Skip to content

Commit

Permalink
Demo_script modified for Revision May 2017
Browse files Browse the repository at this point in the history
  • Loading branch information
@ccaiafa
ccaiafa committed May 29, 2017
1 parent 1130940 commit 77473ac
Show file tree
Hide file tree
Showing 3 changed files with 34 additions and 17 deletions.
Binary file added scripts/demos/Fig_3a_paper.fig
View file
Binary file not shown.
Binary file added scripts/demos/Fig_3a_paper_gray.fig
View file
Binary file not shown.
51 changes: 34 additions & 17 deletions scripts/demos/demo_connectome_data_comparison.m
View file
Expand Up @@ -35,6 +35,11 @@
disp('ERROR: demo dataset either not installed or not on matlab path.')
error('Please, download it from http://purl.dlib.indiana.edu/iusw/data/2022/20995/Demo_Data_for_Multidimensional_Encoding_of_Brain_Connectomes.tar.gz')
end
% s = what('demo_datasets');
% if isempty(s)
% disp('ERROR: demo dataset either not installed or not on matlab path.')
% error('Please, download it from http://purl.dlib.indiana.edu/iusw/data/2022/20995/Demo_Data_for_Multidimensional_Encoding_of_Brain_Connectomes.tar.gz')
% end

%% (1) Figure 3 from Multidimensional encoding of brain connectomes
% Cesar F. Caiafa and Franco Pestilli, submitted.
Expand All @@ -52,18 +57,23 @@
% - the density of a connectome. More specifcially the number of fibers
% supported by the measured diffusion-weighted data in the provided
% tractography solution.
Generate_Fig3_paper_Caiafa_Pestilli('original')
%Generate_Fig3_paper_Caiafa_Pestilli('original')
%savefig('Fig_3a_paper.fig')
openfig('Fig_3a_paper.fig')

% We brighten the symbols to use them as background.
Generate_Fig3_paper_Caiafa_Pestilli('gray')
%Generate_Fig3_paper_Caiafa_Pestilli('gray')
%savefig('Fig_3a_paper_gray.fig')
openfig('Fig_3a_paper_gray.fig')

%% (2) Read HCP3T subject connectome obtained by using Probabilistic tractography
%
% We load data not yet present on the plot.
%
disp('loading fe_structures for 105115 subject in HCP3T dataset (PROB) ...')
feFileName = fullfile(feDemoDataPath('HCP3T','sub-105115','fe_structures'), ...
'fe_structure_105115_STC_run01_SD_PROB_lmax10_connNUM01.mat');
'fe_structure_105115_STC_run01_SD_PROB_lmax10_connNUM01.mat');
%feFileName = fullfile(s.path,'HCP3T','sub-105115','fe_structures', 'fe_structure_105115_STC_run01_SD_PROB_lmax10_connNUM01.mat');
load(feFileName)

% Here we extract two measures we are interested in:
Expand Down Expand Up @@ -113,6 +123,7 @@
disp('loading fe_structures for 105115 subject in HCP3T dataset (DET) ...')
feFileName = fullfile(feDemoDataPath('HCP3T','sub-105115','fe_structures'), ...
'fe_structure_105115_STC_run01_tensor__connNUM01.mat');
%feFileName = fullfile(s.path,'HCP3T','sub-105115','fe_structures','fe_structure_105115_STC_run01_tensor__connNUM01.mat');
load(feFileName)
sbj = retrieve_results(fe,'TENSOR', 'HCP3T');

Expand All @@ -122,8 +133,9 @@
% 3.2 These results were obtained by using CSD-based Probabilistic
% tractography and the STN data set.
disp('loading fe_structures for FP subject in STN dataset (PROB) ...')
feFileName = fullfile(feDemoDataPath('STN','sub-FP','fe_structures'), ...
'fe_structure_FP_96dirs_b2000_1p5iso_STC_run01_SD_PROB_lmax10_connNUM01.mat');
feFileName = fullfile(feDemoDataPath('STN','sub-FP','fe_structures'), ...
'fe_structure_FP_96dirs_b2000_1p5iso_STC_run01_SD_PROB_lmax10_connNUM01.mat');
%feFileName = fullfile(s.path,'STN','sub-FP','fe_structures','fe_structure_FP_96dirs_b2000_1p5iso_STC_run01_SD_PROB_lmax10_connNUM01.mat');
load(feFileName)
sbj = retrieve_results(fe,'PROB', 'STN');

