Dear Victor,
You need to use the tool called FIRST within FSL in order to segment subcortical structures.
It does not have a GUI, but is easy to run from the command line.
There is documentation on the web and also a tutorial, with data, in the FSL Course.
All the best,
Mark
On 26 Jun 2012, at 17:32, Victor DelBene wrote:
> Hi,
>
> I just downloaded FSL so that I can work on a data set I currently have. Specifically, we would like to automatically segment out the amygdala (initially just the amygdala).
>
> So far, I have successfully used the BET brain extraction function to create a brain.nii.gz file. I then ran FAST segmentation using the previously created file. After some time, it created several other .nii.gz files. These are of the whole brain, I feel like I am making progress; however, I cannot seem to find a way to isolate the amygdala in my practice data set so that I can segment it out from the rest of the brain. How can one do this using the GUI?
>
> I am running this on a Macbook (OS X 10.5.8, 2.4 GHz Intel Core Duo, 2 GB 667MHz DDR2 SDRAM) and I am using the FSL GUI. Previously, my only prior neuroimaging experience was in Brain Voyager.
>
> I appreciate any help that can be provided. Thank you.
>
> Sincerely,
> Victor
>
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