Hi,
You could also...
Create a mask for a mean individual structure can be created using FIRST
and the appropriate model.
You'll need to create an identity matrix transformation file:
1 0 0 0
0 1 0 0
0 0 1 0
0 0 0 1
Assuming that its saved as identity.mat, you can now run the command:
run_first -i ${FSLDIR}/data/standard/MNI152_T1_1mm -t ~/eye.mat -n 0 -m
${FSLDIR}/data/first/models_336_bin/L_Hipp_bin.bmv -o L_Hipp_mask
MNI152_T1_1mm.nii.gz
This effectively fills in the mean mesh from the model. It will work for
any of the FIRST models, and on any resolution of the MNI template.
Depending on your application, you could also generate a group specific
mask by running FIRST on all the individual subjects, transforming the
segmentation to standard space, the adding together.
Hopefully this helps,
Cheers,
Brian
> Hi - please have a detailed look at the atlases in FSLView and the
> different structures they contain - for example see the probabilistic
> Harvard-Oxford atlas which contains hippocampus.
>
> Steve.
>
>
>
> On 5 Dec 2008, at 01:01, siamak wrote:
>
>> Hi FSL users,
>>
>> I am looking for a mask for hippocampus. I've seen a subcortical
>> mask in MNI
>> standard template in FSL. I'd like to know that the same is
>> available for each
>> substructure such as hippocampus in the subcortical area or not.
>>
>> Best,
>> Siamak
>>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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>
>
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