Thank you for your reply! Ilona ________________________________________ Lähettäjä: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] käyttäjän Bruce Fischl [fis...@nmr.mgh.harvard.edu] puolesta Lähetetty: 6. syyskuuta 2017 16:56 Vastaanottaja: Freesurfer support list Aihe: Re: [Freesurfer] wm topological defects
Hi Ilona yes, you only need to edit the wm in regions where inaccuracies in the wm.mgz are making the surfaces inaccurate cheers Bruce On Wed, 6 Sep 2017, Ruotsalainen, Ilona wrote: > Dear experts, > > I would have a follow up question for this thread. > > I have erased voxels from areas which are not white matter, but classified as > white matter in wm.mgz (such as blood vessels and tissue outside brain that > clearly are not white matter) or filled "holes" in wm.mgz (example in > pictures hole_wm1 and hole_wm2). I have done this even the surfaces look > accurate. After checking the aparc.stats-file there are sometimes quite > large changes in volumes of specific areas (even over 10%). So my question is > following. Should I only fix those parts in wm.mgz in which the ?h.pial > and/or ?h.white are not accurate and leave other parts of wm.mgz unfixed even > the mask clearly includes regions that are not white matter? I have read the > tutorials, but I'm still not certain about this issue. > > Thank you, > Ilona Ruotsalainen > > > > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: tiistai 4. heinäkuuta 2017 20:43 > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] wm topological defects > > Hi Manuel > > you should examine the ?h.white and ?h.pial for accuracy, and only use the > .nofix surfaces if you are trying to figure out why the white/pial are not as > accurate as you would like Bruce > > > On Tue, 4 Jul 2017, Manuel Delgado wrote: > >> Dear all: >> Regarding wm edits, it is shown in the tutorial how to proceed with "holes" >> that appear in the smoothwm.nofix. However, those holes do not >> necessarily affect the wm matter surface. So is it recommendable to >> check if holes in the smoothwm.nofix surface affect the real wm >> surface before correcting them? And, what is the purpose of the >> smoothwm.nofix, is it used for other issues? >> Thank you >> >> -- >> Manuel Delgado Alvarado, MD >> >> Predoctoral Researcher >> Neuroimaging Unit, IDIVAL >> [LogoIDIVAL.PNG?ver=2015-10-14-180234-000] >> Avda. Cardenal Herrera Oria s/n >> 39011 Santander, Spain >> >> >> > _______________________________________________ > 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
