what different brain images do you mean? You can view them with the
surfaces via:
tkmedit <subject name> norm.mgz lh.white -segmentation aparc+aseg.mgz
or
tkmedit <subject name> norm.mgz lh.white -segmentation aparc2009s+aseg.mgz
the tools will be part of FS 5.2 when it comes out in the next month or so.
If you really need it before then Nick can get you a beta.
cheers
Bruce
On Sat, 1 Dec 2012, Assaf B.
Spanier wrote:
Many thanks for the quick response - I would take a look on your
suggestion!
How about my first question ? About viewing the segmentation results of my
first trial ( without the Flair images)
[Please forgive my English :) ]
On Sat, Dec 1, 2012 at 9:53 PM, Bruce Fischl <[email protected]>
wrote:
Hi Spanier
definitely don't invoke recon-all with the FLAIR image. We have
some tools in 5.2 for this, but you would call it as a
postprocessing step with a different command line in any case.
Instead, you can use bbregister to register the flair to the
surfaces and resample it.
cheers
Bruce
On Sat, 1 Dec 2012, Assaf B. Spanier wrote:
Hi@all,
I have a dataset of several MRI T1 images and one
Flair. All images of the
same subject and were taken in the same session. My
goal is to register and
segment all those MRI images.
= A =
In my first try I have used, "recon-all -i image1 -i
image2 etc'" for all
T1 images (here, I didn't use the Flair images ) .
Follow this, I used the
"recon-all -all" command. (For about two days...)
Here come Question 1: After all this process, I
didn't completely follow the
results I got... As I have noticed that I have only
one segmentation file
(aparc.a2009s+aseg.mgz) ? How can I see the
segmentation result
with tkmedit in the different brain images ?
= B =
As I would like the neuroanatomical labels to be
inspected for accuracy by a
physician. My physician asks to see the segmentation
result on top of the
Flair images (saying it easier for him to do so on
Flair images)
So I've used the "recon-all -i image1 -i image2
etc'" command again
but this time I've also included the Flair image.
Here come Question 2: However, this time,
unfortunately, the "recon-all -i
image1 -i image2 etc'" , failed, saying that:
~~~~~
images have different voxel sizes. Currently not
supported, maybe first
make conform? Debug info: size(1) = 0.5078, 0.5078,
5.5 size(0) = 0.51,
0.51, 5.5
~~~~~
Is there something I can do to fix this ?
Thanks for everyone involved in this great project!
Highly appreciate your time and efforts.
Best,
Spanier
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