Hi, We have manual tracings of the cerebellum (approx. 100 brains), which were done in the Brains2 software. Could these tracings be used to construct an atlas for use with FreeSurfer? If so, which file format would be most convenient? Analyze?
(The data have been described in: Okugawa G, Sedvall G, Agartz I. Smaller cerebellar vermis but not hemisphere volumes in chronic schizophrenia. Am J Psychiatry, 2003; 160:1614-7)
-- yours, Lars M. Rimol
Hi Lars,
I guess in principal you could use it via the standard route for spherical morphing if you segmented it yourself. In general we haven't done a lot with cerebellum as you need something like .3 mm voxels in plane to resolve the majority of the foliations. Could someone point Lars at the wiki page describing how to build your own atlas? Analyze would probably be okay if you keep the orientation info in an associate .mat file (as SPM does)
cheers, Bruce
On Thu, 8 Dec 2005, Lars M. Rimol wrote:
Hi, We have manual tracings of the cerebellum (approx. 100 brains), which were done in the Brains2 software. Could these tracings be used to construct an atlas for use with FreeSurfer? If so, which file format would be most convenient? Analyze?
(The data have been described in: Okugawa G, Sedvall G, Agartz I. Smaller cerebellar vermis but not hemisphere volumes in chronic schizophrenia. Am J Psychiatry, 2003; 160:1614-7)
-- yours, Lars M. Rimol
Hi Bruce and Lars,
Could this be done as a volume atlas and be segmented out by the subcortical segmentation? That may deal with the lack of high resolution images necessary for cerebellar parcellation. And I'm not completely sure, but Lars probably has his data as a volume segmentation if he used the Brains2 software?
Satra
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Thursday, December 08, 2005 8:38 AM To: Lars M. Rimol Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum atlas
Hi Lars,
I guess in principal you could use it via the standard route for spherical morphing if you segmented it yourself. In general we haven't done a lot with cerebellum as you need something like .3 mm voxels in plane to resolve the majority of the foliations. Could someone point Lars at the wiki page describing how to build your own atlas? Analyze would probably be okay if you keep the orientation info in an associate .mat file (as SPM does)
cheers, Bruce
On Thu, 8 Dec 2005, Lars M. Rimol wrote:
Hi, We have manual tracings of the cerebellum (approx. 100
brains), which
were done in the Brains2 software. Could these tracings be used to construct an atlas for use with FreeSurfer? If so, which
file format
would be most convenient? Analyze?
(The data have been described in: Okugawa G, Sedvall G, Agartz I. Smaller cerebellar vermis but not hemisphere volumes in chronic schizophrenia. Am J Psychiatry, 2003; 160:1614-7)
-- yours, Lars M. Rimol
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Satra,
we do segment the cerebellum with the aseg stuff into cerebellar gray and white. I guess it's a question of what your goals are Lars.
Bruce On Thu, 8 Dec 2005, Satrajit Ghosh wrote:
Hi Bruce and Lars,
Could this be done as a volume atlas and be segmented out by the subcortical segmentation? That may deal with the lack of high resolution images necessary for cerebellar parcellation. And I'm not completely sure, but Lars probably has his data as a volume segmentation if he used the Brains2 software?
Satra
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Thursday, December 08, 2005 8:38 AM To: Lars M. Rimol Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum atlas
Hi Lars,
I guess in principal you could use it via the standard route for spherical morphing if you segmented it yourself. In general we haven't done a lot with cerebellum as you need something like .3 mm voxels in plane to resolve the majority of the foliations. Could someone point Lars at the wiki page describing how to build your own atlas? Analyze would probably be okay if you keep the orientation info in an associate .mat file (as SPM does)
cheers, Bruce
On Thu, 8 Dec 2005, Lars M. Rimol wrote:
Hi, We have manual tracings of the cerebellum (approx. 100
brains), which
were done in the Brains2 software. Could these tracings be used to construct an atlas for use with FreeSurfer? If so, which
file format
would be most convenient? Analyze?
(The data have been described in: Okugawa G, Sedvall G, Agartz I. Smaller cerebellar vermis but not hemisphere volumes in chronic schizophrenia. Am J Psychiatry, 2003; 160:1614-7)
-- yours, Lars M. Rimol
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
Lars,
The wiki page describing atlas-building is a work-in-progress, so it's not yet a how-to guide, but the essential information exists. See:
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation
If you decide to try to construct your own atlas, it would be helpful to email me particulars on trouble-spots, so that the wiki page can be improved.
Nick
On Thu, 2005-12-08 at 08:38 -0500, Bruce Fischl wrote:
Hi Lars,
I guess in principal you could use it via the standard route for spherical morphing if you segmented it yourself. In general we haven't done a lot with cerebellum as you need something like .3 mm voxels in plane to resolve the majority of the foliations. Could someone point Lars at the wiki page describing how to build your own atlas? Analyze would probably be okay if you keep the orientation info in an associate .mat file (as SPM does)
cheers, Bruce
On Thu, 8 Dec 2005, Lars M. Rimol wrote:
Hi, We have manual tracings of the cerebellum (approx. 100 brains), which were done in the Brains2 software. Could these tracings be used to construct an atlas for use with FreeSurfer? If so, which file format would be most convenient? Analyze?
(The data have been described in: Okugawa G, Sedvall G, Agartz I. Smaller cerebellar vermis but not hemisphere volumes in chronic schizophrenia. Am J Psychiatry, 2003; 160:1614-7)
-- yours, Lars M. Rimol
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Lars M. Rimol -
Nick Schmansky -
Satrajit Ghosh