[[ReconAllTableStableV7]]

This table shows the recon-all steps for the '''stable''', publicly released, '''version 6.0 '''of !FreeSurfer [[DownloadAndInstall | (available here)]]. 

See also the [[https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags|OtherUsefulFlags]] for other recon-all options.
||<tablestyle="text-align:left;                    ;text-align:left">'''recon-all step''' ||'''Individual Flag''' ||'''Input''' ||'''Command Line''' ||'''Output''' ||
||<style="text-align:left" |20>'''[[https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all|recon-all]] -autorecon1 -subjid <subjid>''' ||
||<style="text-align:left" |1>-i <invol1> ||invol1.dcm ''or .nii or .mgz'' ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert|mri_convert]] invol1.dcm orig/001.mgz ||orig/001.mgz ||
||<style="text-align:left" |1>-i <invol2> ''optional'' ||invol2.dcm'' or .nii or .mgz'' ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert|mri_convert]] invol2.dcm orig/002.mgz ||orig/002.mgz ||
||<style="text-align:left" |1>-T2 <invol> ''or'' -FLAIR <invol> ''optional'' ||<style="text-align:left" |1>invol.dcm ''or .nii or .mgz'' ||<style="text-align:left" |1>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert|mri_convert]] --no_scale 1 invol.dcm orig/T2raw.mgz ''(or orig/FLAIRraw.mgz)'' ||<style="text-align:left" |1>orig/T2raw.mgz ''(or orig/FLAIRraw.mgz)'' ||
||<style="text-align:left" |4>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/motioncor|motioncor]] ||orig/001.mgz ||<style="text-align:left" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_robust_template|mri_robust_template]]  --mov 001.mgz 002.mgz --average 1 --template rawavg.mgz --satit  --inittp 1 --fixtp --noit --iscale --iscaleout --subsample 200 --lta ||<style="text-align:left" |2>rawavg.mgz ||
||orig/002.mgz ||
||rawavg.mgz ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert|mri_convert]] rawavg.mgz orig.mgz --conform ||orig.mgz ||
||orig.mgz ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_add_xform_to_header|mri_add_xform_to_header]] -c transforms/talairach.xfm orig.mgz orig.mgz ||orig.mgz ||
||<style="text-align:left" |5>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/talairach|talairach]] ||orig.mgz ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_nu_correct.mni|mri_nu_correct.mni]] --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz ||orig_nu.mgz ||
||orig_nu.mgz ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/talairach_avi|talairach_avi]] --i orig_nu.mgz --xfm transforms/talairach.auto.xfm ||transforms/talairach.auto.xfm ||
||transforms/talairach.auto.xfm ||cp transforms/talairach.auto.xfm transforms/talairach.xfm ||transforms/talairach.xfm ||
||transforms/talairach.xfm ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/talairach_afd|talairach_afd]] -T 0.005 -xfm transforms/talairach.xfm || ||
|| ||awk -f $FREESURFER_HOME/bin/extract_talairach_avi_QA.awk transforms/talairach_avi.log ||transforms/talairach_avi.log ||
||<style="text-align:left;" |2>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/nuintensitycor|nuintensitycor]] ||orig.mgz ||<style="text-align:left;" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_nu_correct.mni|mri_nu_correct.mni]] --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 ||<style="text-align:left;" |2>nu.mgz ||
||talairach.xfm ||
||<style="text-align:left" |1>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/normalization|normalization]] ||nu.mgz ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_normalize|mri_normalize]] -g 1 -mprage nu.mgz T1.mgz ||T1.mgz ||
||<style="text-align:left" |3>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/skullstrip|skullstrip]] ||nu.mgz ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_em_register|mri_em_register]] -skull nu.mgz $FREESURFER_HOME/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta ||transforms/talairach_with_skull.lta ||
||T1.mgz ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_watershed|mri_watershed]]  -T1 -brain_atlas  $FREESURFER_HOME/average/RB_all_withskull_2016-05-10.vc700.gca  transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz ||brainmask.auto.mgz ||
||brainmask.auto.mgz ||cp brainmask.auto.mgz brainmask.mgz ||brainmask.mgz ||


||<tablestyle="text-align:left;                    ;text-align:left">'''recon-all step''' ||'''Individual Flag''' ||'''Input''' ||'''Command Line''' ||'''Output''' ||
||<style="text-align:left;" |69>'''[[https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all|recon-all]] -autorecon2 -subjid <subjid>''' ||
