Hi Zhennan
if you run recon-all on any dataset it will create an example for you.
The talairach.m3z maps the volume into the atlas coords. If it is
oriented incorrectly then that would explain your problem. You can also
use mri_info to see the direction cosines of the various volumes
cheers
Br
Dear Bruce,
Thank you very much for your suggestions. I have fixed the reslicing
problem and I am still trying to use mri_ca_label to relabel
sub-cortical structures in my data. Now the program output a new seg,
but the display of "tkmedit mysubj norm.mgz -segmentation new_seg.mgz
$FREESURFER_
that might be the problem. Specify nearest nbr resampling with -rt nearest
on the mri_convert cmd line
cheers
Bruce
On Fri, 1 Feb 2013, Zhennan Yan wrote:
> Dear Bruce,
>
> I have mapped my labels to the Freesurfer labels. But when I tried the
> "mri_ca_label -R init_label.mgz norm.mgz transfo
Dear Bruce,
I have mapped my labels to the Freesurfer labels. But when I tried the
"mri_ca_label -R init_label.mgz norm.mgz transforms/talairach.m3z
$FREESURFER_HOME/average/RB_all_2008-03-26.gca new_label.mgz", I got a
"Segmentation fault" after "0 singular and 1812 ill-conditioned
covariance
thanks Zhennan
good luck and let us know if we can help
Bruce
On Fri, 1 Feb 2013, Zhennan Yan
wrote:
> 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, Bru
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:
> 1. 40 subjects, 10 young, 10 middle ages, 10 elderly (healthy) and 10
> with AD.
>
> 2. Many small thing
1. 40 subjects, 10 young, 10 middle ages, 10 elderly (healthy) and 10 with
AD.
2. Many small things, the big one (described in our 2004 paper) is that we
now use a nonlinear warp
3. Yes, hydrocephalus for example is hard, although we have made recent
improvements in the warping that handle enl
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?
1) What subjects were used to train the atlas in the current version?
Were they healthy or diseased subjects?
2) How the current implementati
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
