Hi Charlie,
You have created a single voxel with intensity one with the first fslmaths call, which is then filtered ( smoothed ) across a 15-voxel radius sphere, resulting in values less than 1 in the sphere. The values outside the sphere are numerical noise. When creating masks, it can often be worth applying a final thresholding/binarising step to set the intensity of all masked voxels to 1.
Kind Regards
Matthew
> FSL group,
>
> I have made a sphere mask centred on significant activation coordinates (from a previous TBSS analysis).
> fslmaths $FSLDIR/data/standard/MNI152_T1_1mm -mul 0 -add 1 -roi 116 1 101 1 88 1 0 1 cst_slfroi -odt float
> fslmaths cst_slfroi -kernel sphere 15 -fmean cst_slf_sphere_mask -odt float
>
> My question concerns the intensity values with the sphere. If the -add 1 command adds the value 1 to the region within the sphere, then why is the value in the sphere 7.1e-05, a value far less than 1. Also, the value outside the sphere is not zero. In short, this mask must require additional thresholding and binarising.
>
> While I can combine atlas based masks to cover the area of interest, the combined masked is too dispersed. Any suggestions with the sphere mask would be much appreciated
>
> All the best,
> charlie
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