Hi Matt, Did you try the -c option described in the function's help?
HTH D On Thu, Sep 4, 2014 at 3:30 PM, Sherwood, Matt <matt.sherw...@wright.edu> wrote: > Bruce, > Thanks for the pointer. What is happening is we would like to combine > the skin/skull/CSF volumes with that of the cortical segmentation. The issue > we are having with the output of mris_fill is the volumes are now different > sizes than the aseg output from recon-all. > > Matthew Sherwood > Medical Research Engineer > > Wright State Research Institute > 4035 Colonel Glenn Hwy. > Dayton, OH 45431 > > PH: 937.705.1025 > FAX: 937.705.1095 > EMAIL: matt.sherw...@wright.edu > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Tuesday, September 02, 2014 6:49 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] watershed surface to volume rendering repost > > Hi Matthew, > > yes, you can use mris_fill to fill the interior of a topologically correct, > closed surface. You'll need to run some boolean operations on them to get the > volumes you want, but it should be pretty easy I think. > > cheers > Bruce > On > Tue, 2 Sep 2014, Sherwood, Matt wrote: > >> >> Freesurfer, >> >> Sorry for the repost, but I did not get any further details: >> >> >> >> We have scans that have recon-all completed. Following recon-all, we >> completed watershed (under the MNE toolbox) to extract skull and scalp >> from the T1 scans. The outputs of this algorithm are outer brain, >> inner skull, outer skull and outer scalp surfaces. We are particularly >> interested in these volumes for our study. Is there a way to convert >> these surface to volumes representative of CSF (layer between >> brain/skull), skull (inner to outer skull surface) and skin (outer skull to >> outer scalp)? >> >> >> >> Matthew Sherwood >> Medical Research Engineer >> >> >> >> Wright State Research Institute >> 4035 Colonel Glenn Hwy. >> >> Dayton, OH 45431 >> >> >> >> PH: 937.705.1025 >> >> FAX: 937.705.1095 >> >> EMAIL: matt.sherw...@wright.edu >> >> >> > > _______________________________________________ > 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
