mri_segment \ -v \ -fillv \ -fillbg \ -wlo 104 \ -ghi 118 \ -whi 140 \ -n 4 \ -keep \ brain.mgz wm.mgz
The pial surface in the rest of the brain is ok, it is only the orbitofrontal/piriform cortex that is problematic. I now wanted to add -p 0.7.
Caspar
2013/5/17 Bruce Fischl fischl@nmr.mgh.harvard.edu:
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 matt@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" fischl@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 fischl@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 fischl@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 matt@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" >>>> cschwiedrz@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 > > > > >