||<style="text-align:left;" |2>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/gcareg|gcareg]] ||brainmask.mgz ||<style="text-align:left;" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_em_register|mri_em_register]] -uns 3 -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta ||<style="text-align:left;" |2>transforms/talairach.lta ||
||nu.mgz ||
||<style="text-align:left;" |3>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/canorm|canorm]] ||brainmask.mgz ||<style="text-align:left;" |3>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_ca_normalize|mri_ca_normalize]]  -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz  $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca  transforms/talairach.lta norm.mgz ||<style="text-align:left;" |3>norm.mgz ||
||nu.mgz ||
||transforms/talairach.lta ||
||<style="text-align:left;" |3>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/careg|careg]] ||brainmask.mgz ||<style="text-align:left;" |3>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_ca_register|mri_ca_register]]  -align-after -nobigventricles -mask brainmask.mgz -T  transforms/talairach.lta norm.mgz  $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca  transforms/talairach.m3z ||<style="text-align:left;" |3>transforms/talairach.m3z ||
||transforms/talairach.lta ||
||norm.mgz ||
||<style="text-align:left;" |4>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/calabel|calabel]] ||norm.mgz ||<style="text-align:left;" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_ca_label|mri_ca_label]]  -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz  transforms/talairach.m3z  $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca  aseg.auto_noCCseg.mgz ||<style="text-align:left;" |2>aseg.auto_noCCseg.mgz ||
||transforms/talairach.m3z ||
||aseg.auto_noCCseg.mgz ||<style="text-align:left;" |1>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_cc|mri_cc]] -lta <subjid>/mri/transforms/cc_up.lta -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz <subjid> ||aseg.auto.mgz ||
||aseg.auto.mgz ||cp aseg.auto.mgz aseg.presurf.mgz ||aseg.presurf.mgz ||
||<style="text-align:left;" |3>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/normalization2|normalization2]] ||brainmask.mgz ||<style="text-align:left;" |3>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_normalize|mri_normalize]] -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz ||<style="text-align:left;" |3>brain.mgz ||
||norm.mgz ||
||aseg.presurf.mgz ||
||<style="text-align:left;" |2>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/maskbfs|maskbfs]] ||brain.mgz ||<style="text-align:left;" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_mask|mri_mask]] -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz ||<style="text-align:left;" |2>brain.finalsurfs.mgz ||
||brainmask.mgz ||
||<style="text-align:left;" |6>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/segmentation|segmentation]] ||brain.mgz ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segment|mri_segment]] -mprage brain.mgz wm.seg.mgz ||wm.seg.mgz ||
||wm.seg.mgz ||<style="text-align:left;" |3>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_edit_wm_with_aseg|mri_edit_wm_with_aseg]] wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz ||<style="text-align:left;" |3>wm.asegedit.mgz ||
||aseg.presurf.mgz ||
||brain.mgz ||
||wm.asegedit.mgz ||<style="text-align:left;" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_pretess|mri_pretess]] wm.asegedit.mgz wm norm.mgz wm.mgz ||<style="text-align:left;" |2>wm.mgz ||
||norm.mgz ||
||<style="text-align:left;" |3>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/fill|fill]] ||wm.mgz ||<style="text-align:left;" |3>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_fill|mri_fill]] -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz ||filled.mgz ||
||aseg.auto_noCCseg.mgz ||<style="text-align:left;" |2>../scripts/ponscc.cut.log ||
||transforms/talairach.lta ||
||<style="text-align:left;" |8>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/tessellate|tessellate]] ||filled.mgz ||<style="text-align:left;" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_pretess|mri_pretess]] filled.mgz 255 norm.mgz filled-pretess255.mgz ||<style="text-align:left;" |2>filled-pretess255.mgz ||
||norm.mgz ||
||filled-pretess255.mgz ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_tessellate|mri_tessellate]] filled-pretess255.mgz 255 lh.orig.nofix ||lh.orig.nofix ||
||filled.mgz ||<style="text-align:left;" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_pretess|mri_pretess]] filled.mgz 127 norm.mgz filled-pretess127.mgz ||<style="text-align:left;" |2>filled-pretess127.mgz ||
