cbiSwapNiftiDimensions.m
31022b3a13e6master

cbiSwapNiftiDimensions.m
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			function varargout=cbiSwapNiftiDimensions(varargin);
			% [newdata,newhdr,swapMatrix]=cbiSwapNiftiDimensions(data,hdr,swapvect);
			% - OR -
			% swapMatrix=cbiSwapNiftiDimensions(inputfile,outputfile,swapvect,[outputdatatype]);
			%
			% Swaps the dimensions of a Nifti file or data set.
			% Modifies the qform44 and quaternions accordingly.
			% If sform44 is non-identity, also modifies the sform.
			% Equivalent to avwswapdim except it (hopefully correctly) modifies qform44/sform44 matrices
			% NOTE: Only modifies the first 3 dimensions of a file - but works with data with 4 or more dimensions.
			%
			% swapvect: a 3-vector with entries +/-(1,2,3) indicating axis changes/flips, e.g.:
			% - flip x (dimension 1): swapvect=[-1 2 3]
			% - exchange x and z: swapvect=[3 2 1]
			% - exchange x with flipped y: swapvect=[-2 1 3]
			%
			% NOTE: if the image is acquired in one of the cardinal directions (axial, sagittal, or coronal
			% slice prescription) swapvect can be omitted, in which case the default is to swap the image axes
			% to conform to a 'standard' right-handed coordinate system as follows:
			% - dimension i (fastest changing dimension) corresponds to x (increasing from left to right)
			% - dimension j (second fastest changing dimension) corresponds to y (increasing from back to front)
			% - dimension k (third fastest changing dimension) corresponds to z (increasing from bottom to top)
			%
			% Optionally returns swap matrix
			%

			% File or data input?

			isfile=0;
			isarray=0;
			if (isstr(varargin{1}) & isstr(varargin{2}))
			% Input is a file
			isfile=1;
			[data,hdr]=cbiReadNifti(varargin{1});
			datasize=size(data);
			else
			% Input is a Matlab data array
			if (nargout<2)
			error('Not enough outputs')
			end
			if (~isstruct(varargin{2}))
			error('Second input must be a header struct')
			end
			hdr=varargin{2};
			isarray=1;
			datasize=size(varargin{1});
			end

			if (nargin==3)
			swapvect=varargin{3};
			else
			% check that image is in cardinal planes
			image_axes=hdr.qform44(1:3,1:3);
			ndims_per_axis=sum(abs(image_axes)>0);
			if (any(ndims_per_axis>1))
			error('Image planes not in cardinal planes - image must be rotated to canonical orientation. Aborting...')
			else
			swapvect=[0 0 0];
			swapmat=inv(image_axes);
			for n=1:3
			% row index of nonzero entry in each column == axis index with sign
			ri=find(swapmat(:,n));
			swapvect(n)=ri*sign(swapmat(ri,n));
			end
			end
			disp(['Extracted permutation vector (swapvect): ' num2str(swapvect)])
			end

			if (length(swapvect)~=3)
			error('Permutation (swap) vector must have 3 dimensions!');
			end

			if (~find(abs(swapvect)==1) \| ~find(abs(swapvect)==2) \| ~find(abs(swapvect)==3 ))
			error('swapvect MUST contain 1, 2, and 3')
			end

			% Generate swap matrix P
			% Old coordinates: X
			% New coordinates after flipping: Y = P*X
			% Scanner coordinates: S = Q*X where Q is the qform44
			% Hence the new qform R is given by
			% S = QX = Qinv(P)*Y
			% R = Q*inv(P)
			% and similarly, the new sform Z is given by
			% Z = W*inv(P) where W is the old sform
			% NOTE: swapMatrix == inv(P)

			swapMatrix=eye(4);
			id44=eye(4);
			for n=1:3
			% axis changes correspond to exchanging columns
			srccol=swapvect(n);
			sgn=sign(srccol);
			srccol=abs(srccol);
			swapMatrix(:,n)=sgn*id44(:,srccol);
			if (sgn<0)
			% axis inversions correspond to inverting sign and adding axis dimension-1
			swapMatrix(srccol,4)=datasize(srccol)-1;
			end
			end


			% Calculate new qform & sform. Qform is needed for pixdim etc.
			if (~isfield(hdr,'qform44') \| isempty(hdr.qform44))
			hdr.qform44=eye(4);
			end

			newqform44=hdr.qform44*swapMatrix;
			% Set new qform and update quaternions, qoffset, and pixdim
			fliphdr=cbiSetNiftiQform( hdr, newqform44 );

			if (isfield(hdr,'sform44') & ~isequal(eye(4),hdr.sform44))
			newsform44=hdr.sform44*swapMatrix;
			fliphdr=cbiSetNiftiSform( fliphdr, newsform44 );
			end

			% Flip data
			permutevect=1:length(datasize);
			permutevect(1:3)=abs(swapvect);
			if (isarray)
			flipdata=permute(varargin{1},permutevect);
			else
			flipdata=permute(data,permutevect);
			end
			for n=1:3
			if (swapvect(n)<0)
			flipdata=flipdim(flipdata,n);
			end
			end


			if (isarray)
			varargout{1}=flipdata;
			varargout{2}=fliphdr;
			if (nargout==3)
			varargout{3}=swapMatrix;
			end
			else
			% Save if desired
			if (nargin==4)
			[b,h]=cbiWriteNifti(varargin{2},flipdata,fliphdr,varargin{4});
			else
			[b,h]=cbiWriteNifti(varargin{2},flipdata,fliphdr);
			end
			if (nargout==1)
			varargout{1}=swapMatrix;
			end
			end

iCAPs/packages/cbiNifti/cbiSwapNiftiDimensions.m31022b3a13e6master

cbiSwapNiftiDimensions.mView Options

iCAPs/packages/cbiNifti/cbiSwapNiftiDimensions.m
31022b3a13e6master

cbiSwapNiftiDimensions.m
View Options