If you are going to pass it the UNI, then you will probably need to mask out the stuff outside of the head. One way to do this is to run samseg on the INV1 or INV2 (INV1 probably better), the run mri_mask uni.mgz seg.mgz uni.masked.mgz Then pass uni.masked.mgz to recon-all

On 8/2/2022 8:39 AM, Renew Andrade wrote:

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Dear community:

I need to run recon-all on some subjects with a MP2RAGE sequence. Can I do with any flag or directly -i “mp2rage”.

Best, Rene Andrade.

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