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.sherwood@wright.edumailto:matt.sherwood@wright.edu
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.sherwood@wright.edu
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.sherwood@wright.edu
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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.sherwood@wright.edu
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.sherwood@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.sherwood@wright.edu
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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.sherwood@wright.edu
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Sherwood, Matt