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Hello again, Running concat_bvars again did not solve the problem. All steps were carried out on the same version of FSL (4.1.5) Is there any way of checking the concat command worked properly? I get a 'L_Hipp_all.bvars' file and a 'con_to_dis_L_Hipp.bvars' file so I assumed concat worked.. In the documentation, two concat commands are listed but I'm unclear if both or either need to be used (I've tried both together and seperately but the output seems to be the same..). Can you explain the difference between these commands? 1) concat_bvars L_Hipp_all.bvars con*_L_Hipp_first.bvars dis*_L_Hipp_first.bvars 2) concat_bvars con_to_dis_L_Hipp.bvars con*_L_Hipp_first.bvars dis*_L_Hipp_first.bvars Thanks and regards, Duncan. Hi, This is probably due to the concat_bvars command failing or using outputs from older versions of FIRST. Try running concat_bvars again and see if that fixes the problem. All the best, Mark On 8 Jun 2011, at 14:22, Duncan wrote: > Hi there, > > I'm trying out the vertex analysis function but cannot produce the final .vtk file. > > I've done the segmentation and concatenated the bvars files and produced the design matrix, seemingly without problems. > > I then run the 'first_utils command from my 'test' directory (which contains my bvars files and my con0_dis1.mat file): > > first_utils --vertexAnalysis --usebvars -i con_to_dis_L_Hipp.bvars -d con0_dis1.mat -o shape_analysis/con0_dis1_L_Hipp --useReconNative --useRigidAlign -v >& shape_analysis/con0_dis1_L_Hipp_output.txt > > In my shape_analysis file, the only output is the .txt file. I don't get an error in my terminal when I run the above command but the contents of the text file is: > > read model > Cannot open file. > Cannot open file. > > Any advice greatly appreciated, > > rgds, > Duncan.