Mrgrid/3dresample image cropped

OK, there’s a couple of ways I could interpret that:

  1. you want to register an image to MNI space so that the anatomy in your image maps onto the anatomy of the MNI template.

  2. you want the voxel grid of your image to match that of the MNI template, in terms of voxel size, image dimensions, orientation of the axes, etc.

Note that these are essentially independent concepts. You can have co-registered data defined on a completely different voxel grid, but since we can figure the real-space position of each voxel (via the transform matrix), equivalent locations can overlap in real-space even if the voxel grid is completely different. Likewise, two images can be defined on the same voxel grid, but without alignment of the anatomy in these images. See this wiki post for details.

Your original question implies interpretation 2 only. If that’s all you need is to regrid to match the reference image, then the second example I provided should do that for you:

 mrgrid original.nii regrid -template master.mif resampled.nii

However, if you need to register to MNI space (i.e interpretation 1), then that’s an altogether different problem…