freesurfer: Wrapper Functions for 'Freesurfer'

Wrapper functions that interface with 'Freesurfer' (https:// surfer.nmr.mgh.harvard.edu/), a powerful and commonly-used 'neuroimaging' software, using system commands. The goal is to be able to interface with 'Freesurfer' completely in R, where you pass R objects of class 'nifti', implemented by package 'oro.nifti', and the function executes an 'Freesurfer' command and returns an R object of class 'nifti' or necessary output.

Author
John Muschelli <muschellij2@gmail.com>
Date of publication
2016-09-28 19:34:59
Maintainer
John Muschelli <muschellij2@gmail.com>
License
GPL-3
Version
1.0

View on CRAN

Man pages

aparcstats2table
Parcellation Stats to Table
aparcstats2table.help
Parcellation Stats to Table Help
aparcs_to_bg
Convert Freesurfer aparcs Table to brainGraph
asegstats2table
Parcellation Stats to Table
asegstats2table.help
Parcellation Stats to Table Help
check_fs_result
Check Freesurfer Result
checkmnc-methods
Force object to filename with .mnc extension
construct_subj_dir
Construct Subject Directory
freesurferdir
Get Freesurfer's Directory
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
fs_cmd
FS Command Wrapper
fs_help
Wrapper for getting Freesurfer help
fs_imgext
Determine extension of image based on FSLOUTPUTTYPE
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_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
mris_convert
Use Freesurfers MRIs Converter
mris_convert.help
Help file for Freesurfers MRIs Converter
mri_segment
Use Freesurfers MRI Segmentation Algorithm
mri_segment.help
MRI Segment Help
mris_euler_number
MRI Euler Number
mris_euler_number.help
MRI Euler Number Help
mri_surf2surf
Use Freesurfers 'mri_surf2surf' function to resamples one...
mri_surf2surf.help
Freesurfers mri_surf2surf Help
mri_watershed
Use Freesurfers MRI Watershed Algorithm
mri_watershed.help
MRI Watershed 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_aseg_stats
Read Anatomical Segmentation Statistics
read_fs_table
Read Freesurfer Table Output
recon
Reconstruction from Freesurfer
recon_all
Reconstruction from Freesurfer for All Steps
recon_manual
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
trac_all
Tract Reconstruction Helper for trac-all from Freesurfer for...
tracker
Tract Reconstruction Helper for trac-all from Freesurfer
trac_manual
Tract Reconstruction for Each Step

Files in this package

freesurfer
freesurfer/inst
freesurfer/inst/CITATION
freesurfer/NAMESPACE
freesurfer/R
freesurfer/R/reconner.R
freesurfer/R/checkmnc.R
freesurfer/R/freesurfer_read3.R
freesurfer/R/mri_watershed.R
freesurfer/R/mri_normalize.R
freesurfer/R/run_check_fs_cmd.R
freesurfer/R/mri_mask.R
freesurfer/R/nii2mnc.R
freesurfer/R/recon.R
freesurfer/R/nu_correct.R
freesurfer/R/mri_convert.R
freesurfer/R/mris_euler_number.R
freesurfer/R/check_fs_result.R
freesurfer/R/mri_surf2surf.R
freesurfer/R/trac_manual.R
freesurfer/R/mri_info.R
freesurfer/R/mnc2nii.R
freesurfer/R/construct_subj_dir.R
freesurfer/R/recon_all.R
freesurfer/R/mri_segment.R
freesurfer/R/recon_manual.R
freesurfer/R/surf_convert.R
freesurfer/R/read_aseg_stats.R
freesurfer/R/read_fs_table.R
freesurfer/R/fs_help.R
freesurfer/R/aparcs_to_bg.R
freesurfer/R/tracker.R
freesurfer/R/trac_all.R
freesurfer/R/mris_convert.R
freesurfer/R/asegstats2table.R
freesurfer/R/fs_cmd.R
freesurfer/R/fs_version.R
freesurfer/R/aparcstats2table.R
freesurfer/R/fs_setup.R
freesurfer/MD5
freesurfer/DESCRIPTION
freesurfer/man
freesurfer/man/aparcstats2table.help.Rd
freesurfer/man/fs_version.Rd
freesurfer/man/freesurfer_read3.Rd
freesurfer/man/freesurfer_read_curv.Rd
freesurfer/man/mris_euler_number.Rd
freesurfer/man/nu_correct.help.Rd
freesurfer/man/freesurfer_read3_con.Rd
freesurfer/man/mris_euler_number.help.Rd
freesurfer/man/mri_mask.Rd
freesurfer/man/fs_cmd.Rd
freesurfer/man/mnc2nii.Rd
freesurfer/man/mri_normalize.help.Rd
freesurfer/man/fs_subj_dir.Rd
freesurfer/man/mri_surf2surf.Rd
freesurfer/man/mri_info.Rd
freesurfer/man/aparcstats2table.Rd
freesurfer/man/trac_all.Rd
freesurfer/man/mnc2nii.help.Rd
freesurfer/man/mri_info.help.Rd
freesurfer/man/mri_surf2surf.help.Rd
freesurfer/man/mris_convert.Rd
freesurfer/man/run_check_fs_cmd.Rd
freesurfer/man/reconner.Rd
freesurfer/man/recon_all.Rd
freesurfer/man/freesurferdir.Rd
freesurfer/man/freesurfer_read_surf.Rd
freesurfer/man/fs_imgext.Rd
freesurfer/man/nu_correct.Rd
freesurfer/man/tracker.Rd
freesurfer/man/trac_manual.Rd
freesurfer/man/mri_mask.help.Rd
freesurfer/man/mri_watershed.Rd
freesurfer/man/construct_subj_dir.Rd
freesurfer/man/recon_manual.Rd
freesurfer/man/asegstats2table.Rd
freesurfer/man/read_aseg_stats.Rd
freesurfer/man/nii2mnc.Rd
freesurfer/man/mri_convert.help.Rd
freesurfer/man/mri_normalize.Rd
freesurfer/man/aparcs_to_bg.Rd
freesurfer/man/recon.Rd
freesurfer/man/set_fs_subj_dir.Rd
freesurfer/man/mri_segment.help.Rd
freesurfer/man/read_fs_table.Rd
freesurfer/man/mri_segment.Rd
freesurfer/man/get_fs.Rd
freesurfer/man/mris_convert.help.Rd
freesurfer/man/nii2mnc.help.Rd
freesurfer/man/mri_watershed.help.Rd
freesurfer/man/fs_help.Rd
freesurfer/man/get_fs_output.Rd
freesurfer/man/check_fs_result.Rd
freesurfer/man/have_fs.Rd
freesurfer/man/surf_convert.Rd
freesurfer/man/mri_convert.Rd
freesurfer/man/checkmnc-methods.Rd
freesurfer/man/asegstats2table.help.Rd