Hi,
I'm not sure why you are using the mask options.
With a non-linear registration method like fnirt, the registration
acts locally, and so using a mask like this isn't really helpful, as
the cortical regions tend not to affect the sub-cortical regions
much in a non-linear registration. Hence I would not use the
mask options and just do the registration without them, which
sounds like it is working fine.
All the best,
Mark
On 2 Aug 2009, at 18:17, siamak wrote:
> Hi Mark,
>
> I checked the result of fnirt registration after using the conf
> file. Its result is
> better than the previous fnirt that I was using, but still is far
> from what
> expected. Let me explain the problem in more detail. I have two MRI
> images
> with their manual labels (subcortical labels). The volume of
> subcortical
> structures of both of them is around 132,000 mm^3. When I register
> these
> two images using fnirt with --refmask and --inmask (Registered
> MNI_subbr
> mask to these MRI images) and then propagate the labels using
> applywarp,
> the resulting subcortical structure has the volume around
> 167,000mm^3 in the
> best case using config file you recommended me. It shows that the
> subcortical structures after registration is expanded around 20%. I
> don't have
> this problem when I use fnirt without --refmask or --inmask. Any
> comment is
> highly appreciated.
>
> All the best,
> Siamak
>
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