||norm.mgz ||
||filled-pretess127.mgz ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_tessellate|mri_tessellate]] filled-pretess127.mgz 127 rh.orig.nofix ||rh.orig.nofix ||
||?h.orig.nofix ||mris_extract_main_component ?h.orig.nofix ?h.orig.nofix ||?h.orig.nofix ||
|| ||rm -f filled-pretess255.mgz filled-pretess127.mgz || ||
||-[[https://surfer.nmr.mgh.harvard.edu/fswiki/smooth|smooth1]] ||?h.orig.nofix ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_smooth|mris_smooth]] -nw ?h.orig.nofix ?h.smoothwm.nofix ||?h.smoothwm.nofix ||
||-[[https://surfer.nmr.mgh.harvard.edu/fswiki/inflate|inflate1]] ||?h.smoothwm.nofix ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_inflate|mris_inflate]] -no-save-sulc ?h.smoothwm.nofix ?h.inflated.nofix ||?h.inflated.nofix ||
||-[[https://surfer.nmr.mgh.harvard.edu/fswiki/qsphere|qsphere]] ||?h.inflated.nofix ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_sphere|mris_sphere]] -q ?h.inflated.nofix ?h.qsphere.nofix ||?h.qsphere.nofix ||
||<style="text-align:left;" |6>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/fix|fix]] ||?h.orig.nofix ||cp ?h.orig.nofix ?h.orig ||?h.orig ||
||?h.inflated.nofix ||cp ?h.inflated.nofix ?h.inflated ||?h.inflated ||
||?h.qsphere.nofix ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_fix_topology|mris_fix_topology]] -mgz -sphere qsphere.nofix -ga <subjid> ?h ||?h.orig ||
||?h.orig ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_euler_number|mris_euler_number]] ?h.orig ||?h.orig ||
||?h.orig ||mris_remove_intersection ?h.orig ?h.orig ||?h.orig ||
|| ||rm ?h.inflated || ||
||<style="text-align:left;" |8>-white ||<style="text-align:left;" |1>aseg.presurf.mgz ||<style="text-align:left;" |8>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_make_surfaces|mris_make_surfaces]] -aseg ../mri/aseg.presurf -whiteonly -noaparc -mgz -T1 brain.finalsurfs <subjid> ?h ||<style="text-align:left" |4>?h.white.preaparc ||
||<style="text-align:left">brain.finalsurfs.mgz ||
||<style="text-align:left">wm.mgz ||
||<style="text-align:left">filled.mgz ||
||<style="text-align:left;" |4>?h.orig ||
||?h.curv ||
||?h.area ||
||?h.cortex.label ||
||-[[https://surfer.nmr.mgh.harvard.edu/fswiki/smooth|smooth2]] ||?h.white.preaparc ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_smooth|mris_smooth]] -n 3 -nw ?h.white.preaparc ?h.smoothwm ||?h.smoothwm ||
||<style="text-align:left" |2>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/inflate|inflate2]] ||<style="text-align:left" |2>?h.smoothwm ||<style="text-align:left" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_inflate|mris_inflate]] ?h.smoothwm ?h.inflated ||?h.inflated ||
||?h.sulc ||
||<style="text-align:left" |4>-curvHK ||<style="text-align:left" |2>?h.white.preaparc ||<style="text-align:left" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_curvature|mris_curvature]] -w ?h.white.preaparc ||<style="text-align:left" |1>?h.white.H ||
||?h.white.K ||
||<style="text-align:left" |2>?h.inflated ||<style="text-align:left" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_curvature|mris_curvature]] -thresh .999 -n -a 5 -w -distances 10 10 ?h.inflated ||<style="text-align:left" |1>?h.inflated.H ||
||?h.inflated.K ||
||<style="text-align:left" |3>-curvstats ||<style="text-align:left">?h.smoothwm ||<style="text-align:left" |3>mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/?h.curv.stats -F smoothwm <subjid> ?h curv sulc ||<style="text-align:left" |3>stats/?h.curv.stats ||
||<style="text-align:left">?h.curv ||
||<style="text-align:left">?h.sulc ||


||<tablestyle="text-align:left;                    ;text-align:left">'''recon-all step''' ||'''Individual Flag''' ||'''Input''' ||'''Command Line''' ||'''Output''' ||
||<style="text-align:left;" |85>'''[[https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all|recon-all]] -autorecon3 -subjid <subjid>''' ||
||<style="text-align:left" |2>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/sphere|sphere]] ||?h.inflated ||<style="text-align:left" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_sphere|mris_sphere]] ?h.inflated ?h.sphere ||<style="text-align:left" |2>?h.sphere ||
||<style="text-align:left">?h.smoothwm ||
||-[[https://surfer.nmr.mgh.harvard.edu/fswiki/surfreg|surfreg]] ||?h.sphere ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_register|mris_register]] -curv ?h.sphere $FREESURFER_HOME/average/?h.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ?h.sphere.reg ||?h.sphere.reg ||
