Function reference • freesurfer

All functions
`aparcs_to_bg()`	Convert Freesurfer aparcs Table to brainGraph
`aparcstats2table()`	Parcellation Stats to Table
`aparcstats2table.help()`	Parcellation Stats to Table Help
`asegstats2table()`	Parcellation Stats to Table
`asegstats2table.help()`	Parcellation Stats to Table Help
`check_fs_result()`	Check Freesurfer Result
`checkmnc()` `ensure_mnc()`	Force object to filename with .mnc extension
`construct_subj_dir()`	Construct Subject Directory
`convert_surface()`	Convert Freesurfer Surface
`freesurfer_read3()`	Freesurfer Read 3 records
`freesurfer_read3_con()`	Freesurfer Read 3 records
`freesurfer_read_curv()`	Read Freesufer Curv file
`freesurfer_read_surf()`	Read Freesurfer Surface file
`freesurferdir()` `freesurfer_dir()` `fs_dir()`	Get Freesurfer's Directory
`fs_cmd()`	FS Command Wrapper
`fs_help()`	Wrapper for getting Freesurfer help
`fs_imgext()`	Determine extension of image based on FSLOUTPUTTYPE
`fs_lut`	Freesurfer look up table (LUT)
`fs_subj_dir()`	Determine Freesurfer Subjects Directory
`fs_version()`	Find Freesurfer Version
`get_fs()`	Create command declaring FREESURFER_HOME
`get_fs_output()`	Determine Freesurfer output type
`have_fs()`	Logical check if Freesurfer is accessible
`mnc2nii()`	Convert MNC to NIfTI
`mnc2nii.help()`	MNC to NIfTI Help
`mri_convert()`	Use Freesurfers MRI Converter
`mri_convert.help()`	MRI Normalize Help
`mri_deface()`	MRI Deface
`mri_info()`	MRI information
`mri_info.help()`	MRI information Help
`mri_mask()`	Use Freesurfers MRI Mask
`mri_mask.help()`	MRI Normalize Help
`mri_normalize()`	Use Freesurfers MRI Normalize Algorithm
`mri_normalize.help()`	MRI Normalize Help
`mri_segment()`	Use Freesurfers MRI Segmentation Algorithm
`mri_segment.help()`	MRI Segment Help
`mri_surf2surf()`	Use Freesurfers `mri_surf2surf` function to resamples one cortical surface onto another
`mri_surf2surf.help()`	Freesurfers mri_surf2surf Help
`mri_watershed()`	Use Freesurfers MRI Watershed Algorithm
`mri_watershed.help()`	MRI Watershed Help
`mris_convert()`	Use Freesurfers MRIs Converter
`mris_convert.help()`	Help file for Freesurfers MRIs Converter
`mris_convert_annot()`	Convert Annotation file
`mris_convert_curv()`	Convert Curvature file
`mris_convert_normals()`	Convert Surface to Surface normals
`mris_convert_vertex()`	Convert Surface to vertex file
`mris_euler_number()`	MRI Euler Number
`mris_euler_number.help()`	MRI Euler Number Help
`nii2mnc()`	Convert NIfTI to MNC
`nii2mnc.help()`	Convert NIfTI to MNC Help
`nu_correct()`	Use Freesurfers Non-Uniformity Correction
`nu_correct.help()`	Non-Uniformity Correction Help
`read_annotation()`	Read Freesurfer annotation file
`read_aseg_stats()`	Read Anatomical Segmentation Statistics
`read_fs_label()`	Read Label File
`read_fs_table()`	Read Freesurfer Table Output
`readmgz()` `readmgh()`	Read MGH or MGZ File
`readmnc()`	Read MNC File
`recon()`	Reconstruction from Freesurfer
`recon_all()`	Reconstruction from Freesurfer for All Steps
`recon_con1()` `autorecon1()` `recon_con2()` `autorecon2()` `recon_con3()` `autorecon3()`	Reconstruction from Motion Correction to Skull Strip
`reconner()`	Reconstruction Helper for recon from Freesurfer
`run_check_fs_cmd()`	Run and Check a Freesurfer Command
`set_fs_subj_dir()`	Set Freesurfer Subjects Directory
`surf_convert()`	Convert Surface Data to ASCII
`surface_to_obj()`	Convert Freesurfer Surface to Wavefront OBJ
`surface_to_triangles()`	Convert Freesurfer Surface to Triangles
`trac_all()`	Tract Reconstruction Helper for trac-all from Freesurfer for All Steps
`trac_prep()` `trac_bedpost()` `trac_path()`	Tract Reconstruction for Each Step
`tracker()`	Tract Reconstruction Helper for trac-all from Freesurfer

Reference

All functions