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Hi Taylor, Unfortunately there is not much support for doing things with VTK files in FSL right now. This is one of the main reasons that the new-style vertex analysis was introduced; converting the shape deformations to scalars in a nifti file allows the use of all of FSL’s nifti-based tools. If you want to do further computations of the VTK files, you will probably need to load them into Matlab or Python and do your calculations there. This is not as bad as it may sound - they are simple text files containing the locations of the vertices, the triangles and the values for all vertices (i.e. your p-values/F-stats). As a possible alternative, I think FreeSurfer’s mris_convert will allow you to convert the VTK file to other mesh formats. I am not sure if there are any tools that will allow you to compute the statistics you are interested, but others on the list might know more. Hope that helps, Eelke > On 10 Nov 2015, at 19:55, Kuhn, Taylor <[log in to unmask]> wrote: > > Hello, > I have run within group correlations between neuropsych performance and shape using the older surface-based vertex analysis method. I am interested in computing the percent of the surface that is significant for the different neuropsych tasks. However, I am unsure what to use to compute these stats on .vtk files (the output of the surface-based vertex method). Fslmaths and fslstats aren't able to open .vtk files. How do you convert .vtk to .nii so fslmaths and fslstats can be applied to the file? Or are there separate stats tools for .vtk files? > > Thank you, > Taylor > > Taylor P. Kuhn, Ph.D. > Neuropsychology Postdoctoral Fellow > UCLA Semel Institute for Neuroscience and Human Behavior > [log in to unmask] > > > IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.