Bruce, If I understand you correctly, you’re saying I should tweak my expert options? Should I further change the limits, how so? You previously advised that I not adjust the -p threshold, is this still the case?
Basically, I’m still confused after your response. Sorry to bother, Jon On Nov 4, 2013, at 12:52 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Jon > > this is almost certainly due to a topological defect. Improving the > segmentation quality can frequently reduce the # of defects and get rid of > big ones, so if you find that the wm segmentation isn't as visually > accurate as is usually the case, using expert opts to improve its quality > may also get rid of the problem you are seeing > > cheers > Bruce > > > > On Mon, 4 Nov 2013, Jonathan Holt wrote: > >> Hey Louis, >> >> thanks for your response. It?s actually a bit different, in my case an >> entire sulcus, including the empty space within it has been segmented and >> surfaced as white matter. I?m trying to reduce the WM surface such that the >> empty space is not included. I?ve tried removing segmentation manually and >> running >> >> recon-all -autorecon2-noaseg -subjid <SUBJID> >> >> that doesn?t work, the empty space is simply resegmented and the surface >> doesn?t change.. I should note that this has worked for me in the past on >> some brains. >> >> Since there are no WM voxels to remove I didn?t bother with removing any of >> them. I ran recon-all -autorecon2 -autorecon3 -expert expert.opts -s >> <subjID> with mri_segment -wlo/-ghi/-whi all reduced by 10 and that hasn?t >> worked? >> >> I?m open for ideas. >> >> I should also note that this problem is not an issue in rh.orig.nofix >> >> (sorry about duplicate email, Louis) >> >> >> On Nov 4, 2013, at 11:30 AM, Louis Nicholas Vinke >> <vi...@nmr.mgh.harvard.edu> wrote: >> >>> Hi Jon, >>> The limit numbers correspond to voxel intensities in the brainmask.mgz. I >>> believe you will want a lower number for the -wlo/-wm_low flag to make the >>> wm surf extend further out, assuming that the wm voxels that are not being >>> captured by the surface is hypo-intense (<< 110). >>> -Louis >>> >>> On Thu, 31 Oct 2013, Jonathan Holt wrote: >>> >>>> HI experts, >>>> >>>> I?m wondering how these limits work, and whether the limit numbers >>>> indicate voxel intensity. If I wanted WM to be segmented more aggressively >>>> would I plug in a higher number or a lower number? >>>> >>>> Jon >>>> _______________________________________________ >>>> 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. >> >> >> _______________________________________________ >> 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
