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_output_MNI --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 are some suggestions:
- "–useReconMNI" option could have "_MNI" and the "--useReconNative --useRigidAlign" (those two always go together) could have "_Native".
- "–useRigidAlign" has "_Rigid"
- "–useScale" has "_Scale"
- "--usePCAfilter -n 1000" would use "_PCA1000"