Hi,
The FSL course can be found on a link in the
"Documentation, support and training" page on the
FSL site.
The direct link is:
http://www.fmrib.ox.ac.uk/fslcourse/
As Brian posted earlier today, you can fill the
mesh directly in the native space easily with
first_utils. However, the output of run_first_all
is already in native space normally. So I can
only assume that your modifications have
changed this.
If that's the case then you can transform images
between different spaces as long as you have the
linear matrix or non-linear warp field/coef files. The
FSL course practical will clearly take you through
this process. Whether you need identity matrices
or inverse warps will depend on how you've created
these transformations in the first place, but after
doing the practical in the FSL course it should be
clear how things work.
All the best,
Mark
On 15 Jan 2009, at 16:47, siamak wrote:
> Hi Mark,
>
> No, I've not been through that. Is it available online on the FSL
> documents or
> not? Besides, my question is about how can I use the 4*4 matrix and
> coefficient file in run_first_all to have a segmented image finally
> in native
> space. So, you mean that I segment the image with
> run_first_all_noflirt
> applying an identity matrix and finally apply applywarp (invers) to
> the
> segmented image to transform it to the native space. Am I right?
>
> Siamak
>
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