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iCAPs/packages/spm12/config/spm_cfg_smooth.m
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spm_cfg_smooth.m
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function smooth = spm_cfg_smooth
% SPM Configuration file for Smooth
%__________________________________________________________________________
% Copyright (C) 2005-2016 Wellcome Trust Centre for Neuroimaging
% $Id: spm_cfg_smooth.m 6952 2016-11-25 16:03:13Z guillaume $
%--------------------------------------------------------------------------
% data Images to Smooth
%--------------------------------------------------------------------------
data = cfg_files;
data.tag = 'data';
data.name = 'Images to smooth';
data.help = {
'Specify the images to smooth.'
'The smoothed images are written to the same subdirectories as the original images with a configurable prefix.'
}';
data.filter = 'image';
data.ufilter = '.*';
data.num = [1 Inf];
data.preview = @(f) spm_check_registration(char(f));
%--------------------------------------------------------------------------
% fwhm FWHM
%--------------------------------------------------------------------------
fwhm = cfg_entry;
fwhm.tag = 'fwhm';
fwhm.name = 'FWHM';
fwhm.help = {
'Full width at half maximum (FWHM) of the Gaussian smoothing kernel in mm.'
'Three values should be entered, denoting the FWHM in the x, y and z directions.'
}';
fwhm.strtype = 'r';
fwhm.num = [1 3];
fwhm.def = @(val)spm_get_defaults('smooth.fwhm', val{:});
%--------------------------------------------------------------------------
% dtype Data Type
%--------------------------------------------------------------------------
dtype = cfg_menu;
dtype.tag = 'dtype';
dtype.name = 'Data Type';
dtype.help = {
'Data type of the output images.'
'''SAME'' indicates the same data type as the original images.'
}';
dtype.labels = {
'SAME'
'UINT8 - unsigned char'
'INT16 - signed short'
'INT32 - signed int'
'FLOAT32 - single prec. float'
'FLOAT64 - double prec. float'
}';
dtype.values = {0 spm_type('uint8') spm_type('int16') spm_type('int32') spm_type('float32') spm_type('float64')};
dtype.val = {0};
%--------------------------------------------------------------------------
% im Implicit masking
%--------------------------------------------------------------------------
im = cfg_menu;
im.tag = 'im';
im.name = 'Implicit masking';
im.help = {
'An "implicit mask" is a mask implied by a particular voxel value (0 for images with integer type, NaN for float images).'
'If set to ''Yes'', the implicit masking of the input image is preserved in the smoothed image.'
}';
im.labels = {'Yes' 'No'};
im.values = {1 0};
im.val = {0};
%--------------------------------------------------------------------------
% prefix Filename Prefix
%--------------------------------------------------------------------------
prefix = cfg_entry;
prefix.tag = 'prefix';
prefix.name = 'Filename prefix';
prefix.help = {'String to be prepended to the filenames of the smoothed image file(s). Default prefix is ''s''.'};
prefix.strtype = 's';
prefix.num = [1 Inf];
prefix.def = @(val)spm_get_defaults('smooth.prefix', val{:});
%--------------------------------------------------------------------------
% smooth Smooth
%--------------------------------------------------------------------------
smooth = cfg_exbranch;
smooth.tag = 'smooth';
smooth.name = 'Smooth';
smooth.val = {data fwhm dtype im prefix};
smooth.help = {
'Smooth (ie convolve) image volumes with a Gaussian kernel of a specified width.'
'It is used as a preprocessing step to suppress noise and effects due to residual differences in functional and gyral anatomy during inter-subject averaging.'
}';
smooth.prog = @spm_run_smooth;
smooth.vout = @vout;
%==========================================================================
function dep = vout(varargin)
% Output file names will be saved in a struct with field .files
dep(1) = cfg_dep;
dep(1).sname = 'Smoothed Images';
dep(1).src_output = substruct('.','files');
dep(1).tgt_spec = cfg_findspec({{'filter','image','strtype','e'}});
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