Hi Jennifer, thank you again for your answer. This helped a lot!
Have a nice day! Best Paul Zitat von "Kriegel, Jennifer Lynn Sarai" <jlk130...@utdallas.edu>: > 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 > -- 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
