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
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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.
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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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@nmr.mgh.harvard.edu
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Axelson, Eric D -
Bruce Fischl -
Falk Lüsebrink