Hard to fix if that is the receive field and you don't have another image like a T2w to remove it with. Perhaps mri_normalize can be tuned to improve this with expert options as the white matter that is being correctly segmented appears to be darker as well.
Peace, Matt. On 5/17/13 9:30 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >Hi Caspar > >yes, that might help. There are expert opts for this. Sorry, I have >almost no experience analyzing monkey brains at .5mm, so I'm really not >sure what to advise you. Perhaps one of the other people on list who have >done a bunch can comment? >Bruce >On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote: > >> Hi Bruce, >> I tried adding control points in the white matter in that region, >> however, it does not seem to fix the issue. Also, the brainmask.mgz >> does not seem to exclude this part of the brain, so that is not the >> problem either. >> I am attaching another screenshot (horizontal 119) to illustrate the >>problem. >> White matter pixel values range from the high 80ies to >100 in this >>area. >> Included grey matter pixel values are in the low 80ies. >> Excluded grey matter pixel values range from the low 60ies to low 70ies. >> >> Would it make sense to re-run mri_segment with a different threshold? >> Thanks, Caspar >> >> >> >> 2013/5/16 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >>> Hi Caspar >>> >>> is the closest white matter captured by the white surface? What is the >>> intensity of voxels there? If < 110 you could try putting control >>>points in >>> them and seeing if that helps (that is, in the closest voxels that are >>> entirely white matter). >>> >>> >>> Bruce >>> >>> On Thu, 16 May 2013, Caspar M. Schwiedrzik wrote: >>> >>>> Hi Bruce, >>>> ok. >>>> But in theory, what would you recommend to get around the darkening >>>> issue? Unfortunately, I do not have a field map available for this >>>> data set. >>>> Or should I not expect to get a pial surface in this area since the >>>> white matter is not discernable? >>>> There are five slices without clear white matter (original voxel size >>>> 0.5x0.5x0.5 mm). >>>> Thanks, Caspar >>>> >>>> 2013/5/16 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >>>>> >>>>> Hi Caspar >>>>> >>>>> if it's primate I don't think I'm going to be able to help - you'll >>>>>need >>>>> someone more familiar with primate anatomy >>>>> >>>>> sorry >>>>> Bruce >>>>> On Thu, 16 May 2013, Caspar M. >>>>> Schwiedrzik wrote: >>>>> >>>>>> Hi Bruce and Matt, >>>>>> yes, it is primate data. I just dropped an archive on your FTP >>>>>>server >>>>>> in transfer/incoming. >>>>>> Thanks! >>>>>> Caspar >>>>>> >>>>>> 2013/5/16 Matt Glasser <m...@ma-tea.com>: >>>>>>> >>>>>>> Is the brain extraction removing that part of the brain? Do you >>>>>>>know >>>>>>> where the OFC ends and olfactory bulb begins? >>>>>>> >>>>>>> Peace, >>>>>>> >>>>>>> Matt. >>>>>>> >>>>>>> On 5/16/13 11:43 AM, "Caspar M. Schwiedrzik" >>>>>>> <cschwie...@mail.rockefeller.edu> wrote: >>>>>>> >>>>>>>> Hi! >>>>>>>> I am failing to get a proper pial surface in orbitofrontal cortex. >>>>>>>> See attached screenshot. >>>>>>>> This is NHP data, processed with version 4.5. >>>>>>>> I am not sure how to proceed here, as there is no clear with >>>>>>>>matter. >>>>>>>> Any advice would be appreciated. >>>>>>>> Thanks! >>>>>>>> Caspar >>>>>>>> _______________________________________________ >>>>>>>> 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