||<style="text-align:left;" |2>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/jacobian_white|jacobian_white]] ||?h.white.preaparc ||<style="text-align:left;" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_jacobian|mris_jacobian]] ?h.white.preaparc ?h.sphere.reg ?h.jacobian_white ||<style="text-align:left;" |2>?h.jacobian_white ||
||?h.sphere.reg ||
||-[[https://surfer.nmr.mgh.harvard.edu/fswiki/avgcurv|avgcurv]] ||?h.sphere.reg ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mrisp_paint|mrisp_paint]] -a 5 $FREESURFER_HOME/average/?h.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ?h.sphere.reg ?h.avg_curv ||?h.avg_curv ||
||<style="text-align:left;" |3>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/cortparc|cortparc]] ||aseg.presurf.mgz ||<style="text-align:left;" |3>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_ca_label|mris_ca_label]]  -l ../label/?h.cortex.label -aseg mri/aseg.presurf.mgz <subjid>  ?h ?h.sphere.reg  $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs  ?h.aparc.annot ||<style="text-align:left;" |3>label/?h.aparc.annot ||
||<style="text-align:left">?h.cortex.label ||
||?h.sphere.reg ||
||<style="text-align:left;" |8>-pial ||<style="text-align:left;" |1>aseg.presurf.mgz ||<style="text-align:left;" |8>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_make_surfaces|mris_make_surfaces]] -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs <subjid> ?h ||<style="text-align:left" |4>?h.pial ||
||brain.finalsurfs.mgz ||
||wm.mgz ||
||filled.mgz ||
||<style="text-align:left;" |3>?h.orig ||
||?h.curv.pial ||
||<style="text-align:left">?h.area.pial ||
||<style="text-align:left" |1>label/?h.aparc.annot ||?h.thickness ||
||<style="text-align:left;" |17>-T2pial ''or'' <<BR>>-FLAIRpial ''optional'' ||orig/T2raw.mgz ||bbregister --s <subjid> --mov mri/orig/T2raw.mgz --lta mri/transforms/T2raw.lta --init-fsl --T2 ||transforms/T2raw.lta ||
||orig/T2raw.mgz ||<style="text-align:left" |2>mri_convert -odt float -at mri/transforms/T2raw.lta -rt cubic -ns 1 -rl mri/orig.mgz mri/orig/T2raw.mgz mri/T2.prenorm.mgz ||<style="text-align:left" |2>T2.prenorm.mgz ||
||transforms/T2raw.lta ||
||aseg.presurf.mgz ||<style="text-align:left" |3>mri_normalize -sigma 0.5 -nonmax_suppress 0 -min_dist 1 -aseg mri/aseg.presurf.mgz -surface surf/rh.white identity.nofile -surface surf/lh.white identity.nofile mri/T2.prenorm.mgz mri/T2.norm.mgz ||<style="text-align:left" |3>T2.norm.mgz ||
||?h.white ||
||T2.prenorm.mgz ||
||T2.norm.mgz ||<style="text-align:center" |2>mri_mask mri/T2.norm.mgz mri/brainmask.mgz mri/T2.mgz ||<style="text-align:center" |2>T2.mgz ||
||brainmask.mgz ||
||?h.pial ||cp -v surf/?h.pial surf/?h.woT2.pial ||?h.woT2.pial ||
||aseg.presurf.mgz ||<style="text-align:left" |9>[[mris_make_surfaces]] -orig_white white -orig_pial woT2.pial -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs -T2 ../mri/T2 -nsigma_above 2 -nsigma_below 5 <subjid> ?h ||<style="text-align:left" |3>?h.pial ||
||brain.finalsurfs.mgz ||
||wm.mgz ||
||filled.mgz ||<style="text-align:left" |2>?h.curv.pial ||
||?h.white ||
||<style="text-align:left" |1>label/?h.aparc.annot ||<style="text-align:left" |1>?h.area.pial ||
||<style="text-align:left" |1>T2.mgz ||<style="text-align:left" |3>?h.thickness ||
||?h.woT2.pial ||
|| ||
||<style="text-align:left;" |3>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/cortribbon|cortribbon]] ||aseg.presurf.mgz ||<style="text-align:left" |3>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_volmask|mris_volmask]] --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon <subjid> ||<style="text-align:left;" |2>?h.ribbon.mgz ||
||?h.white ||
||?h.pial ||<style="text-align:left" |1>ribbon.mgz ||
||<style="text-align:left" |5>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/parcstats|parcstats]] ||<style="text-align:left" |1>label/?h.aparc.annot ||<style="text-align:left" |5>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_anatomical_stats|mris_anatomical_stats]]  -th3 -mgz -cortex ../label/?h.cortex.label -f stats/?h.aparc.stats -b  -a label/?h.aparc.annot -c label/aparc.annot.ctab <subjid> ?h <white or pial> ||stats/?h.aparc.stats ||
||<style="text-align:left" |1>wm.mgz, ribbon.mgz ||<style="text-align:left" |4>label/aparc.annot.ctab ||
||?h.white ||
||?h.pial ||
||?h.thickness ||
||<style="text-align:left;" |3>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/cortparc|cortparc2]] ||aseg.presurf.mgz ||<style="text-align:left;" |3>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_ca_label|mris_ca_label]]  -l ../label/?h.cortex.label -aseg aseg.presurf.mgz <subjid> ?h  ?h.sphere.reg  $FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs  label/?h.aparc.a2009s.annot ||<style="text-align:left;" |3>label/?h.aparc.a2009s.annot ||
