If it is in progress, it means that it is not usable by end-users yet? If so, when would the how-to guide be available?
(This would be a wonderful tool for my project in which I need to see a particular region labeled, i.e., lateral portion of the areas between parietal and occipital lobes. I am talking about the 'purple-colored' region in the example image shown in the Wiki page)
Thanks.
Nam.
Nick Schmansky nicks@nmr.mgh.harvard.edu 12/08/05 11:09 AM >>>
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Nam,
The documentation describing how to create your own atlas is the bit that is a 'work-in-progress'. The binary mris_ca_train is used to create your own atlas, following which the binary mris_ca_label will label your subjects. These binaries already exist in the Freesurfer 'dev' distribution.
Freesurfer already includes a default atlas which is used during the 'recon-all' processing stream to label a subject, so in most cases it is not necessary to create your own atlas. Have you used Freesurfer to process your subject(s)? If so, you already have labelled subjects. For example, the Freesurfer 'dev' distribution includes a sample subject, called bert, which you can see the labels:
tksurfer bert rh pial
To view cortical parcellation labels, in tksurfer:
File->Label->Import Annotation
Browse to file rh.aparc.annot and select OK
Move the cursor over the areas to display the labels.
Nick
On Thu, 2005-12-08 at 17:21 -0500, Joongnam Yang wrote:
If it is in progress, it means that it is not usable by end-users yet? If so, when would the how-to guide be available?
(This would be a wonderful tool for my project in which I need to see a particular region labeled, i.e., lateral portion of the areas between parietal and occipital lobes. I am talking about the 'purple-colored' region in the example image shown in the Wiki page)
Thanks.
Nam.
Nick Schmansky nicks@nmr.mgh.harvard.edu 12/08/05 11:09 AM >>>
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Joongnam Yang -
Nick Schmansky