Dear Miguel, Mark, (and FSL Experts),
Hope this finds you well. I was just wondering if you or anyone else had managed to find a solution to this caudate problem (see below)? As I believe we are suffering from the same problem with our data.
Hope to hear from you!
Many thanks and best wishes,
Colm.
Thanks Mark for your reply.
Registrations look fine. The non-boundary corrected segmentations don't cover all the caudate though.
I have uploaded a few problematic T1s, ref 277951 (not sure if you want me to upload the whole data set and/or the outputs, please let me know)
Thanks so much!
Best,
Miguel
On Wed, Jan 23, 2013 at 10:50 AM, Mark Jenkinson <[log in to unmask]> wrote:
Hi,
I'm not sure what to suggest without seeing the images.
Is the registration sufficiently accurate?
If not then try working on that.
Does the non-boundary corrected image cover all of the caudate?
If so then some other option for boundary correction might work.
If you still can't get a good solution then send us the data (see the Support page in the website for details) and we'll have a look.
All the best,
Mark
On 22 Jan 2013, at 17:04, Miguel Burgaleta <[log in to unmask]> wrote:
>
> Hi FSLers,
>
> I think this one is for Mark.
>
> I usually get stunning subcortical segmentations with FIRST, with one exception: the right (and sometimes, left) caudate nucleus. This happens consistently to me across data sets. When I overlay the fast_firstseg.nii.gz over the subject's T1, I often see that an anterosuperior segment of the structure is excluded. I can see this in aprox 15% of the subjects.
>
> This is what I've tried so far:
> - Changing the number of modes. I tried 20, 100, 150 and 200.
> - Disabling boundary correction.
> - Disabling the intref option.
>
> None of these worked (although increasing the number of modes had a small positive impact). I would really appreciate if you could give me some advice to improve these segmentations.
>
> Thanks in advance,
> Miguel
>
>
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