ica_test

 ica_test.m

 My first attempt at running ICA on fMRI data

0001 % ica_test.m
0002 %
0003 % My first attempt at running ICA on fMRI data
0004 %
0005 
0006 % 02/01/01
0007 
0008 GET_FILE_INFO = 0;
0009 LOAD_RAW_DATA = 0;
0010 COMPUTE_ICA = 0;
0011 SAVE_ICA_DATA = 0;
0012 LOAD_ICA_DATA = 0;
0013 COMPUTE_COMPONENTS = 0;
0014 WRITE_COMPONENTS = 0;
0015 WRITE_Z = 0;
0016 
0017 rootdir = '/data1/prime_long/';
0018 outdir = './testimages/';
0019 
0020 sub_id = '25jan01JP';
0021 run_id = 1;
0022 
0023 if GET_FILE_INFO
0024   % Specify the files to load
0025   P = spm_get('Files',fullfile(rootdir,sub_id,'epi', sprintf('run%d',run_id)),'sn*.img');
0026   
0027   nvol = size(P,1);
0028 
0029   % Get the dimension info for the first file
0030   disp(sprintf('Getting info for %d files', nvol))
0031   V = spm_vol(P);
0032 end
0033 
0034 if LOAD_RAW_DATA
0035   % Load the data
0036   clear indata
0037   disp(sprintf('Loading data'))
0038   indata = zeros(nvol,prod(V(1).dim(1:3)));
0039 
0040   for ivol = 1:nvol
0041     fid = fopen(deblank(P(ivol,:)),'rb','l');
0042     indata(ivol,:) = fread(fid,inf,'int16')';
0043     fclose(fid);
0044   end % for ivol
0045 end
0046 
0047 if COMPUTE_ICA
0048   % Run through the ICA algorithm
0049   disp('Running ICA algorithm')
0050   [weights sphere] = runica(indata);
0051 end
0052 
0053 if SAVE_ICA_DATA
0054   disp('Saving data')
0055   save(sprintf('%s_ica.mat',sub_id), 'weights','sphere')
0056 end
0057 
0058 if LOAD_ICA_DATA
0059   disp('Loading ICA data')
0060   load(sprintf('%s_ica.mat',sub_id))
0061 end
0062 
0063 if COMPUTE_COMPONENTS
0064   disp('Computing components')
0065   components = weights * indata;
0066 end
0067 
0068 if WRITE_COMPONENTS
0069   disp('Writing components')
0070   for ivol = 1:nvol
0071     outname = fullfile(outdir,sprintf('%s_comp%04d',sub_id,ivol));
0072     Vo(ivol) = V(ivol);
0073     Vo(ivol).fname = outname;
0074     Vo(ivol).descrip = sprintf('ICA component: %d', ivol);
0075 
0076     tmp = components(ivol,:);
0077     if WRITE_Z
0078       tmp = (tmp-mean(tmp))/std(tmp);
0079       max_z(ivol) = max(tmp);
0080       min_z(ivol) = min(tmp);
0081     end
0082     Vo(ivol) = spm_write_vol(Vo(ivol), reshape(tmp,Vo(ivol).dim(1:3)));
0083   end
0084 end