can you upload a dataset with this problem and tell us exactly (what voxel coords) you see them at? On Thu, 27 Aug 2015, fmri wrote:
> processing attempt on latest dev 8/15 did not resolve the subcortical > annotation within WM tracks, the unknown voxels continue to persist. > > > On Aug 26, 2015, at 7:06 AM, Bruce Fischl wrote: > >> it would fix the hippocampal problems and maybe the cortical ones as well >> >> cheers >> Bruce >> On >> Tue, 25 Aug 2015, fmri wrote: >> >>> I have already processed 88 subjects in this version, >>> >>> would it matter if I process or re-process subjects with another version? >>> >>> >>> On Aug 25, 2015, at 3:44 PM, Bruce Fischl wrote: >>> >>>> that's probably the reason the hippocampus (and maybe cortex) doesn't >>>> look that good. Try grabbing a new dev version and see if it improves. >>>> Doug: has the new atlas been put into the dev recon-all? I think it has, >>>> hasn't it? >>>> >>>> On Tue, 25 Aug 2015, fmri wrote: >>>> >>>>> Version >>>>> >>>>> freesurfer-Darwin-lion-dev-20150701 >>>>> >>>>> >>>>> On Aug 25, 2015, at 3:11 PM, Bruce Fischl wrote: >>>>> >>>>>> Hi Joe >>>>>> >>>>>> what version are you using? That looks a lot like a bug I fixed a month >>>>>> or two ago (the hippocampal stuff). The cortex I'm not so sure about. >>>>>> Some >>>>>> of it might be dura >>>>>> cheers >>>>>> Bruce >>>>>> >>>>>> >>>>>> On Tue, 25 Aug 2015, fmri wrote: >>>>>> >>>>>>> Dear Freesurfer experts, >>>>>>> >>>>>>> on aparc+aseg.mgz there is Hippocampus labeled over WM regions. >>>>>>> >>>>>>> There are cortex "Unknown" voxels that persist through out all of our >>>>>>> scans. >>>>>>> >>>>>>> What files should be edited and what recons should be processed after >>>>>>> edits to get a complete freesurfer data set. >>>>>>> >>>>>>> Thanks >>>>>>> >>>>>>> Joe >>>>>> _______________________________________________ >>>>>> 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 >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
