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Hi Alba > Hello everyone, > > I am creating masks for doing fa mean value statistics and i have a doubt. > > What is the difference between doing a mask with > > fsl4.1-fslmaths /usr/share/fsl/data/atlases/JHU/JHU-ICBM-tracts-prob-1mm.nii.gz -thr 17 -uthr 17 -mas mean_FA_skeleton_mask_p-cp.nii.gz maskcs17 > > fsl4.1-fslmaths /usr/share/fsl/data/atlases/JHU/JHU-ICBM-tracts-prob-1mm.nii.gz -thr 17 -uthr 17 maskcs17 > (without the mean_FA_skeleton_mask ) ??? The image that you're using (JHU-ICBM-tracts-prob-1mm) is a 4D image with one probabilistic tract per volume. You need to use the "maxprob" images if you want to use fslmaths as you suggest above. Alternatively, you can extract your tract from the 4D image using fslroi, then use fslmaths as above but with a threshold that has a different meaning. If you are going to use all_FA_skeletonised to calculate mean FA for each subject and tract, then yes it is a good idea to restrict the atlas to the skeleton. You can do that either with your first command, or when you use fslstats to calculate mean FA you can mask using the skeleton (-k option). > > and between using the > > /usr/share/fsl/data/atlases/JHU/JHU-ICBM-tracts-prob-1mm.nii.gz > atlas or the > > /usr/share/fsl/data/atlases/JHU/JHU-ICBM-tracts-prob-1mm.nii.gz?? I can't see a difference between these two. Did you mean "maxprob"? If so, then see my answer above. Saad > > thanks in advance, > > Alba Garin > PhD Student > Applied Mechanics Department > Simulation Unit > Paseo Manuel Lardizabal, 15 > 20018 Donostia-San Sebastian. Spain > Tel. +34 943 212 800 (Ext. 2111) > -- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.fmrib.ox.ac.uk/~saad