||?h.sphere.reg ||
||label/?h.cortex.label ||
||<style="text-align:left" |5>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/parcstats|parcstats2]] ||<style="text-align:left" |1>label/?h.aparc.a2009s.annot ||<style="text-align:left" |5>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_anatomical_stats|mris_anatomical_stats]]  -th3 -mgz -cortex ../label/?h.cortex.label -f  stats/?h.aparc.a2009s.stats -b -a label/?h.aparc.a2009s.annot -c  label/aparc.annot.a2009s.ctab <subjid> ?h ||stats/?h.aparc.a2009s.stats ||
||<style="text-align:left" |1>wm.mgz, ribbon.mgz ||<style="text-align:left" |4>label/aparc.annot.a2009s.ctab ||
||?h.white ||
||?h.pial ||
||?h.thickness ||
||<style="text-align:left;" |3>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/cortparc|cortparc3]] ||aseg.presurf.mgz ||<style="text-align:left;" |3>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_ca_label|mris_ca_label]]   -l ../label/?h.cortex.label -aseg aseg.presurf.mgz <subjid> ?h  ?h.sphere.reg $FREESURFER_HOME/average/?h.DKTatlas.2016-03-20.gcs  ../label/?h.aparc.DKTatlas.annot ||<style="text-align:left;" |3>label/?h.aparc.DKTatlas.annot ||
||?h.sphere.reg ||
||label/?h.cortex.label ||
||<style="text-align:left" |5>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/parcstats|parcstats3]] ||<style="text-align:left" |1>label/?h.aparc.DKTatlas.annot ||<style="text-align:left" |5>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_anatomical_stats|mris_anatomical_stats]]  -th3 -mgz -cortex ../label/?h.cortex.label -f  stats/?h.aparc.DKTatlas.stats -b -a label/?h.aparc.DKTatlas.annot -c  label/aparc.annot.DKTatlas.ctab <subjid> ?h ||stats/?h.aparc.DKTatlas.stats ||
||<style="text-align:left" |1>wm.mgz, ribbon.mgz ||<style="text-align:left" |4>label/aparc.annot.DKTatlas.ctab ||
||?h.white ||
||?h.pial ||
||?h.thickness ||
||<style="text-align:left;" |4>-pctsurfcon ||rawavg.mgz ||<style="text-align:left;" |4>pctsurfcon --s <subjid> --?h-only ||<style="text-align:left;" |2>?h.w-g.pct.mgh ||
||orig.mgz ||
||?h.cortex.label ||<style="text-align:left" |2>stats/?h.w-g.pct.stats ||
||?h.white ||
||<style="text-align:left" |2>-hyporelabel ||<style="text-align:left" |1>aseg.presurf.mgz ||<style="text-align:left" |2>mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz ||<style="text-align:left" |2>aseg.presurf.hypos.mgz ||
||?h.white ||
||<style="text-align:left;" |12>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/aparc2aseg|aparc2aseg]] ||aseg.presurf.hypos.mgz ||<style="text-align:left;" |4>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_aparc2aseg|mri_aparc2aseg]] --s <subjid> --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt ||<style="text-align:left;" |4>aparc+aseg.mgz ||
||?h.ribbon.mgz ||
||label/?h.aparc.annot ||
||<style="text-align:left">ribbon.mgz ||
||aseg.presurf.hypos.mgz ||<style="text-align:left;" |4>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_aparc2aseg|mri_aparc2aseg]] --s <subjid> --volmask --annot aparc.a2009s --aseg aseg.presurf.hypos --relabel mri/norm.mgz  mri/transforms/talairach.m3z  $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca  mri/aseg.auto_noCCseg.label_intensities.txt ||<style="text-align:left;" |4>aparc.a2009s+aseg.mgz ||
||?h.ribbon.mgz ||
||label/?h.aparc.a2009s.annot ||
||<style="text-align:left">ribbon.mgz ||
||aseg.presurf.hypos.mgz ||<style="text-align:left;" |4>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_aparc2aseg|mri_aparc2aseg]] --s <subjid> --volmask --annot aparc.DKTatlas --aseg aseg.presurf.hypos --relabel mri/norm.mgz  mri/transforms/talairach.m3z  $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca  mri/aseg.auto_noCCseg.label_intensities.txt ||<style="text-align:left;" |4>aparc.DKTatlas+aseg.mgz ||
||?h.ribbon.mgz ||
||label/?h.aparc.DKTatlas.annot ||
||<style="text-align:left">ribbon.mgz ||
||<style="text-align:left;" |1>-apas2aseg ||aparc+aseg.mgz ||<style="text-align:left;" |1>apas2aseg --i aparc+aseg.mgz --o aseg.mgz ||<style="text-align:left;" |1>aseg.mgz ||
||<style="text-align:left" |2>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/segstats|segstats]] ||brainmask.mgz, norm.mgz, aseg.mgz, aseg.presurf.mgz, ribbon.mgz ||<style="text-align:left" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats|mri_segstats]]  --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty  --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0  --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz  --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol  --surf-ctx-vol --totalgray --euler --ctab  $FREESURFER_HOME/ASegStatsLUT.txt --subject <subjid> ||<style="text-align:left" |2>stats/aseg.stats ||
