Nick, Thank you. This recon-all script resolved my problems. I really appreciate this post. -
Josh - Joshua Lee UC Davis On Tue, Apr 17, 2012 at 7:51 AM, Nick Schmansky <ni...@nmr.mgh.harvard.edu> wrote: > 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. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
