rsurfer (version 0.2)

fsimport: 'Freesurfer' Import (Serialise)

Description

This function assumes all the subdirectories of subjectDir are subjects who have been processed in 'Freesurfer'. In then runs various 'Freesurfer' scripts to extract the specified fields into an R data frame.

Usage

fsimport(subjectDir, fields = fsimport.listfields(), verbose = F)

Arguments

subjectDir

The directory containing the subject subdirectories

fields

The field groups to use, see fsimport() for more details

verbose

Whether to log the 'Freesurfer' scripts to the R console

Value

The subject data processed from 'Freesurfer'

Details

The field groups which can be imported from the subject are: The specified fields can be:

lh.cortical.thickness = left hemisphere cortical thicknesses rh.cortical.thickness = right hemisphere cortical thicknesses lh.cortical.volume = left hemisphere cortical volumes rh.cortical.volume = right hemisphere cortical volumes lh.cortical.thickness.std = left hemisphere cortical thickness standard deviations rh.cortical.thickness.std = right hemisphere cortical thickness standard deviations lh.cortical.area = left hemisphere cortical surface areas rh.cortical.area = right hemisphere cortical surface areas lh.subcortical = left hemisphere subcortical volumes rh.subcortical = right hemisphere subcortical volumes lh.hippocampal = left hemisphere hippocampal volumes rh.hippocampal = right hemisphere hippocampal volumes

By default all of the above fields are included. For the hippocampal volumes, the subjects must have been processed with the "hippo-subfields" when 'Freesurfer' was invoked.

Examples

# NOT RUN {
setfshome("/Applications/freesurfer")
fsimport("/Users/alex/Desktop/Subjects")
# }