||?h.orig.nofix, ?h.white, ?h.pial ||
||<style="text-align:left;" |2>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/wmparc|wmparc]] ||aparc+aseg.mgz ||<style="text-align:left;" |1>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_aparc2aseg|mri_aparc2aseg]] --s <subjid> --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz ||<style="text-align:left;" |1>wmparc.mgz ||
||talairach.xfm, brainmask.mgz, norm.mgz, ribbon.mgz, wmparc.mgz, aseg.presurf.mgz, ?h.white, ?h.pial ||<style="text-align:left;" |1>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats|mri_segstats]]  --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz  --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz  --in-intensity-name norm --in-intensity-units MR --etiv --subject  <subjid> --surf-wm-vol --ctab  $FREESURFER_HOME/WMParcStatsLUT.txt ||<style="text-align:left;" |1>stats/wmparc.stats ||
||-[[https://surfer.nmr.mgh.harvard.edu/fswiki/BrodmannAreaMaps|balabels]] ||?h.sphere.reg ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_label2label|mri_label2label]]  --srcsubject fsaverage --srclabel fsaverage/label/?h.BA*.label  --trgsubject <subjid> --trglabel ?h.BA*.label --hemi ?h  --regmethod surface ||label/?h.BA*_exvivo.label label/?h.perirhinal_exvivo.label label/?h.entorhinal_exvivo.label ||





--------------------------------------------------------------
—————————————————————————————————
= ReconAllTableStable7.1.1 =

This table shows the recon-all steps for the '''stable''', publicly released, '''version 7.1.1 '''of !FreeSurfer [[DownloadAndInstall | (available here)]]. 

See also the [[https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags|OtherUsefulFlags]] for other recon-all options.
||<tablestyle="text-align:left;                    ;text-align:left">'''recon-all step''' ||'''Individual Flag''' ||'''Input''' ||'''Command Line''' ||'''Output''' ||
||<style="text-align:left" |20>'''[[https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all|recon-all]] -autorecon1 -subjid <subjid>''' ||
||<style="text-align:left" |1>-i <invol1> ||invol1.dcm ''or .nii or .mgz'' ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert|mri_convert]] invol1.dcm orig/001.mgz ||orig/001.mgz ||
||<style="text-align:left" |1>-i <invol2> ''optional'' ||invol2.dcm'' or .nii or .mgz'' ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert|mri_convert]] invol2.dcm orig/002.mgz ||orig/002.mgz ||
||<style="text-align:left" |1>-T2 <invol> ''or'' -FLAIR <invol> ''optional'' ||<style="text-align:left" |1>invol.dcm ''or .nii or .mgz'' ||<style="text-align:left" |1>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert|mri_convert]] --no_scale 1 invol.dcm orig/T2raw.mgz ''(or orig/FLAIRraw.mgz)'' ||<style="text-align:left" |1>orig/T2raw.mgz ''(or orig/FLAIRraw.mgz)'' ||
||<style="text-align:left" |4>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/motioncor|motioncor]] ||orig/001.mgz ||<style="text-align:left" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_robust_template|mri_robust_template]]  --mov 001.mgz 002.mgz --average 1 --template rawavg.mgz --satit  --inittp 1 --fixtp --noit --iscale --iscaleout --subsample 200 --lta ||<style="text-align:left" |2>rawavg.mgz ||
||orig/002.mgz ||
||rawavg.mgz ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert|mri_convert]] rawavg.mgz orig.mgz --conform ||orig.mgz ||
||orig.mgz ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_add_xform_to_header|mri_add_xform_to_header]] -c transforms/talairach.xfm orig.mgz orig.mgz ||orig.mgz ||
||<style="text-align:left" |5>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/talairach|talairach]] ||orig.mgz ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_nu_correct.mni|mri_nu_correct.mni]] --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz ||orig_nu.mgz ||
||orig_nu.mgz ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/talairach_avi|talairach_avi]] --i orig_nu.mgz --xfm transforms/talairach.auto.xfm ||transforms/talairach.auto.xfm ||
||transforms/talairach.auto.xfm ||cp transforms/talairach.auto.xfm transforms/talairach.xfm ||transforms/talairach.xfm ||
||transforms/talairach.xfm ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/talairach_afd|talairach_afd]] -T 0.005 -xfm transforms/talairach.xfm || ||
|| ||awk -f $FREESURFER_HOME/bin/extract_talairach_avi_QA.awk transforms/talairach_avi.log ||transforms/talairach_avi.log ||
