This may not be correct. Especially, because XYZ is not a 3D matrix, but a 3 x nVox matrix containing the XYZ coords for the voxels with the given "index".
Let's assume that we have an nX x nY x nZ image (img) so the XYZ is a 3 x (nX*nY*nZ) matrix; and we want the "index" for the voxel at X,Y,Z.
There are two options to figure out the "index":
ind = (Z-1)*(nX*nY)+(Y-1)*nX+X; % specific
or
ind = 1:length(XYZ); ind = reshape(ind,size(img)); ind = ind(X,Y,Z); % general
and
XYZ(:,ind)
gives you the coordinates
Cheers,
Auer, Tibor M.D. Ph.D.
MRC Cognition and Brain Sciences Unit
15 Chaucer Road
Cambridge
CB2 7EF
United Kingdom
Phone/Work: +44-(0)1223-355294 (ext. 869)
-----Original Message-----
From: SPM (Statistical Parametric Mapping) [
mailto:[log in to unmask]] On Behalf Of Michael Erb
Sent: Monday, October 14, 2013 10:00 PM
To:
[log in to unmask]
Subject: Re: [SPM] Q) How to figure out the MNI coordinate of matrix x,y,z?
try:
[Img, XYZ]=spm_read_vols(Vol);
XYZ(10,20, 6) will give you the MNI coordinate in mm
How do I know that?
>> help spm_read_vols
Read in entire image volumes
FORMAT [Y,XYZ] = spm_read_vols(V,mask)
V - vector of mapped image volumes to read in (from spm_vol)
mask - implicit zero mask?
Y - 4D matrix of image data, fourth dimension indexes images
XYZ - 3xn matrix of XYZ locations returned (in mm)
__________________________________________________________________________
For image data types without a representation of NaN (see spm_type),
implicit zero masking can be used. If mask is set, then zeros are
treated as masked, and returned as NaN.
__________________________________________________________________________
Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
Hope that helps,
Michael
Am 14.10.2013 22:10, schrieb Glen Lee:
> Hello SPM experts,
>
> I'd like to figure out the MNI coordinate that corresponds to matlab's
> matrix of an image.
> For example, I'd like to know what the MNI x,y,z that corresponds to
> 10,20,6 in matrix below.
>
> Vol=spm_vol('tmap.nii');
> Img=spm_read_vols(Vol);
>
> Img(10,20, 6)-> MNI??
>
>
> thanks in advance,
> Glen
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Dr. Michael Erb
Department of Biomedical Magnetic Resonance University of Tübingen Hoppe-Seyler-Str. 3
72076 Tübingen, Germany
Tel.: +49(0)7071/2987753 priv. +49(0)7071/61559
Fax.: +49(0)7071/294371
www:
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