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bramila_detrend.m
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function vol = bramila_detrend(cfg)
% INPUT
% cfg.infile = location where the subject NII file (4D)
% cfg.vol = input can be a 4D volume, if this exists, then infile is not loaded but used as ID (optional)
% cfg.write = 0 (default 0, set to 1 if you want to store the volume)
% cfg.detrend_type = type of detrend, default is 'linear-nodemean', others are: 'linear-demean', 'spline', 'polynomial-(no)demean'
% cfg.TR = TR (mandatory if detrend spline is used)
% OUTPUT
% vol = a 4D volume detrended
if(isfield(cfg,'vol'))
data=cfg.vol;
% add check that it's a 4D vol
elseif(isfield(cfg,'infile'))
nii=load_nii(cfg.infile);
data=nii.img;
end
data=double(data);
type='linear-nodemean';
if(isfield(cfg,'detrend_type'))
type=cfg.detrend_type;
end
% resize the data into a 2-dim matrix, time in first dimension
kk=size(data);
if(length(kk)==4)
T=kk(4);
tempdata=reshape(data,[],T);
tempdata=tempdata';
fprintf('Detrending data...');
else
T=kk(1);
tempdata=data;
end
m=mean(tempdata,1);
switch type
case 'linear-demean'
tempdata=detrend(tempdata);
case 'linear-nodemean'
tempdata=detrend(tempdata);
for row=1:T
tempdata(row,:)=tempdata(row,:)+m;
end
case 'spline'
error('not implememented')
% add here code
case 'polynomial-demean'
tempdata=detrend_extended(tempdata,2);
case 'polynomial-nodemean'
tempdata=detrend_extended(tempdata,2);
for row=1:T
tempdata(row,:)=tempdata(row,:)+m;
end
case 'Savitzky-Golay'
% see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3929490/
if(T*cfg.TR>=240)
SGlen=round(240/cfg.TR);
else
SGlen=T; % if we have less than 4 minutes, let's use all the data
end
disp(['Performing Savitzky-Golay detrending over ' num2str(SGlen) ' timepoints']);
if(mod(SGlen,2)==0) SGlen=SGlen-1; end % it needs to be odd
trend=sgolayfilt(tempdata,3,SGlen);
for v=1:size(tempdata,2) % foreach voxel
if(var(trend(:,v))==0) continue; end
[aa bb res]=regress(tempdata(:,v),[trend(:,v) ones(T,1)]);
tempdata(:,v)=res;
end
for row=1:T
tempdata(row,:)=tempdata(row,:)+m;
end
end
% resize the data back
if(length(kk)==4)
tempdata=tempdata';
vol=reshape(tempdata,kk);
fprintf(' done\n');
else
vol=tempdata;
end
if cfg.write==1 || nargout<1
cfg.outfile=bramila_savevolume(cfg,vol,'EPI volume after detrending','mask_detrend.nii');
end
function [X,T]=detrend_extended(t,X,p)
% DETREND removes the trend from data, NaN's are considered as missing values
%
% DETREND is fully compatible to previous Matlab and Octave DETREND with the following features added:
% - handles NaN's by assuming that these are missing values
% - handles unequally spaced data
% - second output parameter gives the trend of the data
% - compatible to Matlab and Octave
%
% [...]=detrend([t,] X [,p])
% removes trend for unequally spaced data
% t represents the time points
% X(i) is the value at time t(i)
% p must be a scalar
%
% [...]=detrend(X,0)
% removes the mean
%
% [...]=detrend(X,p)
% removes polynomial of order p (default p=1)
%
% [...]=detrend(X,1) - default
% removes linear trend
%
% [X,T]=detrend(...)
%
% X is the detrended data
% T is the removed trend
%
% see also: SUMSKIPNAN
% This library is free software; you can redistribute it and/or
% modify it under the terms of the GNU Library General Public
% License as published by the Free Software Foundation; either
% Version 2 of the License, or (at your option) any later version.
%
% This library 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
% Library General Public License for more details.
%
% You should have received a copy of the GNU Library General Public
% License along with this library; if not, write to the
% Free Software Foundation, Inc., 59 Temple Place - Suite 330,
% Boston, MA 02111-1307, USA.
% Copyright (C) 1995, 1996 Kurt Hornik <[email protected]>
% Copyright (C) 2001 by Alois Schloegl <[email protected]>
% last revision 13 Apr 2001, Ver 2.74
if (nargin == 1)
p = 1;
X = t;
t = [];
elseif (nargin == 2)
if all(size(X)==1),
p = X;
X = t;
t = [];
else
p = 1;
end;
elseif (nargin == 3)
elseif (nargin > 3)
fprintf (1,'usage: detrend (x [, p])\n');
end;
% check data, must be in culomn order
[m, n] = size (X);
if (m == 1)
X = X';
r=n;
else
r=m;
end
% check time scale
if isempty(t),
t = (1:r).'; % make time scale
elseif ~all(size(t)==size(X))
t = t(:);
end;
% check dimension of t and X
if ~all(size(X,1)==size(t,1))
fprintf (2,'detrend: size(t,1) must same as size(x,1) \n');
end;
% check the order of the polynomial
if (~(all(size(p)==1) & (p == round (p)) & (p >= 0)))
fprintf (2,'detrend: p must be a nonnegative integer\n');
end
if (nargout>1) , % needs more memory
T = zeros(size(X))+nan;
%T=repmat(nan,size(X)); % not supported by Octave 2.0.16
if (size(t,2)>1), % for multiple time scales
for k=1:size(X,2),
idx=find(~isnan(X(:,k)));
b = (t(idx,k) * ones (1, p + 1)) .^ (ones (length(idx),1) * (0 : p));
T(idx,k) = b * (b \ X(idx,k));
end;
else % if only one time scale is used
b = (t * ones (1, p + 1)) .^ (ones (length(t),1) * (0 : p));
for k=1:size(X,2),
idx=find(~isnan(X(:,k)));
T(idx,k) = b(idx,:) * (b(idx,:) \ X(idx,k));
%X(idx,k) = X(idx,k) - T(idx,k); % 1st alternative implementation
%X(:,k) = X(:,k) - T(:,k); % 2nd alternative
end;
end;
X = X-T; % 3nd alternative
if (m == 1)
X = X';
T = T';
end
else % needs less memory
if (size(t,2)>1), % for multiple time scales
for k = 1:size(X,2),
idx = find(~isnan(X(:,k)));
b = (t(idx,k) * ones (1, p + 1)) .^ (ones (length(idx),1) * (0 : p));
X(idx,k) = X(idx,k) - b * (b \ X(idx,k));
end;
else % if only one time scale is used
b = (t * ones (1, p + 1)) .^ (ones (length(t),1) * (0 : p));
for k = 1:size(X,2),
idx = find(~isnan(X(:,k)));
X(idx,k) = X(idx,k) - b(idx,:) * (b(idx,:) \ X(idx,k));
end;
end;
if (m == 1)
X = X';
end
end;