External Email - Use Caution Got it, thank you for your help, Doug! -- 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: Monday, August 05, 2019 1:57 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] WM surface including too much gray matter In general, this would be handled by manual editing, but we are looking into whether a parameter adjustment can be used instead. The problem is that adjustments often result in underlabeling in other places. On 8/5/2019 1:53 PM, Brian Biekman wrote: > External Email - Use Caution > > Hi Doug, I just wanted to follow up on this last message I sent. What do you > suggest that we do about the spots where the white surface "leaks" in the > gray surface? > -- > 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: Brian Biekman > Sent: Tuesday, July 30, 2019 12:51 PM > To: Freesurfer support list > Subject: RE: [Freesurfer] WM surface including too much gray matter > > 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 >>> >>> >> _______________________________________________ >> 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 _______________________________________________ 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
