When I try to specify a different threshold using -p, mri_segment reads in the threshold as the input volume. I tried specifying the input with -i (as explained here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18826.html), but now it does not recognize the -i flag. Caspar
2013/5/17 Matt Glasser <m...@ma-tea.com>: > 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
