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ft_defacevolume.m
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ft_defacevolume.m
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function mri = ft_defacevolume(cfg, mri)
% FT_DEFACEVOLUME allows you to de-identify an anatomical MRI by erasing specific
% regions, such as the face and ears. The interactive graphical user interface allows
% you to position a box over the anatomical data inside which all anatomical voxel
% values will be replaced by zero. You might have to call this function multiple
% times when both face and ears need to be removed. Following defacing, you should
% check the result with FT_SOURCEPLOT.
%
% Use as
% mri = ft_defacevolume(cfg, mri)
%
% The configuration can contain the following options
% cfg.method = 'interactive', 'spm' (default = 'interactive')
%
% If you specify the box method, the following options apply
% cfg.translate = initial position of the center of the box (default = [0 0 0])
% cfg.scale = initial size of the box along each dimension (default is automatic)
% cfg.rotate = initial rotation of the box (default = [0 0 0])
% cfg.selection = which voxels to keep, can be 'inside' or 'outside' (default = 'outside')
% cfg.smooth = 'no' or the FWHM of the gaussian kernel in voxels (default = 'no')
% cfg.keepbrain = 'no' or 'yes', segment and retain the brain (default = 'no')
% cfg.feedback = 'no' or 'yes', whether to provide graphical feedback (default = 'no')
%
% If you specify no smoothing, the selected area will be zero-masked. If you
% specify a certain amount of smoothing (in voxels FWHM), the selected area will
% be replaced by a smoothed version of the data.
%
% The spm method does not have any options, it uses SPM_DEFACE from the
% SPM12 toolbox.
%
% See also FT_ANONYMIZEDATA, FT_DEFACEMESH, FT_ANALYSISPIPELINE, FT_SOURCEPLOT
% Copyright (C) 2015-2022, Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for the documentation and details.
%
% FieldTrip is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% FieldTrip is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with FieldTrip. If not, see <http://www.gnu.org/licenses/>.
%
% $Id$
% these are used by the ft_preamble/ft_postamble function and scripts
ft_revision = '$Id$';
ft_nargin = nargin;
ft_nargout = nargout;
% do the general setup of the function
ft_defaults
ft_preamble init
ft_preamble debug
ft_preamble loadvar mri
ft_preamble provenance mri
% the ft_abort variable is set to true or false in ft_preamble_init
if ft_abort
return
end
% for backward compatibility
cfg = ft_checkconfig(cfg, 'renamedval', {'method', 'box', 'interactive'});
% set the defaults
cfg.method = ft_getopt(cfg, 'method', 'interactive');
cfg.rotate = ft_getopt(cfg, 'rotate', [0 0 0]);
cfg.scale = ft_getopt(cfg, 'scale'); % the automatic default is determined further down
cfg.translate = ft_getopt(cfg, 'translate', [0 0 0]);
cfg.transformorder = ft_getopt(cfg, 'transformorder', {'scale', 'rotate', 'translate'}); % T*R*S
cfg.selection = ft_getopt(cfg, 'selection', 'outside');
cfg.smooth = ft_getopt(cfg, 'smooth', 'no');
cfg.keepbrain = ft_getopt(cfg, 'keepbrain', 'no');
cfg.feedback = ft_getopt(cfg, 'feedback', 'no');
ismri = ft_datatype(mri, 'volume') && isfield(mri, 'anatomy');
ismesh = isfield(mri, 'pos'); % triangles are optional
if ismri
% check if the input data is valid for this function
mri = ft_checkdata(mri, 'datatype', 'volume', 'feedback', 'yes');
end
switch cfg.method
case 'spm'
% this requires SPM12 on the path
ft_hastoolbox('spm12', 1);
% defacing relies on coregistration, which relies on the MRI being reasonably aligned for SPM
