Thank you for your reply!
Ilona ________________________________________ Lähettäjä: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] käyttäjän Bruce Fischl [fischl@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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
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