Hi Nick, It does not work properly, it only produces an error message, even with no option at all:
'nknown option: '- Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ...]. Ed On 17 Apr 2012, at 16:28, Nick Schmansky wrote: > a modified recon-all is attached. it will run nu_correct prior to the > talairach stage, as will be the case with v5.2. so you can just run: > > recon-all -s subjid -all -clean-tal > > n. > > > On Tue, 2012-04-17 at 08:58 +0200, Ed Gronenschild wrote: >> Hi Nick, >> >> The option -talairach-nu is not recognized in version v5.1.0. >> >> How can I proceed now? >> >> Ed >> >> On 16 Apr 2012, at 17:32, Nick Schmansky wrote: >> >>> 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 >>>> >>>> >>> >>> >>> >>> >>> 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. >> >> > > <recon-all> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
