> Date: Mon, 18 Apr 2016 17:43:47 -0400
> From: jonp@nmr.mgh.harvard.edu
> To: yuexm@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu; macara.p@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: fischl@nmr.mgh.harvard.edu
> > To: freesurfer@nmr.mgh.harvard.edu
> > CC: macara.p@libero.it; jonp@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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