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[user@localhost temp]$ first_utils --vertexAnalysis --usebvars -i L_Hipp_all.bvars -d design.mat -o L_Hipp_output_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 are some suggestionsis a convention:
- "–useReconMNI" option could have "_MNI" and the vertexNative" ==>> "--useReconNative --useRigidAlign" (those two always go together) could have "_Native".
- "–useRigidAlign" has "_RigidvertexNativeScale"
"==>> "--useReconNative --useRigidAlign –useScale" has - "_ScalevertexMNI"
==>> "--usePCAfilter useReconMNI --n 1000" would use "_PCA1000useRigidAlign" - "_vertexMNIScale" ==>> "--useReconMNI --useRigidAlign –useScale"