Hi Lucia,

The '-roi' option to fslmaths doesn't extract an ROI - it sets all voxels outside of the ROI to zero.

You can accomplish what you want with fslroi; for example:

fslroi <input> <output> 0 90 89 90 0 90

Cheers,

Paul

On Sun, Feb 1, 2015 at 11:44 PM, Lucia M Li <[log in to unmask]> wrote:

Dear FSL users & experts,

I'm hoping someone will be able to help me with a simple query.

I've trying to slice an image so that I get 2D planes, along the y-axis. I've tried fslslice but that only slices them in the z-axis. Is there an option to use fslslice to slice the image in the y-plane?

As a side note: an alternative I've tried is to trim my image into slices by using "fslmaths <input> -roi 0 90 89 90 0 90 0 1 <output>" (where '89 90' are the y-co-ordinates as I'm trying to get a single-voxel thick image), however, this gives me an image that is definitely more than 1 voxel thick in the y-axis; indeed, the image appears to extend from voxel 89 to the edge of the image.

If anyone can help by suggesting how to make fslslice do it in the y-axis, or figure out why -roi is not working the way I need, or any other suggestions for how I can get these 2D images, I'd be really grateful!

Kind regards,
Lucia