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initialize_vars.m
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function [b] = initialize_vars(subjects,i,directory)
datadir = '/raw_reorient/';
%%%%%%%%%%%%
% SPM info
b.spmDir = fileparts(which('spm'));% path to SPM installation
% Directory information
switch directory
case 'local'
dataDir = '/Users/Pamsfwang/Desktop/VR_nims/';
case 'sni'
dataDir = '/Volumes/group/awagner/sfwang/VR_nims/';
case 'vm'
dataDir = '/share/awagner/sfwang/VR_nims/';
end
b.curSubj = subjects{i};
b.dataDir = strcat(dataDir,b.curSubj,datadir); % make data directory subject-specific
b.funcRuns = {'08_1_Ax_EPI_fMRI_Accel2_15mm' '09_1_Ax_EPI_fMRI_Accel2_15mm'...
'11_1_Ax_EPI_fMRI_Accel2_15mm' '12_1_Ax_EPI_fMRI_Accel2_15mm'...
'14_1_Ax_EPI_fMRI_Accel2_15mm' '15_1_Ax_EPI_fMRI_Accel2_15mm'...
'17_1_Ax_EPI_fMRI_Accel2_15mm' '18_1_Ax_EPI_fMRI_Accel2_15mm'...
'20_1_Ax_EPI_fMRI_Accel2_15mm' '21_1_Ax_EPI_fMRI_Accel2_15mm'...
'23_1_Ax_EPI_fMRI_Accel2_15mm' '24_1_Ax_EPI_fMRI_Accel2_15mm'}; % folders containing functional images
b.runNumbers = 1:12;
b.anatT2_coronal = '02_1_T2_Coronal_Anatomy';% folder containing T2 coronal
b.anatT2_inplane = '03_1_T2_Inplane_Anatomy_15mm';
b.anatT1 = '26_1_Axial_FSPGR_3D';
b.maskDir = fullfile(b.dataDir,'masks');
b.ROImaskDir = fullfile(b.maskDir,'ROImasks');
% Call sub-function to run exceptions
b = run_exceptions(b);
end
% Subject-specific exceptions (e.g., deviations from naming convention)
function b = run_exceptions(b)
if strcmp(b.curSubj,'vr02')
b.funcRuns = {'08_1_Ax_EPI_fMRI_Accel2_15mm' '08_2_Ax_EPI_fMRI_Accel2_15mm'...
'10_1_Ax_EPI_fMRI_Accel2_15mm' '10_2_Ax_EPI_fMRI_Accel2_15mm' ...
'12_1_Ax_EPI_fMRI_Accel2_15mm' '12_2_Ax_EPI_fMRI_Accel2_15mm'...
'14_1_Ax_EPI_fMRI_Accel2_15mm' '14_2_Ax_EPI_fMRI_Accel2_15mm' ...
'16_2_Ax_EPI_fMRI_Accel2_15mm' ...
'18_1_Ax_EPI_fMRI_Accel2_15mm' '18_2_Ax_EPI_fMRI_Accel2_15mm'}; % e.g., if s01 had different run numbers
b.runNumbers = [1:8 10:12];
b.anatT1 = '20_1_Axial_FSPGR_3D';
end
if strcmp(b.curSubj,'vr04')
b.funcRuns = {'09_1_Ax_EPI_fMRI_Accel2_15mm' '10_1_Ax_EPI_fMRI_Accel2_15mm'...
'12_1_Ax_EPI_fMRI_Accel2_15mm' '13_1_Ax_EPI_fMRI_Accel2_15mm'...
'15_1_Ax_EPI_fMRI_Accel2_15mm' '16_1_Ax_EPI_fMRI_Accel2_15mm'...
'18_1_Ax_EPI_fMRI_Accel2_15mm' '19_1_Ax_EPI_fMRI_Accel2_15mm'...
'21_1_Ax_EPI_fMRI_Accel2_15mm' '22_1_Ax_EPI_fMRI_Accel2_15mm'...
