It was version 4.50. I had to walk over to the other room to find out. ;) In any case, I achieved good results by including the use-mritotal flag on the current version.
Josh On Tue, Apr 17, 2012 at 12:00 PM, Alan Francis <alandarkene...@gmail.com>wrote: > Hi Joshua: > > What version of FS 4 did you use? > > best, > > Alan > > On Tue, Apr 17, 2012 at 2:56 PM, Joshua Lee <jki...@ucdavis.edu> wrote: > >> Hi All, >> >> I thought I'd share my recent experiences with the newest Freesurfer v. >> 5.10 and subcortical segmentation. >> >> I ran a large sample of brains using the default stream of Freesurfer v. >> 5.10. The resulting hippocampal segmentations were extremely poor, yet on >> the same sample of brains Freesurfer v. 4.xx did quite well. >> >> Using tkregister, we discovered that the hippocampus is not being >> registered well enough. Nick Schmansky one wrote in another post on this >> list-serve that one difference between versions is that "talairach.xfm >> is needed to compute nu.mgz, [and] talairach stage needs to precede the >> nu_correct stage" He suggested using -use-mritotal in the recon-all command >> to overcome tal-check failures. >> >> I decided to try using -use-mritotal with this sample of my data, despite >> tal-check not failing in the default stream. Resulting segmentations were >> now both realistic and accurate, and near identical to those produced by >> Freesurfer version 4.xx. >> >> Have others experienced poor subcortical segmentation with current >> version of Freesurfer? I should note, that I am having this problem on >> another sample of MPRages of very good quality. I am concerned that future >> versions of Freesurfer will limit use of the old stream to situations in >> which tal-check fails. >> >> Thanks you all. >> Sincerely, >> >> Joshua Lee >> >> >> _______________________________________________ >> 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.