Hi John,

I don't think there's an FSL command to do this, but it is easily done in Python, using numpy and nibabel:

import nibabel as nib

import numpy as np

maskimg = nib.load('/path/to/my_3D_mask.nii.gz')

data = maskimg.get_data()

x, y, z = np.where(data == 0)

Cheers,

Paul

On Thu, Jul 31, 2014 at 11:43 AM, John McLean <[log in to unmask]> wrote:

Dear FSL users,

Is there a way using one or a couple of FSL commands to extract all the voxel co-ordinates for a given binary mask?

I thought for a second fslstats -x might do it, as I want all the co-ordinates for voxels of intensity 1 (the max intensity), but it just outputs a single voxel, which I guess is what it really is intended to do.

Thanks
John