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.
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
no, sorry
On Thu, 8 Dec 2005, peggy christidis wrote:
I'm guessing the answer to this question is "no", but I'll ask it anyway.
Does the sub-cortical segmentation program work on a primate volume? Or do
we have to do things the old way (i.e., with manual editing)?
Thanks for you time,
Peggy
I'm guessing the answer to this question is "no", but I'll ask it
anyway. Does the sub-cortical segmentation program work on a primate
volume? Or do we have to do things the old way (i.e., with manual editing)?
Thanks for you time,
Peggy
___
Freesur
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 parti
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
s
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
Hi Glenn,
we have some estimated total intracranial volume (eTIV) in the new stuff
using something that Randy Buckner showed recently - the determinant of the
tal transform is predictive of TIV. Should be out soon. It's not clear
however that thickness needs to be corrected by it. The MNI fol
you mean by ICV? No, although in our new versions we compute ICV/TIV. Do
you mean volume labels or surface labels? Volume of volume labels can be
computed with mri_label_volume, surfaces can be given to
mris_anatomical_stats -l
cheers,
Bruce
On
Thu, 8 Dec 2005, Glenn Lawyer wrote:
Hi,
W
depends why you needed to improve the talairach. If it's just for
reporting purposes and the filling/intensity normalization all worked
fine then you don't need to.
cheers,
Bruce
On Thu, 8 Dec 2005, Lars M. Rimol wrote:
Hi,
After having redone mri_convert with an edited brain.mgz as input fil
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 t
Hi,
We want to compare grey matter volumes from specific labels. Is the
output of mris_anatomical_stats normalized in any way? It doesn't
appear to be.
Thanks!
+glenn
--
I want to go farther, farther!
A. E. L.
> Glenn Lawyer <
> +352 061 967 244
Hi,
After having redone mri_convert with an edited brain.mgz as input file, in order to improve the talairach transform, and after having changed the file names (brain.xfm -> talairach.xfm), should we then go to autorecon2? (or do we need to re-run some more scripts from autorecon1?)
-- yours,
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
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