mri = ft_checkdata(mri, 'hascoordsys', 'yes');
% remember the original transformation matrix and coordinate system
original = [];
original.transform = mri.transform;
original.coordsys = mri.coordsys;
mri = ft_convert_coordsys(mri, 'acpc');
filename1 = {[tempname '.nii']};
ft_write_mri(filename1{1}, mri, 'dataformat', 'nifti');
% % apply a least squares pre-alignment step in order to make spm_deface more robust
% % this could be done conditional on the modality/contrast, which is part of the BIDS filename
% template = spm_vol(fullfile(spm('Dir'),'canonical','avg152PD.nii'));
% template = spm_vol(fullfile(spm('Dir'),'canonical','avg152T1.nii'));
% template = spm_vol(fullfile(spm('Dir'),'canonical','avg152T2.nii'));
% filevol = spm_vol(filename1{1});
% M = spm_affreg(template, filevol);
% spm_get_space(filename1{1}, M * filevol.mat);
filename2 = spm_deface(filename1);
mri = ft_read_mri(filename2{1});
% put the original transformation matrix and coordinate system back
mri.transform = original.transform;
mri.coordsys = original.coordsys;
% clean up the temporary files
delete(filename1{1});
delete(filename2{1});
case 'interactive'
% this is an alternative implementation of the interactive method usinf FT_INTERACTIVEREALIGN
% it aligns a box to the MRI or mesh, and then removes the points inside that box
if ismri
% enhance the contrast of the volumetric data, see also FT_VOLUMEREALIGN
dat = double(mri.anatomy);
dum = unique(dat(:));
dmin = dum(round(0.05*numel(dum))); % take the 5% value of the histogram
dmax = dum(round(0.95*numel(dum))); % take the 95% value of the histogram
dat = (dat-dmin)./(dmax-dmin);
mri.anatomy = dat;
end
% construct a box with a unit length expressed in the units of the input mri or mesh
% rather than using a triangulation, this specifies polygons for each of the 6 edges of the box
box.unit = mri.unit;
box.pos = [
1 1 1
1 -1 1
-1 -1 1
-1 1 1
1 1 -1
1 -1 -1
-1 -1 -1
-1 1 -1
]/2;
box.poly = [
1 2 3 4
1 5 6 2
2 6 7 3
3 7 8 4
4 8 5 1
5 8 7 6
];
% the default is to scale the box to 75 mm (or equivalent)
defaultscale = [75 75 75] * ft_scalingfactor('mm', mri.unit);
surfaceonly = isfield(mri, 'tet') | isfield(mri, 'hex'); % only for tetrahedral or hexahedral meshes
tmpcfg = keepfields(cfg, {'scale', 'rotate', 'translate', 'transformorder'});
tmpcfg.scale = ft_getopt(cfg, 'scale', defaultscale);
tmpcfg.showlight = 'no';
tmpcfg.showalpha = 'no'; % do not use a global alpha level
tmpcfg.showapply = 'no'; % do not show the apply button
tmpcfg.template.axes = 'yes';
if ismri
tmpcfg.template.mri = mri;
elseif ismesh
tmpcfg.template.mesh = mri;
end
tmpcfg.individual.mesh = box;
tmpcfg.individual.meshstyle = {'edgecolor', 'k', 'facecolor', 'y', 'facealpha', 0.3, 'surfaceonly', surfaceonly};
tmpcfg = ft_interactiverealign(tmpcfg);
% remember these for potential reuse outside of this function
cfg.rotate = tmpcfg.rotate;
cfg.scale = tmpcfg.scale;
cfg.translate = tmpcfg.translate;
% the template remains fixed, the individual is moved around
R = rotate (cfg.rotate);
T = translate(cfg.translate);
S = scale (cfg.scale);
% this is the transformation to get from the individual to the template
transform = combine_transform(R, S, T, cfg.transformorder);
if ismri
% rather than converting the box to the MRI, do it the other way around
[X, Y, Z] = ndgrid(1:mri.dim(1), 1:mri.dim(2), 1:mri.dim(3));
voxpos = ft_warp_apply(mri.transform, [X(:) Y(:) Z(:)]); % voxel positions in head coordinates
voxpos = ft_warp_apply(inv(transform), voxpos); % voxel positions in box coordinates
remove = ...
voxpos(:,1) > -0.5 & ...
voxpos(:,1) < +0.5 & ...
voxpos(:,2) > -0.5 & ...
voxpos(:,2) < +0.5 & ...
voxpos(:,3) > -0.5 & ...
