With the most recent release, does the skullstripping take place with brainmask.auto.mgz and brainmask.mgz? After completing recon-all autorecon-all I checked brain.mgz. I had some frontal areas missing, so ran recon-all -skullstrip -wsthresh 30. Brainmask.mgz looks good.
I believe that I know the answer, but to be safe, after running autorecon2 brain.mgz will reflect these edits? Thanks, Cliff
------------------ Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893
yes, that is correct. I'm attaching some power point slides that show a block diagram of the new stream.
doug
Clifford A. Smith, PhD wrote:
With the most recent release, does the skullstripping take place with brainmask.auto.mgz and brainmask.mgz? After completing recon-all -autorecon-all I checked brain.mgz. I had some frontal areas missing, so ran recon-all -skullstrip -wsthresh 30. Brainmask.mgz looks good.
I believe that I know the answer, but to be safe, after running -autorecon2 brain.mgz will reflect these edits? Thanks, Cliff
Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks.
I¹ve noticed with the newest stream a few posterior inaccuracies (compared to my previously completed stream). I¹ve attached a tiff. You can see the sulcus that is missed. If I am correct, this is a segmentation issue, and one adds control points to help define the white matter intensity?
------------------ Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893
From: Doug Greve greve@nmr.mgh.harvard.edu Date: Tue, 07 Feb 2006 15:57:15 -0500 To: "Clifford A. Smith, PhD" csmith13@rush.edu Cc: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Newest stream
yes, that is correct. I'm attaching some power point slides that show a block diagram of the new stream.
doug
Clifford A. Smith, PhD wrote:
Newest stream With the most recent release, does the skullstripping take place with brainmask.auto.mgz and brainmask.mgz? After completing recon-all autorecon-all I checked brain.mgz. I had some frontal areas missing, so ran recon-all -skullstrip -wsthresh 30. Brainmask.mgz looks good.
I believe that I know the answer, but to be safe, after running autorecon2 brain.mgz will reflect these edits? Thanks, Cliff
Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
no tiff attached, but yes, control points in the occipital wm would probably fix it On Wed, 8 Feb 2006, Clifford A. Smith, PhD wrote:
Thanks.
I¹ve noticed with the newest stream a few posterior inaccuracies (compared to my previously completed stream). I¹ve attached a tiff. You can see the sulcus that is missed. If I am correct, this is a segmentation issue, and one adds control points to help define the white matter intensity?
Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893
From: Doug Greve greve@nmr.mgh.harvard.edu Date: Tue, 07 Feb 2006 15:57:15 -0500 To: "Clifford A. Smith, PhD" csmith13@rush.edu Cc: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Newest stream
yes, that is correct. I'm attaching some power point slides that show a block diagram of the new stream.
doug
Clifford A. Smith, PhD wrote:
Newest stream With the most recent release, does the skullstripping take place with brainmask.auto.mgz and brainmask.mgz? After completing recon-all autorecon-all I checked brain.mgz. I had some frontal areas missing, so ran recon-all -skullstrip -wsthresh 30. Brainmask.mgz looks good.
I believe that I know the answer, but to be safe, after running autorecon2 brain.mgz will reflect these edits? Thanks, Cliff
Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Clifford A. Smith, PhD -
Doug Greve