What should I erase? Sorry, I did mean to say I saw the surface errors overlaid on the volume, but couldn't discern any in the wm.mgz alone. It's 3D FLASH on a Vision 1.5T, TR/TE= 20/5.4 ms, flip=30 deg, 1 acquisition, 1x1x1 mm^3 voxels. Nothing fancy, maybe that's the problem...
-Derin > it looks like there is an (incorrect) connection in the wm.mgz from the > temporal lobe across the insula. The data also looks really noisy - what > is the acquisition? You'll need to erase some stuff form the wm.mgz I > think. > > On Fri, 13 Apr 2007, Derin Cobia wrote: > >> Here is a pic of the inflated.nofix, how do I know what to edit? I've >> checked the wm.mgz and it looks fine (at least I can't see any errors). >> Maybe I'm missing something, I've attached a shot of it as well. >> Thanks. >> >> -Derin >> >>> look at the ?h.inflated.nofix to see what is causing the defect, and >>> correct the wm.mgz manually to remove it. Jenni: can you point Derin at >>> the >>> appropriate wiki page? >>> >>> thanks, >>> Bruce >>> >>> >>> On Fri, 13 Apr 2007, Derin Cobia wrote: >>> >>>> The ?h.orig.nofix looks ok, meaning it follows the white-gray boundary >>>> appropriately. What should I try next? >>>> >>>> -Derin >>>> >>>>> this is probably a topology fixing problem. Look at the ?h.orig.nofix >>>>> and >>>>> see how it is >>>>> On Fri, 13 Apr 2007, Derin Cobia wrote: >>>>> >>>>>> Did you mean wm.mgz? It looks fine. The orig surface is not good >>>>>> either. >>>>>> Here's a pic. >>>>>> >>>>>> -Derin >>>>>> >>>>>> >>>>>> >>>>>>> Hi Derin, >>>>>>> >>>>>>> What does the orig surface look like? and the wm? Are those >>>>>>> correct? >>>>>>> >>>>>>> Jenni >>>>>>> >>>>>>> On Fri, 13 Apr 2007, Derin Cobia wrote: >>>>>>> >>>>>>>> I have two subjects where the white surface does not follow the >>>>>>>> gray-white >>>>>>>> gradient (see attached pic for example). Is there any way to fix >>>>>>>> this? >>>>>>>> I'm assuming it has to do with the limitations of my scan too >>>>>>>> (it's >>>>>>>> FLASH >>>>>>>> data). I'm running 3.0.4, thanks. >>>>>>>> >>>>>>>> -Derin >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> [EMAIL PROTECTED] >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> > _______________________________________________ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
