Thanks Douglas. Just one more quick question: will -nonuintensitycor work if I set the -3T flag? As far as I know, -3T changes some parameters of the N3 correction and makes use of Schwarz atlas. I was wondering whether this flag interferes with -nonuintensitycor.
El El sáb, 3 feb 2018 a las 21:01, Douglas Greve <gr...@nmr.mgh.harvard.edu> escribió: > If you want to just run the recon-all pipeline without using n3, you'll > have to do something else. You can copy orig.mgz to nu.mgz (or create a > symbolic link, which is probably better), then run with -nonuintensitycor > > On 1/29/18 7:14 PM, Alexis Moscoso wrote: > > Hello Freesurfer developers, > > I’m trying to run a recon-all on ADNI T1 images. Since these data have > already been corrected with the N3 correction, I want to turn off N3 > correction in the recon-all process so I added -nonuintensitycor after > -all. However, when I run it, I get an error during the normalization step > since it no nu.mgz file is generated and cannot be found by mri_normalize. > I’d like to know how to do the everything except the N3 correction. > > 1) Freesurfer version: 6.0.0 > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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 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. >
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