Dear Bruce,
Thank you for your help and the great work on Freesurfer!
Best, Zhennan
Zhennan Yan Department of Computer Science Rutgers University
On 1/31/2013 1:43 PM, Bruce Fischl wrote:
- 40 subjects, 10 young, 10 middle ages, 10 elderly (healthy) and 10
with AD.
- Many small things, the big one (described in our 2004 paper) is
that we now use a nonlinear warp
- Yes, hydrocephalus for example is hard, although we have made
recent improvements in the warping that handle enlarged ventricles much better
cheers Bruce
On Thu, 31 Jan 2013, Zhennan Yan wrote:
Dear Bruce,
Thank you very much for your reply. I can convert my labels to Freesurfer labels and try the mri_ca_label now. May I ask some more questions?
- What subjects were used to train the atlas in the current version?
Were they healthy or diseased subjects? 2) How the current implementation differs from the one in your Whole Brain Segmentation (2002) paper? 3) Is there any cases, e.g. on which clinical diseases, FreeSurfer will produce less than ideal results?
Thanks!
Best, Zhennan
Zhennan Yan Department of Computer Science Rutgers University
On 1/30/2013 3:10 PM, Bruce Fischl wrote:
Hi Zhennan
there is an option to mri_ca_label to read in a prior segmentation and iterate the MRF minimization, but unless your labels and conventions are identical to our's it's unlikely to work. You can use mri_ca_train to build the MRF and likelihoods and such if you want.
cheers Bruce
On Wed, 30 Jan 2013, Zhennan Yan wrote:
Dear freesurfer experts,
I have questions about the MRF in Freesurfer:
(1) I have a T1 image and sub-cortical segmentation for it (nifti format). But the segmentation is not perfect and I would like to relabel it using the ICM algorithm as shown
in fig.8 > in paper: Whole Brain Segmentation:
Automated Labeling of Neuroanatomical Structures in the Human
Brain, > Fischl et al., (2002).
How can I do this using Freesurfer?
(2) If I have several subjects with labels, how can I train the
anisotropic nonstationary MRF prior as equation (9) in the same paper? Can I use that MRF prior elsewhere in my
own > program?
Many thanks! Best,
Zhennan
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