Also, quick question . . . How exactly do you run a recon from scratch without nifti images? I’d always delete the directory and restart with mri_convert -i …
Jon On Nov 5, 2013, at 10:40 AM, Louis Nicholas Vinke <vi...@nmr.mgh.harvard.edu> wrote: > Hi Jon, > I see the area you are talking about. I'm rerunning the recon from scratch > to start with a clean copy since the case you sent has been rerun multiple > times and there are a bunch of control points. The fact that the > rh.orig.nofix looks good makes me optimistic that this can be fixed. > > I'll get back to you soon. > -Louis > > On Mon, 4 Nov 2013, Louis Nicholas Vinke wrote: > >> Got it, I'll take a look. >> >> On Mon, 4 Nov 2013, Jonathan Holt wrote: >> >>> OK, >>> >>> been uploaded as JONbrain.tar >>> >>> Please let me know! >>> >>> >>> On Nov 4, 2013, at 1:15 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: >>> >>>> 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 >>> >>> >>> >>> >> _______________________________________________ >> 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
