PROJECT VOXEL PERCENT SIGNAL MAP ON THE BRAIN SURFACE MODEL
[Notice]
con_*.img must be coregistered to T1-structural image used for creating
a brain file
[Syntax]
vb_fmri_project_PSmap_cortex(brain_file,act_file,area_file,PSthres,SPMimginfo)
[Example]
> brain_file = 'hoge.brain.mat';
> act_file = 'hoge.act.mat';
> area_file = 'hoge.area.mat';
> PSthres = 1.0;
> Rthres = 3;
> SPMimginfo = struct('dirname', '/home/hoge/hoge/spm/',...
> imgfilename,{'con_0001.img','con_0002.img'},imglabel,{'Right index',...
> 'Right hand gripping'},'basefilename','beta0010.img','2','1.17');
> vbdot_fmri_project_PSmap_cortex(brain_file,act_file,areafile,PSthres,Rthres,SPMimginfo)
[Input]
brain_file : cortical surface model
act_file : act file
area_file : area file
PSthres : PS-value threshold (%)
Rthres : radius threshold (mm)
SPMimginfo(ii) : arrays of struct containing information of T-image
.dirname : directory name for image file
.imgfilename : file name of image to be projected
.imglabel : label of image to be projected. These label
are used as actkey and areakey
.baseimgfilename : file name for the baseline image
.ncon : the number of positive contrast for each CON image
.peak : regressor peak value
[Optional]
loadVmni : if specfied as 1, loading coordinate of brain file as MNI coordinate
[Output]
Acts are added to "act_file" and Areas are added to "area_file"
Reference : see http://cibsr.stanford.edu/documents/FMRIPercentSignalChange.pdf
2016/07/12 O.Yamashita
* add loadVmni to input arguments to switch coordinate of brain file
2016/07/06 O.Yamashita
* solve the region expansion problem
2016/07/01 O.Yamashita
* first version based on vbdot_fmri_project_Tmap_corext.m
Copyright (C) 2011, ATR All Rights Reserved.
License : New BSD License(see VBMEG_LICENSE.txt)0001 function vb_fmri_project_PSmap_cortex(brain_file,act_file,area_file,PSthres,Rthres,SPMimginfo,loadVmni) 0002 % PROJECT VOXEL PERCENT SIGNAL MAP ON THE BRAIN SURFACE MODEL 0003 % 0004 % [Notice] 0005 % con_*.img must be coregistered to T1-structural image used for creating 0006 % a brain file 0007 % 0008 % [Syntax] 0009 % vb_fmri_project_PSmap_cortex(brain_file,act_file,area_file,PSthres,SPMimginfo) 0010 % 0011 % [Example] 0012 % > brain_file = 'hoge.brain.mat'; 0013 % > act_file = 'hoge.act.mat'; 0014 % > area_file = 'hoge.area.mat'; 0015 % > PSthres = 1.0; 0016 % > Rthres = 3; 0017 % > SPMimginfo = struct('dirname', '/home/hoge/hoge/spm/',... 0018 % > imgfilename,{'con_0001.img','con_0002.img'},imglabel,{'Right index',... 0019 % > 'Right hand gripping'},'basefilename','beta0010.img','2','1.17'); 0020 % > vbdot_fmri_project_PSmap_cortex(brain_file,act_file,areafile,PSthres,Rthres,SPMimginfo) 0021 % 0022 % [Input] 0023 % brain_file : cortical surface model 0024 % act_file : act file 0025 % area_file : area file 0026 % PSthres : PS-value threshold (%) 0027 % Rthres : radius threshold (mm) 0028 % SPMimginfo(ii) : arrays of struct containing information of T-image 0029 % .dirname : directory name for image file 0030 % .imgfilename : file name of image to be projected 0031 % .imglabel : label of image to be projected. These label 0032 % are used as actkey