Expand All @@ -133,8 +145,9 @@
% 3.3 These results were obtained by using tensor-based deterministic
% tractography and the STN data set.
disp('loading fe_structures for FP subject in STN dataset (DET) ...')
feFileName = fullfile(feDemoDataPath('STN','sub-FP','fe_structures'), ...
'fe_structure_FP_96dirs_b2000_1p5iso_STC_run01_tensor__connNUM01.mat');
feFileName = fullfile(feDemoDataPath('STN','sub-FP','fe_structures'), ...
'fe_structure_FP_96dirs_b2000_1p5iso_STC_run01_tensor__connNUM01.mat');
%feFileName = fullfile(s.path,'STN','sub-FP','fe_structures', 'fe_structure_FP_96dirs_b2000_1p5iso_STC_run01_tensor__connNUM01.mat');
load(feFileName)
sbj = retrieve_results(fe,'TENSOR', 'STN');

Expand All @@ -144,8 +157,9 @@
% 3.4 These results were obtained by using CSD-based probabilistic
% tractography and the HCP7T data set.
disp('loading fe_structures for 108323 subject in HCP7T dataset (PROB) ...')
feFileName = fullfile(feDemoDataPath('HCP7T','sub-108323','fe_structures'), ...
'fe_structure_108323_STC_run01_SD_PROB_lmax8_connNUM01.mat');
feFileName = fullfile(feDemoDataPath('HCP7T','sub-108323','fe_structures'), ...
'fe_structure_108323_STC_run01_SD_PROB_lmax8_connNUM01.mat');
%feFileName = fullfile(s.path,'HCP7T','sub-108323','fe_structures','fe_structure_108323_STC_run01_SD_PROB_lmax8_connNUM01.mat');
load(feFileName)
sbj = retrieve_results(fe,'PROB', 'HCP7T');

Expand All @@ -156,8 +170,9 @@
% tractography and the HCP7T data set.
disp('loading fe_structures for 108323 subject in HCP7T dataset (DET) ...')

feFileName = fullfile(feDemoDataPath('HCP7T','sub-108323','fe_structures'), ...
'fe_structure_108323_STC_run01_tensor__connNUM01.mat');
feFileName = fullfile(feDemoDataPath('HCP7T','sub-108323','fe_structures'), ...
'fe_structure_108323_STC_run01_tensor__connNUM01.mat');
%feFileName = fullfile(s.path,'HCP7T','sub-108323','fe_structures','fe_structure_108323_STC_run01_tensor__connNUM01.mat');
load(feFileName)
sbj = retrieve_results(fe,'TENSOR', 'HCP7T');

Expand All @@ -174,11 +189,12 @@
% the one in Figure 3 of Caiafa and Pestilli under review.
%

DataPath = feDemoDataPath('Figs_data');
%DataPath = feDemoDataPath('Figs_data');
DataPath = '/N/dc2/projects/lifebid/code/ccaiafa/Caiafa_Pestilli_paper2015/Revision_Feb2017/Results/Variability/';

HCP_subject_set = {'111312','105115','113619','110411'};
STN_subject_set = {'KK_96dirs_b2000_1p5iso','FP_96dirs_b2000_1p5iso','HT_96dirs_b2000_1p5iso','MP_96dirs_b2000_1p5iso'};
HCP7T_subject_set = {'108323','131217','109123','910241'};
HCP7T_subject_set = {'108323','109123','111312_7T','125525','102311_Paolo_masks'};

fh = figure('name','combined scatter mean +-sem across repeats','color','w');
set(fh,'Position',[0,0,800,600]);
Expand All @@ -197,8 +213,8 @@
Gen_plot(HCP7T_subject_set,'hot',DataPath,Nalg,'HCP7T60',color_mode)

set(gca,'tickdir','out', 'ticklen',[0.025 0.025], ...
'box','off','ytick',[2 10 18].*10^4, 'xtick', [0.04 0.07 0.1], ...
'ylim',[2 18].*10^4, 'xlim', [0.04 0.1],'fontsize',20)
'box','off','ytick',[2 15 32].*10^4, 'xtick', [0.04 0.07 0.1], ...
'ylim',[2 32].*10^4, 'xlim', [0.04 0.1],'fontsize',20)
axis square
ylabel('Fascicles number','fontsize',20)
xlabel('Connectome error (r.m.s.)','fontsize',20)
Expand Down Expand Up @@ -299,7 +315,7 @@
case 'original'
c = getNiceColors(color_type);
case 'gray'
c = repmat([.9,.9,.9], [4,1]);
c = repmat([.9,.9,.9], [length(subject_set),1]);
end


Expand Down Expand Up @@ -379,7 +395,8 @@
case 'medium'
c = [c1([12 16 19 23],:) ];
case 'hot'
c = [c2([32 25 13 5],:)];
%c = [c2([32 25 13 5],:)];
c = [c2([32 27 19 12 2],:)];
end

end
Expand Down

0 comments on commit 77473ac

Please sign in to comment.