Hi Sarah, Nick will be out of the office until next week. I would suggest just trying to run the default gcut and if you find you need to tweak it a bit, doing mri_gcut --help will describe the parameter (-T) that you can adjust for a cleaner skullstrip. You could also run -skullstrip a second time on already stripped data to potentially get a better skullstrip. Allison
On Wed, 20 Apr 2011, Sarah Whittle wrote: > Hi, > > Just wondering if Nick or one of the gcut developers could help me with > this issue? > > Regards, > > Sarah > > -----Original Message----- > From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] > Sent: Wednesday, 13 April 2011 9:43 AM > To: Sarah Whittle > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] hyperintense artifact causing problems for > segmentation > > I'll leave that for Nick, or one of the gcut developers. > > cheers > Bruce > On Wed, 13 Apr > 2011, Sarah Whittle wrote: > >> Thanks for your reply. I guess it could be dura. Here's a picture pre >> FreeSurfer with skull on. This is a particularly bad image. No, it's >> not gado enhanced. >> >> gcut is automatically implemented in version 5 isn't it?? Would you >> suggest altering the parameters if the default doesn't help and if so, >> what would you suggest? >> >> Regards, >> >> Sarah. >> >> -----Original Message----- >> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] >> Sent: Tuesday, 12 April 2011 10:24 PM >> To: Sarah Whittle >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] hyperintense artifact causing problems for >> segmentation >> >> wow, that is noisy. Looks like the bright ring is dura. This isn't >> gado enhanced, is it? You could try using the gcut stuff >> >> On Tue, 12 Apr 2011, Sarah Whittle wrote: >> >>> Hi, >>> >>> >>> >>> I'm working with some poor quality images and having a lot of trouble >>> with FreeSurfer segmentation. The main issue is that for a lot of >>> images, there is a bright "strip" of hyperintense signal forming a >> ring >>> around the cortex. I'm not sure what this is or where it comes from. >>> I've attached an example image that shows where FreeSurfer has >>> misinterpreted the GM/WM border due to this artefact. It will be > quite >>> labour intensive to manually remove the artefact, as it appears > across >>> most of the cortex. >>> >>> >>> >>> Has anyone seen this before and/or could offer advice as to the best >> way >>> to proceed? Using the 3T flag in version 5 helps a little but far > from >>> perfect. >>> >>> >>> >>> Thanks, >>> >>> >>> >>> Sarah >>> >>> >> >> >> 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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
