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. > >
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