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_HOME/FreeSurferColorLUT.txt showed the orientation wrong
(upside down and maybe left-right fliped). This is very weird since I
have used tkmedit mysubj norm.mgz -segmentation old_seg.mgz
$FREESURFER_HOME/FreeSurferColorLUT.txt to confirm that old_seg.mgz has
the same orientation with norm.mgz. Do you have any idea about this?
What's the function of transforms/talairach.m3z in mri_ca_label? Could
you please send me a simple example T1, init_seg and relabeled result
archived by mri_ca_label?
Thanks!
Best,
Zhennan
Zhennan Yan
Department of Computer Science
Rutgers University
On 2/1/2013 7:44 PM, Bruce Fischl wrote:
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 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 matrices regularized.
I noticed that my initial segmentation image is not 255 cubed and has
only 30+ different subcortical labels (for example labels
0,2,3,4,5,7,8,10,...,60,62). Then I tried to use the command
mri_convert init_label.mgz init_label_c.mgz --conform to conform
it. But the output init_label_c.mgz is not as I expected. I guess the
reslicing interpolation might introduce some new labels to my
initial segmentation?
My question is do I need to conform the initial seg into 255 cubed
image? How can I do this in my case? And what do you think is the
problem cause the failure of the mri_ca_label?
Thanks!
Zhennan
Zhennan Yan
Department of Computer Science
Rutgers University
On 2/1/2013 10:28 AM, Bruce Fischl wrote:
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, Bruce Fischl wrote:
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 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?
1) 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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