Hi,
The video only shows the process for a probabilistic atlas, but not all atlases in FSL are probabilistic (this is a minor error in what is said in the video). The JHU white matter labels are a case in point, and the atlas is not stored in the same format as the probabilistic atlases. The easiest way to work with this atlas is to do the following:
fslview $FSLDIR/data/atlases/JHU/JHU-ICBM-labels-1mm.nii.gz
(or the 2mm version if you prefer)
Within this FSLView window, add a suitable background template (if you like) and select the label of interest. Note what the "intensity" value is at a voxel within the label that you are interested in (click on the voxel to see this).
Then, you can extract this label with fslmaths as such:
fslmaths $FSLDIR/data/atlases/JHU/JHU-ICBM-labels-1mm.nii.gz -thr 40 -uthr 40 -bin ROImask
The output is an image (ROImask) which you can name as you like. You need to change the numbers "40" to whatever the label number is that you selected with FSLView (the "intensity" referred to above).
This method will work with any non-probabilistic atlas in FSL.
All the best,
Mark
On 7 Apr 2014, at 14:24, Vera Steinheuser <[log in to unmask]> wrote:
> Dear FSL-users,
>
> do you know if there is a way to create masks from specific regions of the JHU WHITE MATTER LABELS atlas? I created masks of regions of the Tractography and the Juelich atlas already after I found this video:
>
> https://www.youtube.com/watch?v=fIu4tUjRfUE
>
> Since the WM Labels atlas contains more structures, I would like to use it as well but unfortunately it does not work as it is described in the video..
>
> Any ideas?
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