crop option not cropping image tightly

[soichih]

I have an input image that looks like this.

If I pass it through ACPC alignment app, it crops nicely on X and Z axis but leaves good chunk of empty space for Y axis.

I believe this causes Freesurfer to fail with following error message.

****************************************
ERROR! FOV=318.000 > 256
Include the flag -cw256 with recon-all!
Inspect orig.mgz to ensure the head is fully visible.
****************************************

Is there something we can do to make the image crop more of the white space on Y?

[kitchell]

I think robustfov (which is what we are using for crop) only focuses on the z direction:

Reduce FOV of image to remove lower head and neck.

Usage:
robustfov [options] -i -r
robustfov [options] -i

Compulsory arguments (You MUST set one or more of):
-i input filename

Optional arguments (You may optionally specify one or more of):
-b size of brain in z-dimension (default 170mm)
-m matrix output name (roi to full fov)
-r ROI volume output name
--debug turn on debugging output
-v,--verbose switch on diagnostic messages
-h,--help display this message

We could look into other cropping options