This repository has been archived by the owner on Aug 3, 2018. It is now read-only.
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Gen_niftis_crossing_tracts.m
180 lines (156 loc) · 6.78 KB
/
Gen_niftis_crossing_tracts.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
function [] = Gen_niftis_crossing_tracts(info, tract_name_1, tract_name_2, other_tracts)
%% INPUT: two crossing tracts (AFQ)
%% Number Name Full Name
% 1 Thal_Rad_L Left Thalamic Radiation
% 2 Thal_Rad_R Right Thalamic Radiation
% 3 CST_L Left Corticospinal
% 4 CST_R Right Corticospinal
% 5 Cing_L Left Cingulum Cingulate
% 6 Cing_R Right Cingulum Cingulate
% 7 Hipp_L Left Cingulum Hippocampus
% 8 Hipp_R Right Cingulum Hippocampus
% 9 Call_Maj Callosum Forceps Major
% 10 Call_Min Callosum Forceps Minor
% 11 IFOF_L Left IFOF
% 12 IFOF_R Right IFOF
% 13 ILF_L Left ILF
% 14 ILF_R Right ILF
% 15 SLF_L Left SLF
% 16 SLF_R Right SLF
% 17 Unc_L Left Uncinate
% 18 Unc_R Right Uncinate
% 19 ARC_L Left Arcuate
% 20 ARC_R Right Arcuate
%% INPUT: two crossing tracts (Dan tracts)
%% Number Name Full Name
% 1 Thal_Rad_L Left Thalamic Radiation
% 2 Thal_Rad_R Right Thalamic Radiation
% 3 CST_L Left Corticospinal
% 4 CST_R Right Corticospinal
% 5 Cing_L Left Cingulum Cingulate
% 6 Cing_R Right Cingulum Cingulate
% 7 Hipp_L Left Cingulum Hippocampus
% 8 Hipp_R Right Cingulum Hippocampus
% 9 Call_Maj Callosum Forceps Major
% 10 Call_Min Callosum Forceps Minor
% 11 IFOF_L Left IFOF
% 12 IFOF_R Right IFOF
% 13 Unc_L Left Uncinate
% 14 Unc_R Right Uncinate
% 15 ARC_L Left Arcuate
% 16 ARC_R Right Arcuate
% 17 VOF_L Left VOF
% 18 VOF_R Right VOF
% 19 pARC_L Left pArc
% 20 pARC_R Right pArc
% 21 TPC_L Left TPC
% 22 TPC_R Right TPC
% 23 MdLF-SPL_L Left MdLF-SPL
% 24 MdLF-SPL_R Right MdLF-SPL
% 25 MdLF-Ang_L Left MdLF-Ang
% 26 MdLF-Ang_R Right MdLF-Ang
% 27 Meyer_L Left Meyer
% 28 Meyer_R Right Meyer
% 29 Baum_L Left Baum
% 30 Baum_R Right Baum
% 31 SLF1_L Left SLF1
% 32 SLF1_R Right SLF1
% 33 SLF2_L Left SLF2
% 34 SLF2_R Right SLF2
% 35 SLF3_L Left SLF3
% 36 SLF3_R Right SLF3
% 37 ILF_L Left ILF
% 38 ILF_R Right ILF
%% Get tract numbers
other_tract_number = [];
if info.segmentation_type == 'AFQ'
tract_number_1 = Get_tract_number(tract_name_1);
tract_number_2 = Get_tract_number(tract_name_2);
for i=1:size(other_tracts,2)
other_tract_number = [other_tract_number, Get_tract_number(other_tracts{i})];
end
else
tract_number_1 = Get_tract_number_Dan(tract_name_1);
tract_number_2 = Get_tract_number_Dan(tract_name_2);
for i=1:size(other_tracts,2)
other_tract_number = [other_tract_number, Get_tract_number(other_tracts{i})];
end
end
%% Set the Path for the output
dataOutputPath = info.output.niftis;
%% load fe structure
%FileName = deblank(ls(fullfile(dataInputPath,strcat('fe_*.mat'))));
FileName = info.input.optimal;
load(FileName);
%dwiFile = fe.path.dwifile;
dwiFile = info.input.dwi_path;
%% Save .b file (mrtrix format)
%bvecsFile = strcat(dwiFile(1:end-6),'bvecs');
%bvalsFile = strcat(dwiFile(1:end-6),'bvals');
%% TODO - is this necessary?
