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
> > >
> > >
> >
> > _______________________________________________
> > 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
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.
