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cat_conf_stoolsexp.m
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cat_conf_stoolsexp.m
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function stoolsexp = cat_conf_stoolsexp
%_______________________________________________________________________
% wrapper for calling CAT surface utilities
% ______________________________________________________________________
%
% Christian Gaser, Robert Dahnke
% Structural Brain Mapping Group (https://neuro-jena.github.io)
% Departments of Neurology and Psychiatry
% Jena University Hospital
% ______________________________________________________________________
% $Id$
%% average surface mesh
%-----------------------------------------------------------------------
avg.data = cfg_files;
avg.data.tag = 'data';
avg.data.name = 'Sample';
avg.data.filter = 'gifti';
avg.data.ufilter = '^[rl]h.central';
avg.data.num = [1 Inf];
avg.data.help = {
'Select surfaces.'
};
avg.meshsmooth = cfg_entry;
avg.meshsmooth.tag = 'meshsmooth';
avg.meshsmooth.name = 'Surface Smoothing Iterations';
avg.meshsmooth.strtype = 'r';
avg.meshsmooth.num = [1 Inf];
avg.meshsmooth.val = {[0 2 32]};
avg.meshsmooth.help = {
'Smoothing of the average surface. '
''
};
avg.surfside = cfg_menu;
avg.surfside.tag = 'surfside';
avg.surfside.name = 'Side Handling';
avg.surfside.labels = {'separate','mirror'};
avg.surfside.values = {1,2};
avg.surfside.val = {1};
avg.surfside.help = {
'Handling of the cortical hemispheres.'
''
};
avg.surfname = cfg_entry;
avg.surfname.tag = 'surfname';
avg.surfname.name = 'Surface Filename';
avg.surfname.strtype = 's';
avg.surfname.num = [1 Inf];
avg.surfname.val = {'average'};
avg.surfname.help = {'Name of the surface.'};
avg.outdir = cfg_files;
avg.outdir.tag = 'outdir';
avg.outdir.name = 'Output Directory';
avg.outdir.filter = 'dir';
avg.outdir.ufilter = '.*';
avg.outdir.num = [0 1];
avg.outdir.val{1} = {''};
avg.outdir.dir = fullfile(fileparts(mfilename('fullpath')));
avg.outdir.help = {'Select a directory where files are written.'};
avg.main = cfg_exbranch;
avg.main.tag = 'avg_surf';
avg.main.name = 'Average Surface Mesh';
avg.main.val = {
avg.data ...
avg.meshsmooth ...
avg.surfside ...
avg.surfname ...
avg.outdir ...
};
avg.main.vfiles = @vfiles_avg;
avg.main.prog = @cat_surf_avg;
avg.main.help = {
'Averaging of cortical surfaces.'
''
};
%}
%% data smoothing
%-----------------------------------------------------------------------
smooth.data = cfg_files;
smooth.data.tag = 'data';
smooth.data.name = 'Sample';
smooth.data.filter = 'any';
smooth.data.ufilter = '^[rl]h.(?!cent|pial|white|sphe|defe|hull).*';
smooth.data.num = [1 Inf];
smooth.data.help = {'Select surface data (texture) files for smoothing.'};
smooth.fwhm = cfg_entry;
smooth.fwhm.tag = 'fwhm';
smooth.fwhm.name = 'Smoothing filter size in fwhm';
smooth.fwhm.strtype = 'r';
smooth.fwhm.num = [1 1];
smooth.fwhm.val = {15};
smooth.fwhm.help = {
'Select filter size for smoothing. For cortical thickness a good starting value is 15mm, while other surface parameters based on cortex folding (e.g. gyrification, cortical complexity) need a larger filter size of about 25mm.'};
smooth.main = cfg_exbranch;
smooth.main.tag = 'datasmooth';
smooth.main.name = 'Smooth Surface Data';
smooth.main.val = {
smooth.data ...
smooth.fwhm ...
};
smooth.main.vfiles = @vfiles_smooth;
smooth.main.prog = @cat_surf_smooth;
smooth.main.help = {
'Gaussian smoothing of surface data (texture).'
''
};
%% Toolset
%-----------------------------------------------------------------------
stoolsexp = cfg_choice;
stoolsexp.name = 'Surface Developer Tools';
stoolsexp.tag = 'stoolsexp';
stoolsexp.values = {...
smooth.main, ...
avg.main, ...
};
return
%% Result files
%_______________________________________________________________________
function vf = vfiles_smooth(job)
vf = job.data;
sinfo = cat_surf_info(job.data);
for i=1:numel(vf)
vf(i) = cat_surf_rename(sinfo(i),'dataname',sprintf('s%d%s',job.fwhm,sinfo(i).dataname));
end
return;
%_______________________________________________________________________
function vf = vfiles_avg(job)
if isempty(job.outdir{1})
outdir = spm_fileparts(job.data{1});
else
outdir = job.outdir{1};
end
if job.surfside==2
side = {'lh','rh'};
else
side = {};
sinfo = cat_surf_info(job.data);
if ~isempty(strfind([sinfo.side],'lh')), side{end+1}= 'lh'; end
if ~isempty(strfind([sinfo.side],'rh')), side{end+1}= 'rh'; end
end
vf = cell(numel(side),numel(job.meshsmooth));
for si = 1:numel(side)
for smi=1:numel(job.meshsmooth)
if job.meshsmooth(smi)>0
vf{si,smi} = fullfile(outdir,sprintf('%s.%s_%dmm.gii',side{si},job.surfname,job.meshsmooth(smi)));
else
vf{si,smi} = fullfile(outdir,sprintf('%s.%s.gii',side{si},job.surfname));
end
end
end
return;