[Nibabel] Get raw values for voxels?

[John Richey]

Hi everyone,

I have what is probably a straightforward question about Nibabel... this is my first time using this tool, so please forgive me if the answer is obvious! 

For a single 3D image, I wish to obtain a matrix of values corresponding to the raw voxel intensity of each voxel. In other words, is there a way to produce a [x1, ..., Xn; Y1, ..., Yn; Z1, ..., Zn] matrix that I can use to explore the data in its numerical form?

Thanks in advance!

[Yaroslav Halchenko]

http://nipy.sourceforge.net/nibabel/gettingstarted.html

get_data would be your friend

--
Yaroslav O. Halchenko
Postdoctoral Fellow, Department of Psychological and Brain Sciences
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419
WWW: http://www.linkedin.com/in/yarik

[Ariel Rokem]

Hi John, 

For most cases I've seen, this should do it: 

import nibabel as ni

d = ni.load(file_name).get_data()

Where d is now the matrix you are interested in. 

Cheers, 

Ariel 

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[John Richey]

Exactly what was needed!  Many thanks!