Package: freesurfer 1.6.10

John Muschelli

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.

Authors:John Muschelli [aut, cre], Athanasia Mo Mowinckel [ctb]

freesurfer_1.6.10.tar.gz
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freesurfer_1.6.10.tgz(r-4.4-any)freesurfer_1.6.10.tgz(r-4.3-any)
freesurfer_1.6.10.tar.gz(r-4.5-noble)freesurfer_1.6.10.tar.gz(r-4.4-noble)
freesurfer_1.6.10.tgz(r-4.4-emscripten)freesurfer_1.6.10.tgz(r-4.3-emscripten)
freesurfer.pdf |freesurfer.html✨
freesurfer/json (API)
NEWS

# Install 'freesurfer' in R:
install.packages('freesurfer', repos = c('https://ggseg.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/muschellij2/freesurfer/issues

Datasets:
  • fs_lut - Freesurfer look up table

On CRAN:

7.69 score 10 stars 1 packages 55 scripts 300 downloads 50 mentions 78 exports 20 dependencies

Last updated 6 months agofrom:19ed2662cd. Checks:OK: 5 NOTE: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 09 2024
R-4.5-winNOTENov 09 2024
R-4.5-linuxNOTENov 09 2024
R-4.4-winOKNov 09 2024
R-4.4-macOKNov 09 2024
R-4.3-winOKNov 09 2024
R-4.3-macOKNov 09 2024

Exports:aparcs_to_bgaparcstats2tableaparcstats2table.helpasegstats2tableasegstats2table.helpautorecon1autorecon2autorecon3check_fs_resultcheckmncconstruct_subj_dirconvert_surfaceensure_mncfreesurfer_dirfreesurfer_read_curvfreesurfer_read_surffreesurfer_read3freesurfer_read3_confreesurferdirfs_cmdfs_dirfs_helpfs_imgextfs_subj_dirfs_versionget_fsget_fs_outputhave_fsmnc2niimnc2nii.helpmri_convertmri_convert.helpmri_defacemri_infomri_info.helpmri_maskmri_mask.helpmri_normalizemri_normalize.helpmri_surf2surfmri_surf2surf.helpmri_watershedmri_watershed.helpmris_convertmris_convert_annotmris_convert_curvmris_convert_normalsmris_convert_vertexmris_convert.helpmris_euler_numbermris_euler_number.helpnii2mncnii2mnc.helpnu_correctnu_correct.helpread_annotationread_aseg_statsread_fs_labelread_fs_tablereadmghreadmgzreadmncreconrecon_allrecon_con1recon_con2recon_con3reconnerrun_check_fs_cmdset_fs_subj_dirsurf_convertsurface_to_objsurface_to_trianglestrac_alltrac_bedposttrac_pathtrac_preptracker

Dependencies:abindbitopscligluelifecyclemagrittrmatrixStatsneurobaseoro.niftiplyrR.methodsS3R.ooR.utilsRcppreshape2rlangRNiftistringistringrvctrs

Exploring Included Subject Freesurfer Data

Vignette Author

Rendered fromexploring_included_data.Rmdusingknitr::rmarkdownon Nov 09 2024.

Last update: 2020-12-08
Started: 2017-03-06

Readme and manuals

Help Manual

Help pageTopics
Convert Freesurfer aparcs Table to brainGraphaparcs_to_bg
Parcellation Stats to Tableaparcstats2table
Parcellation Stats to Table Helpaparcstats2table.help
Parcellation Stats to Tableasegstats2table
Parcellation Stats to Table Helpasegstats2table.help
Check Freesurfer Resultcheck_fs_result
Force object to filename with .mnc extensioncheckmnc checkmnc,character-method checkmnc,list-method checkmnc,nifti-method checkmnc-methods ensure_mnc
Construct Subject Directoryconstruct_subj_dir
Convert Freesurfer Surfaceconvert_surface
Read Freesufer Curv filefreesurfer_read_curv
Read Freesurfer Surface filefreesurfer_read_surf
Freesurfer Read 3 recordsfreesurfer_read3
Freesurfer Read 3 recordsfreesurfer_read3_con
Get Freesurfer's Directoryfreesurferdir freesurfer_dir fs_dir
FS Command Wrapperfs_cmd
Wrapper for getting Freesurfer helpfs_help
Determine extension of image based on FSLOUTPUTTYPEfs_imgext
Freesurfer look up table (LUT)fs_lut
Determine Freesurfer Subjects Directoryfs_subj_dir
Find Freesurfer Versionfs_version
Create command declaring FREESURFER_HOMEget_fs
Determine Freesurfer output typeget_fs_output
Logical check if Freesurfer is accessiblehave_fs
Convert MNC to NIfTImnc2nii
MNC to NIfTI Helpmnc2nii.help
Use Freesurfers MRI Convertermri_convert
MRI Normalize Helpmri_convert.help
MRI Defacemri_deface
MRI informationmri_info
MRI information Helpmri_info.help
Use Freesurfers MRI Maskmri_mask
MRI Normalize Helpmri_mask.help
Use Freesurfers MRI Normalize Algorithmmri_normalize
MRI Normalize Helpmri_normalize.help
Use Freesurfers MRI Segmentation Algorithmmri_segment
MRI Segment Helpmri_segment.help
Use Freesurfers 'mri_surf2surf' function to resamples one cortical surface onto anothermri_surf2surf
Freesurfers mri_surf2surf Helpmri_surf2surf.help
Use Freesurfers MRI Watershed Algorithmmri_watershed
MRI Watershed Helpmri_watershed.help
Use Freesurfers MRIs Convertermris_convert
Convert Annotation filemris_convert_annot
Convert Curvature filemris_convert_curv
Convert Surface to Surface normalsmris_convert_normals
Convert Surface to vertex filemris_convert_vertex
Help file for Freesurfers MRIs Convertermris_convert.help
MRI Euler Numbermris_euler_number
MRI Euler Number Helpmris_euler_number.help
Convert NIfTI to MNCnii2mnc
Convert NIfTI to MNC Helpnii2mnc.help
Use Freesurfers Non-Uniformity Correctionnu_correct
Non-Uniformity Correction Helpnu_correct.help
Read Freesurfer annotation fileread_annotation
Read Anatomical Segmentation Statisticsread_aseg_stats
Read Label Fileread_fs_label
Read Freesurfer Table Outputread_fs_table
Read MGH or MGZ Filereadmgh readmgz
Read MNC Filereadmnc
Reconstruction from Freesurferrecon
Reconstruction from Freesurfer for All Stepsrecon_all
Reconstruction from Motion Correction to Skull Stripautorecon1 autorecon2 autorecon3 recon_con1 recon_con1,recon_con2,recon_con3 recon_con2 recon_con3
Reconstruction Helper for recon from Freesurferreconner
Run and Check a Freesurfer Commandrun_check_fs_cmd
Set Freesurfer Subjects Directoryset_fs_subj_dir
Convert Surface Data to ASCIIsurf_convert
Convert Freesurfer Surface to Wavefront OBJsurface_to_obj
Convert Freesurfer Surface to Trianglessurface_to_triangles
Tract Reconstruction Helper for trac-all from Freesurfer for All Stepstrac_all
Tract Reconstruction for Each Steptrac_bedpost trac_path trac_prep
Tract Reconstruction Helper for trac-all from Freesurfertracker