Hi all, I've noticed you can set expert preferences to align before averaging in the GUI, but how do you do it from the command line?
My understanding of the following from the usage is that it assumes that the transform already exists in the /transforms dir, but how do I create this?
"The volume can be resampled into another space by supplying a transform using the --apply_transform flag. This reads the transform file and applies the transform (when --apply_inverse_transform is used, the transform is inverted and then applied). An example of a transform file is talairach.xfm as found in subjectid/mri/transforms."
Do you create it separately through the MNI tools before proceeding with freesurfer, or is there some way to do it through Fressurfer? Thanks, Alex