we got it. I'm out of town but will try to look at it soon cheers Bruce On Mon, 29 Jul 2019, 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
