After running the individual segmentations, checking the output, and creating the files, we are ready to run the "Vertex Analysis." A model is created with a single command, but there are several options.
first_utils --vertexAnalysis --usebvars -i concatenated_bvars -d design.mat -o output_basename [--useReconNative --useRigidAlign ] [--useReconMNI] [--usePCAfilter -n number_of_modes]
Based on earlier examples, this is one possible command line (assuming you are in the directory with the files):
[user@localhost temp]$ first_utils --vertexAnalysis --usebvars -i L_Hipp_all.bvars -d design.mat -o L_Hipp_vertexMNI --useReconMNI
The various options are specified in the User Guide under Vertex Analysis, Usage. It is important to come up with a naming convention for the output files. I suggest starting with the structure name, adding "_output_" to indicate this file is the output of the vertex analysis, then add suffixes. Here is a convention:
- "_vertexNative" ==>> "--useReconNative --useRigidAlign"
- "_vertexNativeScale" ==>> "--useReconNative --useRigidAlign –useScale"
- "_vertexMNI" ==>> "--useReconMNI --useRigidAlign"
- "_vertexMNIScale" ==>> "--useReconMNI --useRigidAlign –useScale"