Hi Jon maybe you should upload your data and we'll take a look
cheers Bruce On Mon, 4 Nov 2013, Jonathan Holt wrote: > 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
