Is there a tool to crop 3D brain volumes efficiently across multiple subjects

The large amount of empty space in my T1w volumes is giving me problem with freesurfer’s recon-all. So i’ll have to crop out the empty space as shown in the screenshot above. i’m wondering if there is an easier and more efficient method to crop these T1w volumes across multiple subjects?

Hi @gerardyu,

Two examples, probably more available:
https://mrtrix.readthedocs.io/en/3.0.4/reference/commands/mrgrid.html?highlight=mrcrop#pad-and-crop-options-no-image-interpolation-is-performed-header-transformation-is-adjusted

Best,
Steven

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