Hi experts, A quick question: I installed FS 5.1 a month ago, should I replace with this recon-all file and run it with flag -clean-tal in the future? why the steps have to be switched?
Thanks! 2012-04-19 Chunhui Chen _________________ State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875 发件人： Nick Schmansky 发送时间： 2012-04-17 22:53:40 收件人： Ed Gronenschild 抄送： freesurfer 主题： Re: [Freesurfer] How to switch order of Talairach and nu-correctionstages in recon-all Ed, email probably trounced it. recon-all is a text file. attached is a gzipped version. use gunzip to unpack it. N. On Tue, 2012-04-17 at 16:45 +0200, Ed Gronenschild wrote: > 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 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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