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Hi, Try to edit the file all.bvars and replace all instances of /usr/local/fsl with /usr/share/fsl/5.0 All the best, Mark On 4 Mar 2013, at 08:11, Gayane Aghakhanyan <[log in to unmask]> wrote: > Dear Mark, > > As I mentioned before, I've already had fsl-first-data, > I've tried vertexAnalysis tutorial data following instructions here http://www.fmrib.ox.ac.uk/fslcourse/lectures/practicals/seg_struc/index.html#first > However, after command below > > first_utils --usebvars --vertexAnalysis -i all.bvars \ > -o diff_con1_dis2_L_Hipp_mni -d design_con1_dis2.mat --useReconMNI > > I've got the same output in the terminal window: > > Warning: does not exist. Attempting to switch to: /usr/share/fsl/5.0 > Not a vtk file (error in line 1). > Not a vtk file (error in line 1). > > It is said In the tutorial - If you are running the above command on a personal install of FSL, it may fail unless FSL is installed at /usr/local/fsl. > However, as you know perfectly in Debian/Ubuntu, FSL by default is installed at /usr/share/fsl/5.0. I'm not sure whether this could cause problem, couldn't it? > > Thanks for your time > Gayane >