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: > External Email - Use Caution > > 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. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
