Wrapper Functions for 'Freesurfer'
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Documentation for package ‘freesurfer’ version 1.6.10
Help 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 |
| autorecon1 | Reconstruction from Motion Correction to Skull Strip |
| autorecon2 | Reconstruction from Motion Correction to Skull Strip |
| autorecon3 | Reconstruction from Motion Correction to Skull Strip |
| checkmnc | Force object to filename with .mnc extension |
| checkmnc-method | Force object to filename with .mnc extension |
| checkmnc-methods | Force object to filename with .mnc extension |
| check_fs_result | Check Freesurfer Result |
| construct_subj_dir | Construct Subject Directory |
| convert_surface | Convert Freesurfer Surface |
| ensure_mnc | Force object to filename with .mnc extension |
| freesurferdir | Get Freesurfer's Directory |
| freesurfer_dir | 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_dir | Get Freesurfer's Directory |
| 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 |
| 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 |
| 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 |
| 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 |
| readmgh | Read MGH or MGZ File |
| readmgz | Read MGH or MGZ File |
| readmnc | Read MNC File |
| 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 |
| recon | Reconstruction from Freesurfer |
| reconner | Reconstruction Helper for recon from Freesurfer |
| recon_all | Reconstruction from Freesurfer for All Steps |
| recon_con1 | Reconstruction from Motion Correction to Skull Strip |
| recon_con1,recon_con2,recon_con3 | Reconstruction from Motion Correction to Skull Strip |
| recon_con2 | Reconstruction from Motion Correction to Skull Strip |
| recon_con3 | Reconstruction from Motion Correction to Skull Strip |
| run_check_fs_cmd | Run and Check a Freesurfer Command |
| set_fs_subj_dir | Set Freesurfer Subjects Directory |
| surface_to_obj | Convert Freesurfer Surface to Wavefront OBJ |
| surface_to_triangles | Convert Freesurfer Surface to Triangles |
| surf_convert | Convert Surface Data to ASCII |
| tracker | Tract Reconstruction Helper for trac-all from Freesurfer |
| trac_all | Tract Reconstruction Helper for trac-all from Freesurfer for All Steps |
| trac_bedpost | Tract Reconstruction for Each Step |
| trac_path | Tract Reconstruction for Each Step |
| trac_prep | Tract Reconstruction for Each Step |