure... \n',mfilename,V1(ih).name)
%roiPeri = dtiReadRoi(fullfile(roiDir,pericalcarine(ih).name));
roiV1 = dtiReadRoi(fullfile(roiDir,V1(ih).name));
%roiV2 = dtiReadRoi(fullfile(roiDir,V2(ih).name));
% Make a spherical ROi at the location fo the Anteriro commissure
radius = 5;
sphere_center = [0,0,0];
roi2 = dtiNewRoi('AC_sphere');
roi2.coords = dtiBuildSphereCoords(sphere_center, radius);
roi = dtiNewRoi('AC_V1');
roi.coords = roiV1.coords;%[roiPeri.coords; roiV1.coords; roiV2.coords; roi2.coords];toc
% Extract fibers touching early visual cortex and the AC
tic, fprintf('\n[%s] Segmenting the TRACT connecting Visual Cortex and the Anterior Commissure... \n',mfilename)
[tract{iSbj,ifb,ih}, keepFascicles{iSbj,ifb,ih}] = feSegmentFascicleFromConnectome(fg, {roiV1, roi2}, {'and','and'}, 'tmp');toc
fprintf('\n[%s] Found tract with %i fibers. \n',mfilename,length(tract{iSbj,ifb,ih}.fibers))
% Get some statistics:
if ~isempty(tract{iSbj,ifb,ih}.fibers)
tic, fprintf('\n[%s] Getting information about the TRACT... \n',mfilename)
fgInfo{iSbj,ifb,ih}.roiname = [V1(ih).name,'_',roi2.name, num2str(radius),'mm'];
fgInfo{iSbj,ifb,ih}.volume = size(fefgGet(tract{iSbj,ifb,ih},'uniqueimagecoords'),1) * prod([1 1 1]); % mm-cube
fgInfo{iSbj,ifb,ih}.length = fefgGet(tract{iSbj,ifb,ih},'length'); % in mm
dtFileName = fullfile(datapath,subjects{iSbj},'dtiInit','dt6.mat');
fgInfo{iSbj,ifb,ih}.fa = fefgGet(tract{iSbj,ifb,ih},'fa',dtFileName); % fractional anysotropy
else
tic, fprintf('\n[%s] TRACT is emapyt information set to nan... \n',mfilename)
fgInfo{iSbj,ifb,ih}.roiname = [V1(ih).name,'_',roi2.name, num2str(radius),'mm'];
fgInfo{iSbj,ifb,ih}.volume = nan; % mm-cube
fgInfo{iSbj,ifb,ih}.length = nan; % in mm
fgInfo{iSbj,ifb,ih}.fa = nan; % fractional anysotropy
toc
end
end
end
end
% Show and save the fascicles
for iSbj = 1:length(subjects)
t1File = fullfile(datapath,subjects{iSbj},'anatomy','t1.nii.gz');
% Display the tract and save the figure
% Load the T1 file for display
t1 = niftiRead(t1File);
for ih = 1:length(hemisphere)
fprintf('Subject: %i Hemisphere: %i\n',iSbj,ih)
switch hemisphere{ih}
case {'left'}
axisLims = [-60 5 -120 10 0 30];
vw = [-55,30];
slices = {[-3 0 0],[0 5 0],[0 0 -17 ]};
histcolor{1} = [0.4 0.4 0.4];
histcolor{2} = [.6 0.4 0.4];
case {'right'}
axisLims = [-20 60 -90 5 0 30];
vw = [55,40];
slices = {[-2 0 0],[0 5 0],[0 0 -17]};
histcolor{1} = [0 0 0];
histcolor{2} = [.8 0.4 0.4];
otherwise
keyboard
end
for ifb = 1:length(fibs)
if ~isempty(tract{iSbj,ifb,ih}.fibers)
% Show te new fiber group
if ifb == 1
str = 'REJECTED';
else
str = 'OPTIMIZED';
end
figName = sprintf('V1_AC_tract_%s_HEMI_%s_%s',str,hemisphere{ih},subjects{iSbj});
fh = figure('name',figName);
hold on
h = mbaDisplayBrainSlice(t1, slices{1});
h = mbaDisplayBrainSlice(t1, slices{2});
h = mbaDisplayBrainSlice(t1, slices{3});
view(vw(1),vw(2)); axis(axisLims);
tract2plot = mbaComputeFibersOutliers(tract{iSbj,ifb,ih},2,1.4);
[fh,ligh] = mbaDisplayConnectome(tract2plot.fibers,fh,[.98 .55 .45],'single',[], [], .6,[]);
delete(ligh);camlight(hemisphere{ih})
saveFig(fh,fullfile(saveDir,figName),'jpg')
end
end
end
end
% Plot the FA and fiber length
Opt.length = []; Opt.n = []; Opt.fa = [];
Rej.length = []; Rej.n = []; Rej.fa = [];
for iSbj = 1:length(subjects)
for ih = 1:length(hemisphere)
for ifb = 1:length(fibs)
if ~isnan(fgInfo{iSbj,ifb,ih}.length)
if ifb == 2 % Optimized
