Hello,
You can use the xml file in $FSLDIR/data/atlases (e.g. HarvardOxford-Subcortical.xml ) to find the index number of the region you are interested in - the Left Hippocampus is 8. You can them use fslroi to extract this region from ( e.g. HarvardOxford-sub-prob-2mm.nii.gz ). The values in this mask will in units of percent probability ( 0…100) and can then be thresholded/binarised with fslmaths.
Kind Regards
Matthew
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Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
> On 19 Jun 2018, at 09:14, Will Khan <[log in to unmask]> wrote:
>
> Dear FSL community.
>
> Could anyone please advise of a way to generate a subcortical mask of a given region, say the hippocampus solely through the command line? i.e. without having to specify the hippocampus using atlas tools in fslview/fsleyes first?
>
> I wanted to create several subcortical masks in FSL but would prefer to generate a script that can automate this process.
>
> Cheers,
>
> Will
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