Ed, Hi, no there is not an option to switch them. The nu correct stage in 5.1 needs the talairach to run.
However, if your intent is to get a better talairach result by using the nu corrected input (as it did prior to v5.1), then you can do the following: recon-all -s subjid -motioncor -talairach -nuintensitycor then run: recon-all -s subjid -all -talairach-nu -clean-tal on the second run, it will use the nu.mgz in the talairach stage. Note that in the next version, v5.2, one iteration of nu_correct will be run prior to the talairach stage to use as input to the talairach stage, in order to get the better talairach results that people were seeing prior to v5.1. it will still run the current nu_correct stage to create nu.mgz (the nu used in talairach gets discarded). Nick On Mon, 2012-04-16 at 09:10 +0200, Ed Gronenschild wrote: > Hi, > > As of version 5.1 the Talairach stage precedes the nu-correction stage. > Is there an option or possibility to switch this order? > > Cheers, > Ed > _______________________________________________ > 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 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.