Opt.length = [Opt.length; mean(fgInfo{iSbj,ifb,ih}.length)];
Opt.n = [Opt.n; length(fgInfo{iSbj,ifb,ih}.length)];
Opt.fa = [Opt.fa; mean((cellfun(@mean,fgInfo{iSbj,ifb,ih}.fa)))];
else % Rejected
Rej.length = [Rej.length; nanmean(fgInfo{iSbj,ifb,ih}.length)];
Rej.n = [Rej.n; length(fgInfo{iSbj,ifb,ih}.length)];
Rej.fa = [Rej.fa; nanmean((cellfun(@nanmean,fgInfo{iSbj,ifb,ih}.fa)))];
end
end
end
end
end
% Make a plot of the length of the fibers and of the FA
figName = sprintf('length_%s_%s',hemisphere{ih},subjects{iSbj});
fh = figure('name',figName,'color','w');
plot([1 1],[mean(Rej.length),mean(Rej.length)] + [-std(Rej.length)./sqrt(length(Rej.n)), std(Rej.length)./sqrt(length(Rej.n))],'r-')
hold on
plot([1 2],[mean(Rej.length),Opt.length],'ro')
set(gca,'tickdir','out','ticklen',[.01 0],'xlim',[0 3],'ylim',[100 140],'ytick',[100 120 140],'box','off','FontSize',14)
ylabel('Tract length (mm)','FontSize',14)
saveFig(fh,fullfile(saveDir,figName),'eps')
figName = sprintf('fa_%s_%s',hemisphere{ih},subjects{iSbj});
fh = figure('name',figName,'color','w');
plot([1 1],[mean(Rej.fa),mean(Rej.fa)] + [-std(Rej.fa)./sqrt(length(Rej.n)), std(Rej.fa)./sqrt(length(Rej.n))],'r-')
hold on
plot([1 2],[mean(Rej.fa),Opt.fa],'ro')
set(gca,'tickdir','out','ticklen',[.01 0],'xlim',[0 3],'ylim',[0.2 .6],'ytick',[.2 .4 .6],'box','off','FontSize',14)
ylabel('FA','FontSize',14)
saveFig(fh,fullfile(saveDir,figName),'eps')
figName = sprintf('n_%s_%s',hemisphere{ih},subjects{iSbj});
fh = figure('name',figName,'color','w');
plot([1 1],[mean(Rej.n),mean(Rej.n)] + [-std(Rej.n)./sqrt(length(Rej.n)), std(Rej.n)./sqrt(length(Rej.n))],'r-')
hold on
plot([1 2],[mean(Rej.n),Opt.n],'ro')
set(gca,'tickdir','out','ticklen',[.01 0],'xlim',[0 3],'ylim',[0 16],'ytick',[0 8 16],'box','off','FontSize',14)
ylabel('Number of fascicles','FontSize',14)
saveFig(fh,fullfile(saveDir,figName),'eps')
save(fullfile(saveDir),'fgInfo')
end % Main function
%%%%%%%%%%%%%%%%%%%%%%%
function FS_SUBJECT = matchSubject2FSSUBJ(subject)
switch subject
case {'FP_96dirs_b2000_1p5iso'}
FS_SUBJECT = 'pestilli_test';
case {'KW_96dirs_b2000_1p5iso'}
FS_SUBJECT = 'weiner';
case {'MP_96dirs_b2000_1p5iso'}
FS_SUBJECT = 'lmperry';
case {'HT_96dirs_b2000_1p5iso'}
FS_SUBJECT = 'takemura';
case {'JW_96dirs_b2000_1p5iso'}
FS_SUBJECT = 'winawer';
case {'KK_96dirs_b2000_1p5iso'}
FS_SUBJECT = 'knk';
otherwise
keyboard
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function saveFig(h,figName,type)
% MAke sure the folder to save the figure exists
[p,f,e] = fileparts(figName);
[success,message] = mkdir(p);
if ~isempty(message), disp(sprintf('%s.',message));end
% Find out which type of figure and geenerate the proper printing command.
switch type
case {0,'jpeg','jpg'}
printCommand = (sprintf('print(%s, ''-djpeg80'',''-r300'' , ''-noui'', ''-opengl'', ''%s'')', num2str(h),figName));
case {1,'eps'}
printCommand = (sprintf('print(%s, ''-cmyk'', ''-depsc2'',''-tiff'',''-r300'' , ''-noui'', ''%s'')', num2str(h),figName));
case 'png'
printCommand = (sprintf('print(%s, ''-dpng'',''-r300'', ''%s'')', num2str(h),figName));
case 'tiff'
printCommand = (sprintf('print(%s, ''-dtiff'',''-r300'', ''%s'')', num2str(h),figName));
case 'bmp'
printCommand = (sprintf('print(%s, ''-dbmp256'',''-r300'', ''%s'')', num2str(h),figName));
otherwise
keyboard
end
% do the printing here:
fprintf('[%s] saving figure... \n%s\n',mfilename,figName);
eval(printCommand);
end