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I substituted the code from the previous email with a combination of fslcreatehd and fslmaths to create a binary sphere in the correct standardized space. I then multiplied this sphere by the mean_FA_skeleton_mask to further restrict the region within the sphere to tracts. On Sat, Sep 20, 2014 at 9:29 PM, charlie <[log in to unmask]> wrote: > 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 >