OK. I will do it. Xiaomin Date: Tue, 19 Apr 2016 10:56:15 -0400 From: fis...@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
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 > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > 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.
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