and areakey 0033 % .baseimgfilename : file name for the baseline image 0034 % .ncon : the number of positive contrast for each CON image 0035 % .peak : regressor peak value 0036 % 0037 % [Optional] 0038 % loadVmni : if specfied as 1, loading coordinate of brain file as MNI coordinate 0039 % 0040 % [Output] 0041 % Acts are added to "act_file" and Areas are added to "area_file" 0042 % 0043 % Reference : see http://cibsr.stanford.edu/documents/FMRIPercentSignalChange.pdf 0044 % 0045 % 0046 % 2016/07/12 O.Yamashita 0047 % * add loadVmni to input arguments to switch coordinate of brain file 0048 % 2016/07/06 O.Yamashita 0049 % * solve the region expansion problem 0050 % 2016/07/01 O.Yamashita 0051 % * first version based on vbdot_fmri_project_Tmap_corext.m 0052 % 0053 % Copyright (C) 2011, ATR All Rights Reserved. 0054 % License : New BSD License(see VBMEG_LICENSE.txt) 0055 0056 fprintf('============== NOTICE ==========================\n') 0057 fprintf('Please confirm con_*.img have been coregistered \n') 0058 fprintf('to the T1-structural image used for creating \n'); 0059 fprintf('a brain file. \n'); 0060 fprintf('================================================\n') 0061 0062 if nargin < 7 0063 loadVmni = 0; 0064 end 0065 0066 spmdir = SPMimginfo(1).dirname; 0067 0068 fprintf('Image directory name : %s,...\n', spmdir); 0069 for jj = 1 : length(SPMimginfo), 0070 fprintf('%s will be registered as %s ...\n', SPMimginfo(jj).imgfilename, SPMimginfo(jj).imglabel); 0071 end 0072 0073 % scale factor for con image 0074 0075 for jj = 1 : length(SPMimginfo), 0076 loadimgfile = [spmdir SPMimginfo(jj).imgfilename]; 0077 key = SPMimginfo(jj).imglabel; 0078 0079 baseimgfile = [spmdir SPMimginfo(jj).baseimgfilename]; 0080 [B] = vb_load_analyze_to_right(baseimgfile); 0081 bmean = mean(B(~isnan(B(:)))); 0082 scale = 1./SPMimginfo(jj).ncon/bmean*SPMimginfo(jj).peak*100; 0083 0084 % surface mesh 0085 if loadVmni 0086 V = vb_load_cortex(brain_file, 'MNI'); 0087 else 0088 V = vb_load_cortex(brain_file, 'subj'); 0089 end 0090 V = V * 1000; % mm 0091 0092 0093 % vox image and coordinates 0094 VG=spm_vol(loadimgfile); 0095 [map,XYZ] = spm_read_vols(VG); 0096 map = map * scale; 0097 0098 % 0099 % thresholding affects resulting surface image !!! 0100 % 0101 % map(abs(map) < PSthres) = NaN; 0102 % ix=find(~isnan(map)); 0103 % XYZ = XYZ(:,ix); 0104 % map = map(ix)'; 0105 ix = find(~isnan(map)); % brain mask 0106 XYZ = XYZ(:,ix); 0107 map = map(ix); 0108 map(abs(map) < PSthres) = 0; % 0109 0110 r2thres = Rthres^2; 0111 0112 0113 % vox --> surf 0114 Tval = vb_voximg2surimg(XYZ',map,V, r2thres, 1); 0115 0116 0117 0118 % add act 0119 fprintf('\nAdd PS-map to %s with act-key %s \n', act_file, key) 0120 act.xxP = Tval; 0121 act.key = key; 0122 act.spmdir = spmdir; 0123 act.imgname = SPMimginfo(jj).imgfilename; 0124 vb_add_act(act_file, act, [], OFF); 0125 0126 % % add area 0127 % fprintf('Add PS-map to %s with area-key %s \n', area_file, key) 0128 % area.Iextract = find(Tval~=0); 0129 % area.key = key; 0130 % area.spmdir = spmdir; 0131 % area.imgname = SPMimginfo(jj).imgfilename; 0132 % vb_add_area(area_file, area); 0133 0134 0135 end