chiaming-PORTEGE-R835:~> setenv FREESURFER_HOME Desktop/freesurfer chiaming-PORTEGE-R835:~> source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME Desktop/freesurfer FSFAST_HOME Desktop/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR Desktop/freesurfer/subjects MNI_DIR Desktop/freesurfer/mni chiaming-PORTEGE-R835:~> which mri_convert Desktop/freesurfer/bin/mri_convert chiaming-PORTEGE-R835:~> recon-all USAGE: recon-all Required Arguments: -subjid - Fully-Automated Directive: -all : performs all stages of cortical reconstruction -autorecon-all : same as -all Manual-Intervention Workflow Directives: -autorecon1 : process stages 1-5 (see below) -autorecon2 : process stages 6-23 after autorecon2, check white surfaces: a. if wm edit was required, then run -autorecon2-wm b. if control points added, then run -autorecon2-cp c. proceed to run -autorecon3 -autorecon2-cp : process stages 12-23 (uses -f w/ mri_normalize, -keep w/ mri_seg) -autorecon2-wm : process stages 15-23 -autorecon2-inflate1 : 6-18 -autorecon2-perhemi : tess, sm1, inf1, q, fix, sm2, inf2, finalsurf, ribbon -autorecon3 : process stages 24-34 if edits made to correct pial, then run -autorecon-pial -hemi ?h : just do lh or rh (default is to do both) Autorecon Processing Stages (see -autorecon# flags above): 1. Motion Correction and Conform 2. NU (Non-Uniform intensity normalization) 3. Talairach transform computation 4. Intensity Normalization 1 5. Skull Strip 6. EM Register (linear volumetric registration) 7. CA Intensity Normalization 8. CA Non-linear Volumetric Registration 9. Remove neck 10. EM Register, with skull 11. CA Label (Aseg: Volumetric Labeling) and Statistics 12. Intensity Normalization 2 (start here for control points) 13. White matter segmentation 14. Edit WM With ASeg 15. Fill (start here for wm edits) 16. Tessellation (begins per-hemisphere operations) 17. Smooth1 18. Inflate1 19. QSphere 20. Automatic Topology Fixer 21. White Surfs (start here for brain edits for pial surf) 22. Smooth2 23. Inflate2 24. Spherical Mapping 25. Spherical Registration 26. Spherical Registration, Contralater hemisphere 27. Map average curvature to subject 28. Cortical Parcellation (Labeling) 29. Cortical Parcellation Statistics 30. Pial Surfs 31. WM/GM Contrast 32. Cortical Ribbon Mask 33. Cortical Parcellation mapped to ASeg 34 Brodmann and exvio EC labels Step-wise Directives See -help Expert Preferences -pons-crs C R S : col, row, slice of seed point for pons, used in fill -cc-crs C R S : col, row, slice of seed point for corpus callosum, used in fill -lh-crs C R S : col, row, slice of seed point for left hemisphere, used in fill -rh-crs C R S : col, row, slice of seed point for right hemisphere, used in fill -nofill : do not use the automatic subcort seg to fill -watershed cmd : control skull stripping/watershed program -wsless : decrease watershed threshold (leaves less skull, but can strip more brain) -wsmore : increase watershed threshold (leaves more skull, but can strip less brain) -wsatlas : use atlas when skull stripping -no-wsatlas : do not use atlas when skull stripping -no-wsgcaatlas : do not use GCA atlas when skull stripping -wsthresh pct : explicity set watershed threshold -wsseed C R S : identify an index (C, R, S) point in the skull -nuiterations N : set number of iterations for nu intensity correction (default is 2) -norm3diters niters : number of 3d iterations for mri_normalize -normmaxgrad maxgrad : max grad (-g) for mri_normalize. Default is 1. -norm1-b N : in the _first_ usage of mri_normalize, use control point with intensity N below target (default=10.0) -norm2-b N : in the _second_ usage of mri_normalize, use control point with intensity N below target (default=10.0) -norm1-n N : in the _first_ usage of mri_normalize, do N number of iterations -norm2-n N : in the _second_ usage of mri_normalize, do N number of iterations -cm : conform volumes to the min voxel size -no-fix-with-ga : do not use genetic algorithm when fixing topology -fix-diag-only : topology fixer runs until ?h.defect_labels files are created, then stops -seg-wlo wlo : set wlo value for mri_segment and mris_make_surfaces -seg-ghi ghi : set ghi value for mri_segment and mris_make_surfaces -nothicken : pass '-thicken 0' to mri_segment -no-ca-align-after : turn off -align-after with mri_ca_register -no-ca-align : turn off -align with mri_ca_label -deface : deface subject, written to orig_defaced.mgz -expert file : read-in expert options file -xopts-use : use pre-existing expert options file -xopts-clean : delete pre-existing expert options file -xopts-overwrite : overwrite pre-existing expert options file -mprage : assume scan parameters are MGH MP-RAGE protocol -washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol. both mprage flags affect mri_normalize and mri_segment, and assumes a darker gm. -use-gpu : use GPU versions of mri_em_register, mri_ca_register, mris_inflate and mris_sphere Notification Files (Optional) -waitfor file : wait for file to appear before beginning -notify file : create this file after finishing Status and Log files (Optional) -log file : default is scripts/recon-all.log -status file : default is scripts/recon-all-status.log -noappend : start new log and status files instead of appending -no-isrunning : do not check whether this subject is currently being processed Other Arguments (Optional) -sd subjectsdir : specify subjects dir (default env SUBJECTS_DIR) -mail username : mail user when done -umask umask : set unix file permission mask (default 002) -grp groupid : check that current group is alpha groupid -onlyversions : print version of each binary and exit -debug : print out lots of info -allowcoredump : set coredump limit to unlimited -dontrun : do everything but execute each command -version : print version of this script and exit -help : voluminous bits of wisdom