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