Multidimensional array (76x93x76), displaying as [x y z]

Hi all, I'm a beginner in matlab and i'd like some help with this problem. I have a 3D data file(.nii), loads into a messy looking array with many columns and rows, and >> [m n o] = size(Array) gives a 76x93x76 data array.

How can I display this as a [DimensionX DimensionY DimensionZ] array? I need it for simple matrice calculations. Also, how do i turn it back into that [76x93x76] again for saving?

Thanks!

--Robertte

[Stephen23]

What exactly do you mean? Can you give an example of what "display this as a [DimensionX DimensionY DimensionZ] array" really means?

Given that your data is already an array, and has 76*93*76 (=537168) elements, what do you hope to gain by displaying it? Are you going to scroll through all half-a-million elements and correct them by hand?

Displaying this data is not going to help you. You should instead actaully tell us what the calculations are that you want to perform, and we can help you with those instead.

[Robert Te]

Hi Stephen,

I have this .nii NIFTI file that contains a 3D image of the brain, and the data format is 76x93x76. I need it to be in [DimX DimY DimZ] form to calculate, and the goal is to convert it from brain image type "mni305" to "icbm152". If you'll look at this link, it describes a simple way to do so:

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-November/034417.html

Where to convert image type mni305('P305') to icbm152('P152'), 'P305' is the array format i am seeking, the [DimX DimY DimZ] to do the following calculation.:

% 
> M = [   0.9975   -0.0073    0.0176   -0.0429

          0.0146    1.0009   -0.0024    1.5496

         -0.0130   -0.0093    0.9971    1.1840

           0            0            0  1.0000]
> P305 = [MNI305x MNI305y MNI305z 1]';
> P152 = M*P305

Thanks in advance!

[Stephen23]

What exactly does "data format is 76x93x76" mean? I certainly understand what an 3D array is, but where are the X, Y, and Z coordinates that this formula requires? Are you are wanting to somehow extract X, Y, and Z values from this 3D array?

That link states "x, y, z coordinates", but you have not provided us with these coordinates. Do you have separate coordinate vectors?

[Robert Te]

Yes you got it! Apologies for the awkward phrasing. I have the 3D array stored in a 76x93x76 array, and i need to find a way to extract each dimension(x,y,z) and make it into an [x y z] array.

The "x,y,z co-ordinates" make up the 3D array i am talking about. Hope this clarifies!

[Stephen23]

The problem is you have not described how the X, Y and Z dimensions can be extracted from this array. If this is a a simple numeric data array (which you don't say), then the coordinates of the data locations are completely unknown. Lets have a look at a simple 2D example:

data = [1,2,3;4,5,6]; % 2x3

If we only have this data matrix, then _we know nothing about its X and Y coordinates of these data points, ie where the data was sampled. It is possible to define them separately:

X = [-40,20,80]; % 3
Y = [0.3,0.6]; % 2

You can see that the data matrix itself does not imply anything about the values of these coordinates. Until you actually tell us how to "extract" the coordinates from your 3D array there is not much more that we can do for you.

Answer 1

[Jan]

Did you ask your favorite internet search engine already? Perhaps others have solved the problem already, e.g. FEX: nifti-data-viewer or FEX: tools for nifti images.