'24_1_Ax_EPI_fMRI_Accel2_15mm' '25_1_Ax_EPI_fMRI_Accel2_15mm'}; % e.g., if s01 had different run numbers
b.anatT2_coronal = '03_1_T2_Coronal_Anatomy';% folder containing T2 coronal
b.anatT2_inplane = '04_1_T2_Inplane_Anatomy_15mm';
b.anatT1 = '27_1_Axial_FSPGR_3D';
end
if strcmp(b.curSubj,'vr06')
b.funcRuns = {'08_1_Ax_EPI_fMRI_Accel2_15mm' '09_1_Ax_EPI_fMRI_Accel2_15mm'...
'11_1_Ax_EPI_fMRI_Accel2_15mm' ...
'14_1_Ax_EPI_fMRI_Accel2_15mm' '15_1_Ax_EPI_fMRI_Accel2_15mm'...
'17_1_Ax_EPI_fMRI_Accel2_15mm' '18_1_Ax_EPI_fMRI_Accel2_15mm'...
'20_1_Ax_EPI_fMRI_Accel2_15mm' '21_1_Ax_EPI_fMRI_Accel2_15mm'...
'23_1_Ax_EPI_fMRI_Accel2_15mm' '24_1_Ax_EPI_fMRI_Accel2_15mm'}; % folders containing functional images
b.anatT1 = '';
b.runNumbers = [1:3 5:12];
end
if strcmp(b.curSubj,'vr08')
b.funcRuns = {'08_1_Ax_EPI_fMRI_Accel2_15mm' '09_1_Ax_EPI_fMRI_Accel2_15mm'...
'11_1_Ax_EPI_fMRI_Accel2_15mm' '12_1_Ax_EPI_fMRI_Accel2_15mm'}; % folders containing functional images
b.runNumbers = 1:4;
end
if strcmp(b.curSubj,'vr09')
b.funcRuns = {'12_1_Ax_EPI_fMRI_Accel2_15mm'...
'14_1_Ax_EPI_fMRI_Accel2_15mm' '15_1_Ax_EPI_fMRI_Accel2_15mm'...
'17_1_Ax_EPI_fMRI_Accel2_15mm' '18_1_Ax_EPI_fMRI_Accel2_15mm'...
'20_1_Ax_EPI_fMRI_Accel2_15mm' '21_1_Ax_EPI_fMRI_Accel2_15mm'...
'23_1_Ax_EPI_fMRI_Accel2_15mm' '24_1_Ax_EPI_fMRI_Accel2_15mm'}; % folders containing functional images
b.runNumbers = 4:12;
end
if strcmp(b.curSubj,'vr11')
b.funcRuns = {'08_1_Ax_EPI_fMRI_Accel2_15mm' ...
'11_1_Ax_EPI_fMRI_Accel2_15mm' '12_1_Ax_EPI_fMRI_Accel2_15mm'...
'14_1_Ax_EPI_fMRI_Accel2_15mm' '15_1_Ax_EPI_fMRI_Accel2_15mm'...
'18_1_Ax_EPI_fMRI_Accel2_15mm'...
'20_1_Ax_EPI_fMRI_Accel2_15mm' '21_1_Ax_EPI_fMRI_Accel2_15mm'...
'23_1_Ax_EPI_fMRI_Accel2_15mm' '24_1_Ax_EPI_fMRI_Accel2_15mm'};
b.runNumbers = [1 3:6 8:12];
end
if strcmp(b.curSubj,'vr19')
b.funcRuns = {'08_1_Ax_EPI_fMRI_Accel2_15mm' '09_1_Ax_EPI_fMRI_Accel2_15mm'...
'11_1_Ax_EPI_fMRI_Accel2_15mm' '12_1_Ax_EPI_fMRI_Accel2_15mm'...
