Sorry, I meant to answer another email...
Roberto > 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 > -- 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
