Dear all, I have some questions I could not find an answer to myself, I'd really appreciate it if anyone could help out.
1) How should recon-all be used to process all subjects' data (i.e. obtain the surface for each subject) before taking it to QDEC (or command prompt) for a group thickness analysis? The QDEC tutorial mentions a separate tutorial for the recon-all preprocessing part, but it is not at all clear which one that is. Is there more to it than just typing "recon-all --i file.nii –i file.dcm –subject bert –all" for each subject (assuming NIFTI structurals)? 2) Is mri_glmfit FreeSurfer's equivalent of the randomise command in FSL, i.e. it does nonparametric permutation-based inference based on the given design matrix and produces statistical maps? Or are there differences between the two in how the GLM is applied? 3) Freeview and tksurfer seem to overlap in scope - when would you use one rather than the other? Does it have to do with viewing structurals vs statistically-generated maps? 4) I see that points on reconall-generated surfaces are always referred to in tutorials as vertices rather than voxels. Since both represent the "unit of space", what exactly is the difference between them? Many thanks in advance! Tudor
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