%% Generate nifti for original data
ni = niftiRead(dwiFile);
fName = fullfile(dataOutputPath,strcat('original.nii.gz'));
niftiWrite(ni,fName);
%% Generate nifti using the predicted diffusion signal based on the model fit to the original data
% fe is already loaded
name = fullfile(dataOutputPath,strcat('pred_full.nii.gz'));
coords = fe.roi.coords; % Get the coordinates of the nodes in each voxel of the connectome
%dwi = feGet(fe, 'dwi'); % load dwi structure
dwi = dwiLoad(info.input.dwi_path); % load dwi structure
diff_signal = feGet(fe,'pred full');
Generate_nifti(ni,name,coords,dwi,diff_signal);
%% Load classification file
load(info.input.classification_path);
%% Generate niftis for single tracts prediction
tract_set = [tract_number_1, tract_number_2];
tract_names = {tract_name_1, tract_name_2};
for i=1:length(tract_set)
Gen_nifti_single_tract(fe,classification,tract_set(i),tract_names{i}, dataOutputPath, ni, info)
end
%% Generate niftis for crossing tracts prediction
Gen_nifti_crossing_tracts(fe,classification, tract_number_1, tract_number_2, other_tract_number, ...
strcat(tract_name_1, '_', tract_name_2,'_new'), dataOutputPath, ni, info)
end
function [] = Gen_nifti_single_tract(fe,classification,tract,fgName,dataOutputPath,ni,info)
name = fullfile(dataOutputPath,strcat(fgName,'.nii.gz'));
coords = fe.roi.coords; % Get the coordinates of the nodes in each voxel of the connectome
dwi = dwiLoad(info.input.dwi_path); % load dwi structure
fibers = find(classification.index == tract);
diff_signal = feGet(fe,'pred tract',fibers);
diff_signal(diff_signal==0) = NaN;
Generate_nifti(ni,name,coords,dwi,diff_signal);
end
function [] = Gen_nifti_crossing_tracts(fe,classification,tract1,tract2,other_tract_number,fgName,dataOutputPath,ni,info)
name = fullfile(dataOutputPath,strcat(fgName,'.nii.gz'));
coords = fe.roi.coords; % Get the coordinates of the nodes in each voxel of the connectome
dwi = dwiLoad(info.input.dwi_path); % load dwi structure
fibers1 = find(classification.index == tract1);
fibers2 = find(classification.index == tract2);
fibers = [fibers1; fibers2];
for i=1:length(other_tract_number)
fibers = [fibers ;find(classification.index == other_tract_number(i))];
end
diff_signal = feGet(fe,'pred tract',fibers);
diff_signal(diff_signal==0) = NaN;
Generate_nifti(ni,name,coords,dwi,diff_signal);
end
function [] = Generate_nifti(ni_in,name,coords,dwi,dwisignal)
ni_out = ni_in;
ni_out.fname = name;
bvals = dwi.bvals;
indexes = find(bvals~=0);
b0indexes = find(bvals==0);
% Copy original S0 values
b0_data = nan(size(b0indexes,1),size(coords,1));
for ivx = 1:size(coords,1)
b0_data(:,ivx) = ni_out.data(coords(ivx,1),coords(ivx,2),coords(ivx,3),b0indexes);
end
ni_out.data = nan(size(ni_in.data));
% Replace Nans with b0_data
ni_out.data = feReplaceImageValues(ni_out.data,b0_data,coords,b0indexes);
% Replace Nans with dw_vals
ni_out.data = feReplaceImageValues(ni_out.data,dwisignal,coords,indexes);
% save nifti to disk
niftiWrite(ni_out,ni_out.fname);
end