then you need to put some control points in the white matter. 70 is way
too low
On Tue, 19 Apr 2016, Xiaomin Yue wrote:
The white matter in the anterior temporal lobe is around 70, the gray matter
is about 30. The number is read from brain.finalsurfs.mgz.
Xiaomin
> Date: Tue, 19 Apr 2016 09:29:50 -0400
> From: fis...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> CC: macar...@libero.it; yu...@hotmail.com
> Subject: Re: [Freesurfer] temporal lobe pial surface problem
>
> yes, you can do that for both mris_make_surfaces and mri_segment, but
> that will only help if you've removed the majority of the bias field. Is
> anterior temporal white matter near 110? If so, what is the gray matter
> at?
> On Tue, 19 Apr 2016, Falk Lüsebrink wrote:
>
> > Hi Xiaomin,
> > currently I don't have access to my notes, however, if I remember
correctly,
> > you can specify thresholds in mris_make_surfaces for consideration in
the
> > surface placement. This obviously works well only if the contrast
between
> > WM/GM/CSF is high enough.
> >
> > If you are interested and nobody jumps in giving you the according
flags,
> > let me know.
> >
> > Best,
> > Falk
> >
> >___________________________________________________________________________
_
> > Von: freesurfer-boun...@nmr.mgh.harvard.edu
> > [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Xiaomin Yue
> > [yu...@hotmail.com]
> > Gesendet: Dienstag, 19. April 2016 01:13
> > An: Freesurfer support list
> > Cc: macar...@libero.it
> > Betreff: Re: [Freesurfer] temporal lobe pial surface problem
> >
> > Hi Jon,
> > Thanks for your answers. There is gray-white contrast in the temporal
> > lobe, but same as you said that the gray-csf is low. Attached is a
> > screenshot. let's me know if you need more information.
> >
> > Xiaomin
> >
> > > Date: Mon, 18 Apr 2016 17:43:47 -0400
> > > From: j...@nmr.mgh.harvard.edu
> > > To: yu...@hotmail.com
> > > CC: freesurfer@nmr.mgh.harvard.edu; macar...@libero.it
> > > Subject: Re: [Freesurfer] temporal lobe pial surface problem
> > >
> > >
> > > hi Xiaomin,
> > >
> > > it is tough to say what might be causing the problem since a lot can
go
> > > wrong in the anterior temporal lobes at 7T. you say that your contrast
is
> > > low there? it is possible to have OK gray-white contrast but low
overall
> > > signal levels (so poor gray-CSF contrast) due to dielectric effects as
> > > bruce mentioned, which can make the MP2RAGE ratio images noisy in that
> > > region. also some adiabatic inversion pulses break down around the
> > > temporal poles due to the B0 inhomogeneity around the ear canals. if
you
> > > could send a screenshot we'd have a better chance at diagnosing the
> > > problem.
> > >
> > >
> > > -jon
> > >
> > >
> > >
> > >
> > > On Mon, 18 Apr 2016, Xiaomin Yue wrote:
> > >
> > > > Hi Jon Polimeni,
> > > > Do you have any suggestions on the following questions?
> > > > Thanks,Xiaomin
> > > >
> > > > Date: Fri, 15 Apr 2016 12:07:48 -0400
> > > > From: fis...@nmr.mgh.harvard.edu
> > > > To: freesurfer@nmr.mgh.harvard.edu
> > > > CC: macar...@libero.it; j...@nmr.mgh.harvard.edu
> > > > Subject: Re: [Freesurfer] temporal lobe pial surface problem
> > > >
> > > > Hi Xiaomin
> > > >
> > > > it's really hard to say without seeing more detail in your images.
Do
> > you
> > > > have contrast in the temporal lobe? Frequently it goes away at 7T
due to
> > > > dielectric effects. I'll cc Jon Polimeni who is our 7T (among other
> > > > things!) expert.
> > > >
> > > > cheers
> > > > Bruce
> > > >
> > > >
> > > > On Fri, 15 Apr 2016, Xiaomin Yue wrote:
> > > >
> > > > > Hi Bruce,
> > > > > I have done the recon-all (fs5.3) with the data collected from a
7T
> > scanner
> > > > > using MP2Rage. The recon went well without problem. But the the
> > temporal
> > > > > reconstruction looks clearly not correct (see attached). I tried
to
> > push
> > > > > the pial surface outside by editing the white matter evidenced in
the
> > > > > attached figures, but has no effect to genera correct pial
surface. I
> > do
> > > > > realize that the contrast is low in the anterior temporal lobes.
> > However, I
> > > > > am wondering if there are expert parameters I can use to push the
pial
> > > > > surface into the right place. If that isn't a option, can I use
some
> > other
> > > > > images collected during the MP2rage scan to help the segmentation
in
> > the
> > > > > anterior temporal lobe? Those extract scans are: inv1_nd,
inv1_phs_nd,
> > ,
> > > > > t1, inv2_nd, invs_phas_nd,
> > > > >
> > > > > thanks very much.
> > > > >
> > > > > Xiaomin
> > > > >
> > > > >
> > > >
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