voxpos(:,3) < +0.5;
elseif ismesh || issource
% rather than converting the box to the mesh, do it the other way around
meshpos = ft_warp_apply(inv(transform), mri.pos); % vertex positions in box coordinates
remove = ...
meshpos(:,1) > -0.5 & ...
meshpos(:,1) < +0.5 & ...
meshpos(:,2) > -0.5 & ...
meshpos(:,2) < +0.5 & ...
meshpos(:,3) > -0.5 & ...
meshpos(:,3) < +0.5;
end
if strcmp(cfg.selection, 'inside')
% invert the selection, i.e., keep the voxels inside the box
remove = ~remove;
end
if ismri
if istrue(cfg.keepbrain)
tmpcfg = [];
tmpcfg.output = {'brain'};
seg = ft_volumesegment(tmpcfg, mri);
fprintf('keeping voxels in brain segmentation\n');
% keep the tissue of the brain
remove(seg.brain) = 0;
clear seg
end
if istrue(cfg.feedback)
tmpmri = keepfields(mri, {'anatomy', 'transform', 'coordsys', 'units', 'dim'});
tmpmri.remove = remove;
tmpcfg = [];
tmpcfg.funparameter = 'remove';
ft_sourceplot(tmpcfg, tmpmri);
end
if isequal(cfg.smooth, 'no')
fprintf('zero-filling %.0f%% of the volume\n', 100*mean(remove));
mri.anatomy(remove) = 0;
else
tmp = mri.anatomy;
tmp = (1 + 0.5.*randn(size(tmp))).*tmp; % add 50% noise to each voxel
tmp = volumesmooth(tmp, cfg.smooth, 'anatomy');
fprintf('smoothing %.0f%% of the volume\n', 100*mean(remove));
mri.anatomy(remove) = tmp(remove);
end
elseif ismesh
% determine all fields that might need to be defaced
fn = setdiff(fieldnames(mri), ignorefields('deface'));
dimord = cell(size(fn));
for i=1:numel(fn)
dimord{i} = getdimord(mri, fn{i});
end
% this applies to headshapes and meshes in general
fprintf('keeping %d and removing %d vertices in the mesh\n', sum(remove==0), sum(remove==1));
if isfield(mri, 'tri')
[mri.pos, mri.tri] = remove_vertices(mri.pos, mri.tri, remove);
elseif isfield(mri, 'tet')
[mri.pos, mri.tet] = remove_vertices(mri.pos, mri.tet, remove);
elseif isfield(mri, 'hex')
[mri.pos, mri.hex] = remove_vertices(mri.pos, mri.hex, remove);
else
mri.pos = mri.pos(~remove,1:3);
end
for i=1:numel(fn)
dimtok = tokenize(dimord{i}, '_');
% do some sanity checks
if any(strcmp(dimtok, '{pos}'))
ft_error('not supported');
end
if numel(dimtok)>5
ft_error('too many dimensions');
end
% remove the same positions from each matching dimension
if numel(dimtok)>0 && strcmp(dimtok{1}, 'pos')
mri.(fn{i}) = mri.(fn{i})(~remove,:,:,:,:);
end
if numel(dimtok)>1 && strcmp(dimtok{2}, 'pos')
mri.(fn{i}) = mri.(fn{i})(:,~remove,:,:,:);
end
if numel(dimtok)>2 && strcmp(dimtok{3}, 'pos')
mri.(fn{i}) = mri.(fn{i})(:,:,~remove,:,:);
end
if numel(dimtok)>3 && strcmp(dimtok{4}, 'pos')
mri.(fn{i}) = mri.(fn{i})(:,:,:,~remove,:);
end
if numel(dimtok)>4 && strcmp(dimtok{5}, 'pos')
mri.(fn{i}) = mri.(fn{i})(:,:,:,:,~remove);
end
end % for fn
mri = removefields(mri, {'dim', 'transform'}); % these fields don't apply any more
end % ismesh
otherwise
ft_error('unsupported method');
end % switch method
% do the general cleanup and bookkeeping at the end of the function
ft_postamble debug
ft_postamble previous mri
ft_postamble provenance mri
ft_postamble history mri
ft_postamble savevar mri