Re: [Freesurfer] wm topological defects
Thank you for your reply! Ilona Lähettäjä: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] kyttjn 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
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 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.
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] wm topological defects
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* *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.
