You need to consider where the coordinates of the voxels (i,j,k) should be
within a mm coordinate system (x,y,z). Doing this involves figuring out a
4x4 matrix M, such that
x = m11*i + m12*j + m13*k + m14
y = m21*i + m22*j + m23*k + m24
z = m31*i + m32*j + m33*k + m34
m41 = m42 = m43 = 0
m44 = 1
Once you have figured out this matrix, you can create an image from data by:
dim = size(data);
Nii = nifti;
Nii.dat = file_array('filename.nii',dim, 'float32',352,1,0);
Nii.mat = M;
Nii.mat0 = M;
Nii.descrip = 'My Image';
create(Nii);
Nii.dat(:,:,:) = data;
Best regards,
-John
On 18 November 2014 11:20, Janki Mehta <[log in to unmask]> wrote:
> Hi,
>
> I have a 3D matrix in MATLAB which I need to convert to NIfTI or ANALYZE
> format so as to view it in SPM8. For this I am using "Tools for NIfTI and
> ANALYZE image by Jimmy Shen" available on
> http://in.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image.
> My problem is once I convert this 3D matrix to ANALYZE format using
> make_ana command, I get the brain volume that is rotated/flipped w.r.t the
> original volume.
> HOw can I resolve this?
> NOTE: co-registering this to original brain volume did not help, the
> result was still flipped.
>
> Thanks,
>
> Janki
>