||<style="text-align:left;" |2>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/nuintensitycor|nuintensitycor]] ||orig.mgz ||<style="text-align:left;" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_nu_correct.mni|mri_nu_correct.mni]] --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 ||<style="text-align:left;" |2>nu.mgz ||
||talairach.xfm ||
||<style="text-align:left" |1>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/normalization|normalization]] ||nu.mgz ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_normalize|mri_normalize]] -g 1 -mprage nu.mgz T1.mgz ||T1.mgz ||
||<style="text-align:left" |3>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/skullstrip|skullstrip]] ||nu.mgz ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_em_register|mri_em_register]] -skull nu.mgz $FREESURFER_HOME/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta ||transforms/talairach_with_skull.lta ||
||T1.mgz ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_watershed|mri_watershed]]  -T1 -brain_atlas  $FREESURFER_HOME/average/RB_all_withskull_2016-05-10.vc700.gca  transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz ||brainmask.auto.mgz ||
||brainmask.auto.mgz ||cp brainmask.auto.mgz brainmask.mgz ||brainmask.mgz ||


||<tablestyle="text-align:left;                    ;text-align:left">'''recon-all step''' ||'''Individual Flag''' ||'''Input''' ||'''Command Line''' ||'''Output''' ||
||<style="text-align:left;" |69>'''[[https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all|recon-all]] -autorecon2 -subjid <subjid>''' ||
||<style="text-align:left;" |2>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/gcareg|gcareg]] ||brainmask.mgz ||<style="text-align:left;" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_em_register|mri_em_register]] -uns 3 -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta ||<style="text-align:left;" |2>transforms/talairach.lta ||
||nu.mgz ||
||<style="text-align:left;" |3>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/canorm|canorm]] ||brainmask.mgz ||<style="text-align:left;" |3>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_ca_normalize|mri_ca_normalize]]  -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz  $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca  transforms/talairach.lta norm.mgz ||<style="text-align:left;" |3>norm.mgz ||
||nu.mgz ||
||transforms/talairach.lta ||
||<style="text-align:left;" |3>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/careg|careg]] ||brainmask.mgz ||<style="text-align:left;" |3>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_ca_register|mri_ca_register]]  -align-after -nobigventricles -mask brainmask.mgz -T  transforms/talairach.lta norm.mgz  $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca  transforms/talairach.m3z ||<style="text-align:left;" |3>transforms/talairach.m3z ||
||transforms/talairach.lta ||
||norm.mgz ||
||<style="text-align:left;" |4>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/calabel|calabel]] ||norm.mgz ||<style="text-align:left;" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_ca_label|mri_ca_label]]  -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz  transforms/talairach.m3z  $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca  aseg.auto_noCCseg.mgz ||<style="text-align:left;" |2>aseg.auto_noCCseg.mgz ||
||transforms/talairach.m3z ||
||aseg.auto_noCCseg.mgz ||<style="text-align:left;" |1>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_cc|mri_cc]] -lta <subjid>/mri/transforms/cc_up.lta -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz <subjid> ||aseg.auto.mgz ||
||aseg.auto.mgz ||cp aseg.auto.mgz aseg.presurf.mgz ||aseg.presurf.mgz ||
||<style="text-align:left;" |3>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/normalization2|normalization2]] ||brainmask.mgz ||<style="text-align:left;" |3>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_normalize|mri_normalize]] -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz ||<style="text-align:left;" |3>brain.mgz ||
||norm.mgz ||
||aseg.presurf.mgz ||
||<style="text-align:left;" |2>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/maskbfs|maskbfs]] ||brain.mgz ||<style="text-align:left;" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_mask|mri_mask]] -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz ||<style="text-align:left;" |2>brain.finalsurfs.mgz ||
||brainmask.mgz ||
||<style="text-align:left;" |6>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/segmentation|segmentation]] ||brain.mgz ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segment|mri_segment]] -mprage brain.mgz wm.seg.mgz ||wm.seg.mgz ||
