[Neuroimaging] Looping through 3D NIFTI Image: Help

[Jose Rey López]

Using nilearn you could do:

niimage = nilearn.image.load_img(‘path’)
Voxels = niimage.get_data()

You get a numpy array, with Voxel[i,j,k] would allow you to access any voxel

Voxels[:,x,y] to acces a single line

Voxels[:,:,x]  to access any slice

Or to iterate over all voxels

for i ....
     for j ....
          for k .....
                Voxels[i,j,k]


On 4 Jan 2019, at 17:58, Arnav Lohe <arnavlohe15 at gmail.com<mailto:arnavlohe15 at gmail.com>> wrote:

Dear Neuroimaging List Members,

My name is Arnav Lohe, and I am a junior at Rutgers University working on a neuroimaging project. I want to write an original piece of code to calculate the total tissue volume in a (.nii) MRI image, and to do this I need to loop through the multidimensional array. The loop is what I do not know how to do. I tried triple indexing, I tried converting the .nii image into a numpy array, and got nowhere with my approaches. Does someone know how to loop through the individual voxels and extract the numerical information inside each one?

https://stackoverflow.com/questions/54031899/how-can-i-loop-through-3d-nifti-image-in-python

I have also posted this to StackOverflow, all additional relevant details should be there.

Sincerely,
Thanking you,
Arnav Lohe
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