Hi Eric, I think the easiest way to avoid N3 is to simply add the -nonuintensitycor flag to recon-all and create a symbolic link from nu.mgz to orig.mgz it as otherwise recon-all will end with an error. I'm not sure about the nomenclature of the T2 file, but you should do the same.
Best, Falk -----Ursprüngliche Nachricht----- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Dienstag, 20. Februar 2018 17:17 An: Freesurfer support list Betreff: Re: [Freesurfer] How would one run N4 bias corrected T1 and T2 images through FreeSurfer v6.0 REPOST Hi Eric the easiest thing would be to give your n4-corrected image to recon-all and let it run n3 on it. N3 is pretty gentle so I would think this would be fine. The alternative would be harder I think cheers Bruce On Tue, 20 Feb 2018, Axelson, Eric D wrote: > > > > We are using N4 to correct some large inhomogeneities in some samples > and wanted to insert these images into the v6.0 pipeline and bypass > the N3 bias correction done within. What would be the correct > sequence of freesurfer commands to achieve this? Thanks > > > > Eric > > > > > > ______________________________________________________________________ > ______________________________ > Notice: This UI Health Care e-mail (including attachments) is covered > by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and > is intended only for the use of the individual or entity to which it > is addressed, and may contain information that is privileged, > confidential, and exempt from disclosure under applicable law. If you > are not the intended recipient, any dissemination, distribution or > copying of this communication is strictly prohibited. If you have > received this communication in error, please notify the sender immediately > and delete or destroy all copies of the original message and attachments > thereto. Email sent to or from UI Health Care may be retained as required by > law or regulation. Thank you. > > ______________________________________________________________________ > ______________________________ > > _______________________________________________ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
