wait it was Nick that told me to use this a while back when I had tal-check failures...I just posted about my current issues where I discuss my recent experiences with a high rate of talairach failures in the current version. - Josh
On Tue, Apr 17, 2012 at 12:49 PM, Joshua Lee <jki...@ucdavis.edu> wrote: > I was told to use this recon-all flag and my talairach problem went away: > -use-mritotal > - > Josh > > 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 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.
