Hello, It is working fine for me
regards Roberto On Vie, 24 de Abril de 2009, 10:38 am, Kathryn Devaney dijo: > Hi Bruce, > > Thanks! The lh.orig.nofix surface follows the white matter perfectly, > but the lh.orig surface does not. So I suspect that the topology fixing > step is creating this problem. > > However, when I load lh.defect_labels this area is not marked as a > defect, nor are there any major defects labeled nearby (see > http://nmr.mgh.harvard.edu/~kdevaney/monkrecon/lh_wm_defect.tif for > image). Does this mean that the topology fixing is not editing this area? > > If it is the topology fixing, are there parameters of mris_fix_topology, > mris_euler_number or mris_remove_intersection that I can alter in order > to fix this problem, without wreaking havoc in other areas? Or any > other suggestions would be much appreciated! > > Best, > Katie > > Bruce Fischl wrote: >> Hi Katie, >> >> try looking at the lh.orig.nofix and lh.inflated.nofix surfaces to see >> if you can see the defect. >> >> cheers, >> Bruce >> On Thu, 23 Apr 2009, Kathryn Devaney wrote: >> >>> Hi Bruce & surfers, >>> >>> That's what I thought initially, but then I did edit the wm.mgz to >>> remove topological defects, and re-ran the reconstruction from the >>> 'fill' step, and this problem remains. I can't find a nearby defect >>> in the wm.mgz volume to edit, but maybe there is something that isn't >>> obvious to me. >>> >>> I put up coronal, axial, and sagittal views of the problem area & >>> neighborhood up at: >>> >>> http://nmr.mgh.harvard.edu/~kdevaney/monkrecon/coronal_wm_defect.tif >>> http://nmr.mgh.harvard.edu/~kdevaney/monkrecon/horizontal_wm_defect.tif >>> http://nmr.mgh.harvard.edu/~kdevaney/monkrecon/sagittal_wm_defect.tif >>> >>> Maybe there is a defect around this area which I'm not seeing? >>> Otherwise, is there something else that I can do? Also, let me know >>> if you'd like to check out the data, and I can put it somewhere >>> accessible. >>> >>> Thanks! >>> Katie >>> >>> >>> >>> Bruce Fischl wrote: >>>> Hi Katie, >>>> >>>> looks like an incorrectly fixed topological defect. You need to edit >>>> the wm.mgz to remove the defect and rerun autorecon2-wm >>>> >>>> cheers, >>>> Bruce >>>> On Wed, 22 Apr 2009, Kathryn Devaney wrote: >>>> >>>>> Hello freesurfers, >>>>> >>>>> I am running a reconstruction of a macaque in stabe4, and I am >>>>> having a >>>>> problem with the smooth white matter surface not following the wm >>>>> boundary >>>>> in the wm.mgz volume (please see attached for examples in the wm >>>>> and T1 >>>>> volumes). >>>>> >>>>> The non-wm area included in the surface was never part of the wm >>>>> volume, >>>>> but I edited the other defects in wm.mgz and re-ran fill, tessellate, >>>>> smooth1, inflate1, qsphere, fix, finalsurfs, smooth2, amd inflate2. >>>>> Unsurprisingly, this problem persisted. >>>>> >>>>> Is there anything that I can do to fix this? >>>>> >>>>> Thanks! >>>>> Katie >>>>> >>>>> >>>> >>>> >>> >>> >>> >>> >> >> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Roberto Roiz Santiáñez Laboratorio de Neuroimagen en Psiquiatría Hospital Universitario Marqués de Valdecilla Santander, España Tel: +34 942202520 Ext: 73958 rr...@humv.es _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
