Hi Paul, My apologies - what I meant was PRIOR to running skull strip, that freesurfer mistakenly made my surfaces the dura and pial, which meant removing the dura was a corrective issue. A prior member of my lab, and others whom I have asked advice on freesurfer said the same thing - the dura actually interferes with your measures of brain. From the attachment you sent, nothing vital is being removed. I wouldn't worry about re-running it.
Best, Jennifer -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Paul Schauer Sent: Tuesday, June 30, 2015 7:49 AM To: Freesurfer support list Subject: Re: [Freesurfer] Skullstrip problems Hi Jennifer, thank you for your speedy answer.:-) Unfortunately I didn't understand all of it. The problems with the skullstrip did not (!) affect any of the surfaces in this case and no grey or white matter was cut out. What I was interested in is whether any other measures might be affected (except for the dura volume which I am not interested in). Especially whether it affects any of the volume-based analysis? To put it in a nutshell: Would you rerun the skullstrip with different watershed-parameters so as to prevent the skullstrip to be overly aggressive and "bite" these chunks out of the dura? Or would you leave it like it is? Thanks again! Best, Paul Quoting "Kriegel, Jennifer Lynn Sarai" <jlk130...@utdallas.edu>: > Hi Paul, > >> From my understanding, that's the stuff that can interfere with your >> surfaces. I've run g-cut skullstrip on volumes where the surface of >> the pial is seen as the white matter, and the dura is seen as the >> cortical/pial surface. I think in terms of cortical measures, such as >> cortical thickness, you're better off having run the stripping. I >> could be wrong, but unless you're interested specifically in the dura >> volume as well, it's not going to affect your brain volume measure. > > Best regards, > Jennifer Kriegel > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Paul > Schauer > Sent: Tuesday, June 30, 2015 7:03 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: [Freesurfer] Skullstrip problems > > Hi all, > > I ran the normal recon-all -i... -s... -all on a couple of subjects > and I realized that the skullstrip often seems to "bite" a chunk out > of the meninges (see attached screenshot). Whilst the wm- and > pial-surfaces seem unaffected and no grey or white matter seems to be > missing I didn't bother too much. But I was asking myself whether > these missing chunks did not indirectly affect these measures? Or any > other measures such as the whole brain volume? > > Any help would be greatly appreciated! > > Best, > > Paul > > -- > > Paul Schauer, M.Sc. Psychologie > Biological Psychology & Neuropsychology Faculty of Psychology & Human > Movement Science | University of Hamburg Von-Melle-Park 11 | Room 204 > | 20146 Hamburg, Germany > +49 (0)40 42838 4573 > > _______________________________________________ > 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. > > -- Paul Schauer, M.Sc. Psychologie Biological Psychology & Neuropsychology Faculty of Psychology & Human Movement Science | University of Hamburg Von-Melle-Park 11 | Room 204 | 20146 Hamburg, Germany +49 (0)40 42838 4573 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
