glad to hear it worked. it can be tricky getting the stream to work in a 'one size fits all' kind of way.
n. On Thu, 2012-04-19 at 16:45 -0700, Joshua Lee wrote: > 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
