what is your command line? You are probably better off setting gray_hi, gray_low, wm_hi, wm_low, etc... Bruce On Fri, 17 May 2013, Caspar M. Schwiedrzik wrote:
> 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
