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iCAPs/packages/spm12/config/spm_cfg_parrec.m
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spm_cfg_parrec.m
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function parrec = spm_cfg_parrec
% SPM Configuration file for Philips PAR/REC Import
%__________________________________________________________________________
% Copyright (C) 2015 Wellcome Trust Centre for Neuroimaging
% Guillaume Flandin
% $Id: spm_cfg_parrec.m 6315 2015-01-23 17:09:06Z guillaume $
%--------------------------------------------------------------------------
% data PAR files
%--------------------------------------------------------------------------
data = cfg_files;
data.tag = 'data';
data.name = 'PAR files';
data.help = {'Select the PAR files to convert.'};
data.filter = 'any';
data.ufilter = '.*(par|PAR)';
data.num = [1 Inf];
%--------------------------------------------------------------------------
% outdir Output directory
%--------------------------------------------------------------------------
outdir = cfg_files;
outdir.tag = 'outdir';
outdir.name = 'Output directory';
outdir.help = {'Select a directory where files are written.'};
outdir.filter = 'dir';
outdir.ufilter = '.*';
outdir.num = [1 1];
%--------------------------------------------------------------------------
% ext Output image format
%--------------------------------------------------------------------------
ext = cfg_menu;
ext.tag = 'ext';
ext.name = 'Output image format';
ext.help = {'Output files can be written as .img + .hdr, or the two can be combined into a .nii file.'};
ext.labels = {
'Two file (img+hdr) NIfTI'
'Single file (nii) NIfTI'
}';
ext.values = {'img', 'nii'};
ext.def = @(val)spm_get_defaults('images.format', val{:});
%--------------------------------------------------------------------------
% opts Options
%--------------------------------------------------------------------------
opts = cfg_branch;
opts.tag = 'opts';
opts.name = 'Options';
opts.val = {outdir ext};
opts.help = {'Conversion options'};
%--------------------------------------------------------------------------
% parrec ECAT Import
%--------------------------------------------------------------------------
parrec = cfg_exbranch;
parrec.tag = 'parrec';
parrec.name = 'PAR/REC Import';
parrec.val = {data opts};
parrec.help = {'Philips PAR/REC Import.'};
parrec.prog = @convert_parrec;
parrec.vout = @vout;
%==========================================================================
function out = convert_parrec(job)
for i=1:numel(job.data)
spm_parrec2nifti(job.data{i},job.opts);
end
out.files = cell(size(job.data));
for i=1:numel(job.data)
out.files{i} = spm_file(job.data{i}, 'path',pwd, 'ext',job.opts.ext);
end
%==========================================================================
function dep = vout(job)
dep = cfg_dep;
dep.sname = 'Converted Images';
dep.src_output = substruct('.','files');
dep.tgt_spec = cfg_findspec({{'filter','image','strtype','e'}});
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