External Email - Use Caution
Hi Doug,
Yes that is exactly the concern that we have.
--
Brian Biekman
Graduate Student, University of Houston
Clinical Psychology, Neuropsychology Concentration
Laboratory of Early Experience and Development (LEED)
bdbiek...@uh.edu
brian.biek...@times.uh.edu
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greve, Douglas N.,Ph.D.
[dgr...@mgh.harvard.edu]
Sent: Tuesday, July 30, 2019 10:55 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] WM surface including too much gray matter
Hi Brian, I'm looking at your data. For the most part, it looks like the
surface placement is accurate. I do find a few places where the white
surface "leaks" into the cortex like in the attached picture just to the
left of the cursor. Is this the type of thing you are worried about? If
not, please send a pic of your concern.
doug
On 7/29/19 11:47 AM, Brian Biekman wrote:
> External Email - Use Caution
>
> Hi Bruce, I uploaded a subject's output via the Martinos Center File Drop.
> Let me know if there is anything else you need.
> --
> Brian Biekman
> Graduate Student, University of Houston
> Clinical Psychology, Neuropsychology Concentration
> Laboratory of Early Experience and Development (LEED)
> bdbiek...@uh.edu
> brian.biek...@times.uh.edu
>
> ________________________________________
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, July 29, 2019 9:29 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] WM surface including too much gray matter
>
> Hi Brian
>
> usually this is fixable by changing some default parameters in recon-all.
> You can try this yourself (the intensity bounds used in mri_segment and
> mris_make_surfaces - look at the help), or you can upload a subject
> to our ftp site and we can recommend some
>
> cheers
> Bruce
>
> On Sun, 28 Jul 2019, Brian Biekman wrote:
>
>> External Email - Use Caution
>>
>> To whom it may concern:
>> I'm dealing with an issue in my subjects' recon-all output where the
>> white matter
>> surface extends into the gray matter, especially in the parietal and
>> posterior temporal
>> regions. This is caused by the wm.mgz including too much gray matter. This
>> issue occurs to
>> some degree in every subject's scans. This can be fixed with extensive wm
>> volume edits but
>> since this appears to be a systematic problem, I wanted to find a solution
>> that could be
>> applied to every subject, possibly in the recon-all pipeline. I've tried
>> using an expert
>> parameters 2 different ways to no avail. I've changed the -wlo values in
>> mri_segment but it
>> removes wm voxels in the temporal lobe from the wm.mgz surface. I've tried
>> adding the
>> -prune and -gentle flags to mri_normalize but that appears to make the
>> problem worse. Is
>> there a better approach to try? If necessary, I can send a subject's
>> recon-all output.
>>
>> --
>> Brian Biekman Graduate Student, University of Houston
>> Clinical Psychology, Neuropsychology Concentration
>> Laboratory of Early Experience and Development (LEED)
>> bdbiek...@uh.edu
>> brian.biek...@times.uh.edu
>>
>>
>
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