'14_1_Ax_EPI_fMRI_Accel2_15mm'};
b.runNumbers = 1:5;
end
if strcmp(b.curSubj,'vr21')
b.funcRuns = {'08_1_Ax_EPI_fMRI_Accel2_15mm' '09_1_Ax_EPI_fMRI_Accel2_15mm'...
'11_1_Ax_EPI_fMRI_Accel2_15mm' '12_1_Ax_EPI_fMRI_Accel2_15mm'...
'14_1_Ax_EPI_fMRI_Accel2_15mm' ...
'17_1_Ax_EPI_fMRI_Accel2_15mm' '18_1_Ax_EPI_fMRI_Accel2_15mm'...
'20_1_Ax_EPI_fMRI_Accel2_15mm' '21_1_Ax_EPI_fMRI_Accel2_15mm'...
'23_1_Ax_EPI_fMRI_Accel2_15mm' '24_1_Ax_EPI_fMRI_Accel2_15mm'}; % folders containing functional images
b.runNumbers = [1:5 7:12];
end
if strcmp(b.curSubj,'vr23')
b.funcRuns = {'08_1_Ax_EPI_fMRI_Accel2_15mm' '09_1_Ax_EPI_fMRI_Accel2_15mm'...
'11_1_Ax_EPI_fMRI_Accel2_15mm' '12_1_Ax_EPI_fMRI_Accel2_15mm'...
'14_1_Ax_EPI_fMRI_Accel2_15mm' '15_1_Ax_EPI_fMRI_Accel2_15mm'...
'20_1_Ax_EPI_fMRI_Accel2_15mm' ...
'23_1_Ax_EPI_fMRI_Accel2_15mm' '24_1_Ax_EPI_fMRI_Accel2_15mm'};
b.runNumbers = [1:6 9 11:12];
end
if strcmp(b.curSubj,'vr24')
b.funcRuns = {'08_1_Ax_EPI_fMRI_Accel2_15mm' '09_1_Ax_EPI_fMRI_Accel2_15mm'...
'11_1_Ax_EPI_fMRI_Accel2_15mm' '12_1_Ax_EPI_fMRI_Accel2_15mm'};
b.runNumbers = 1:4;
end
if strcmp(b.curSubj,'vr27')
b.funcRuns = {'08_1_Ax_EPI_fMRI_Accel2_15mm' '09_1_Ax_EPI_fMRI_Accel2_15mm'...
'11_1_Ax_EPI_fMRI_Accel2_15mm' '12_1_Ax_EPI_fMRI_Accel2_15mm'...
'14_1_Ax_EPI_fMRI_Accel2_15mm' '15_1_Ax_EPI_fMRI_Accel2_15mm'...
'17_1_Ax_EPI_fMRI_Accel2_15mm' ...
'20_1_Ax_EPI_fMRI_Accel2_15mm' '21_1_Ax_EPI_fMRI_Accel2_15mm'...
'23_1_Ax_EPI_fMRI_Accel2_15mm' '24_1_Ax_EPI_fMRI_Accel2_15mm'};
b.runNumbers = [1:7 9:12];
end
if strcmp(b.curSubj,'vr28')
b.funcRuns = {'08_1_Ax_EPI_fMRI_Accel2_15mm' '09_1_Ax_EPI_fMRI_Accel2_15mm'...
'11_1_Ax_EPI_fMRI_Accel2_15mm' '12_1_Ax_EPI_fMRI_Accel2_15mm'...
'14_1_Ax_EPI_fMRI_Accel2_15mm'};
b.runNumbers = 1:5;
end
if strcmp(b.curSubj,'vr29')
b.funcRuns = {'08_1_Ax_EPI_fMRI_Accel2_15mm' '09_1_Ax_EPI_fMRI_Accel2_15mm'...
'11_1_Ax_EPI_fMRI_Accel2_15mm' '12_1_Ax_EPI_fMRI_Accel2_15mm'...
'14_1_Ax_EPI_fMRI_Accel2_15mm'};
b.runNumbers = 1:5;
end
end