Thanks, I'll try that. Will I then need to redo all steps fromm -ccseg onwards if I want a correct wmparc at the end, or can I safely skip some? For instance, I could do -ccseg -cortribbon -cortparc -aparc2aseg -wmparc?
Best, Kristine > Kristine, > You should be able to use -ccseg which occurs after the aseg is created in > -autorecon2. First, you will need to copy your aseg.mgz to aseg.auto.mgz > as this is the file that -ccseg will work on (in the dev version of FS, it > uses the aseg.mgz). > Allison > > > On Tue, 22 Jan 2008 > [EMAIL PROTECTED] wrote: > >> Thanks! >> >> The MRI_cc works fine. It's just that I want to use the entire wmparc, >> and >> I worry that it may be skewed when the cc is not in there. The cingulate >> parcellations look a little off. Do you think there's any step in >> -autorecon2 (before -cortribbon) after the aseg I might try to start >> reprocessing to fix this? >> >> Best, >> >> Kristine >> >>> Hi Kristine, >>> >>> you can just run mri_cc directly if you want: >>> >>> mri_cc -o aseg_with_cc.mgz $subject >>> >>> cheers, >>> Bruce >>> On Tue, 22 Jan 2008 >>> [EMAIL PROTECTED] wrote: >>> >>>> Hi >>>> >>>> I have a dataset originally processed with the Autumn 2005 FS version >>>> (2.2?). I know need wm segs, and in order to get this, I've tried to >>>> run >>>> >>>> -cortribbon -cortparc -cortparc2 -aparc2aseg -wmparc >>>> >>>> But the cc doesn't get labeled in the cortparc, and consequently (?) >>>> not >>>> in the wmparc either. >>>> >>>> I've also tried to rerun all of -autorecon3, but w/o difference. >>>> >>>> When rerunning recon-all -all, it gets fixed, but I would like to keep >>>> as >>>> much as possible as is, since I did lots of edits due to a temporal >>>> bias >>>> field problem. I've edited the asegs in some instances, and that is >>>> not >>>> kept by default. >>>> >>>> Grateful for tips on how far down in the processing stream I need to >>>> go >>>> to >>>> get correct wmparcs w/cc. >>>> >>>> Thanks, >>>> >>>> Kristine >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> [email protected] >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