||wm.seg.mgz ||<style="text-align:left;" |3>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_edit_wm_with_aseg|mri_edit_wm_with_aseg]] wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz ||<style="text-align:left;" |3>wm.asegedit.mgz ||
||aseg.presurf.mgz ||
||brain.mgz ||
||wm.asegedit.mgz ||<style="text-align:left;" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_pretess|mri_pretess]] wm.asegedit.mgz wm norm.mgz wm.mgz ||<style="text-align:left;" |2>wm.mgz ||
||norm.mgz ||
||<style="text-align:left;" |3>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/fill|fill]] ||wm.mgz ||<style="text-align:left;" |3>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_fill|mri_fill]] -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz ||filled.mgz ||
||aseg.auto_noCCseg.mgz ||<style="text-align:left;" |2>../scripts/ponscc.cut.log ||
||transforms/talairach.lta ||
||<style="text-align:left;" |8>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/tessellate|tessellate]] ||filled.mgz ||<style="text-align:left;" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_pretess|mri_pretess]] filled.mgz 255 norm.mgz filled-pretess255.mgz ||<style="text-align:left;" |2>filled-pretess255.mgz ||
||norm.mgz ||
||filled-pretess255.mgz ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_tessellate|mri_tessellate]] filled-pretess255.mgz 255 lh.orig.nofix ||lh.orig.nofix ||
||filled.mgz ||<style="text-align:left;" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_pretess|mri_pretess]] filled.mgz 127 norm.mgz filled-pretess127.mgz ||<style="text-align:left;" |2>filled-pretess127.mgz ||
||norm.mgz ||
||filled-pretess127.mgz ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_tessellate|mri_tessellate]] filled-pretess127.mgz 127 rh.orig.nofix ||rh.orig.nofix ||
||?h.orig.nofix ||mris_extract_main_component ?h.orig.nofix ?h.orig.nofix ||?h.orig.nofix ||
|| ||rm -f filled-pretess255.mgz filled-pretess127.mgz || ||
||-[[https://surfer.nmr.mgh.harvard.edu/fswiki/smooth|smooth1]] ||?h.orig.nofix ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_smooth|mris_smooth]] -nw ?h.orig.nofix ?h.smoothwm.nofix ||?h.smoothwm.nofix ||
||-[[https://surfer.nmr.mgh.harvard.edu/fswiki/inflate|inflate1]] ||?h.smoothwm.nofix ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_inflate|mris_inflate]] -no-save-sulc ?h.smoothwm.nofix ?h.inflated.nofix ||?h.inflated.nofix ||
||-[[https://surfer.nmr.mgh.harvard.edu/fswiki/qsphere|qsphere]] ||?h.inflated.nofix ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_sphere|mris_sphere]] -q ?h.inflated.nofix ?h.qsphere.nofix ||?h.qsphere.nofix ||
||<style="text-align:left;" |6>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/fix|fix]] ||?h.orig.nofix ||cp ?h.orig.nofix ?h.orig ||?h.orig ||
||?h.inflated.nofix ||cp ?h.inflated.nofix ?h.inflated ||?h.inflated ||
||?h.qsphere.nofix ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_fix_topology|mris_fix_topology]] -mgz -sphere qsphere.nofix -ga <subjid> ?h ||?h.orig ||
||?h.orig ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_euler_number|mris_euler_number]] ?h.orig ||?h.orig ||
||?h.orig ||mris_remove_intersection ?h.orig ?h.orig ||?h.orig ||
|| ||rm ?h.inflated || ||
||<style="text-align:left;" |8>-white ||<style="text-align:left;" |1>aseg.presurf.mgz ||<style="text-align:left;" |8>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_make_surfaces|mris_make_surfaces]] -aseg ../mri/aseg.presurf -whiteonly -noaparc -mgz -T1 brain.finalsurfs <subjid> ?h ||<style="text-align:left" |4>?h.white.preaparc ||
||<style="text-align:left">brain.finalsurfs.mgz ||
||<style="text-align:left">wm.mgz ||
||<style="text-align:left">filled.mgz ||
||<style="text-align:left;" |4>?h.orig ||
||?h.curv ||
||?h.area ||
||?h.cortex.label ||
||-[[https://surfer.nmr.mgh.harvard.edu/fswiki/smooth|smooth2]] ||?h.white.preaparc ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_smooth|mris_smooth]] -n 3 -nw ?h.white.preaparc ?h.smoothwm ||?h.smoothwm ||
||<style="text-align:left" |2>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/inflate|inflate2]] ||<style="text-align:left" |2>?h.smoothwm ||<style="text-align:left" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_inflate|mris_inflate]] ?h.smoothwm ?h.inflated ||?h.inflated ||
||?h.sulc ||
||<style="text-align:left" |4>-curvHK ||<style="text-align:left" |2>?h.white.preaparc ||<style="text-align:left" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_curvature|mris_curvature]] -w ?h.white.preaparc ||<style="text-align:left" |1>?h.white.H ||
||?h.white.K ||
||<style="text-align:left" |2>?h.inflated ||<style="text-align:left" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_curvature|mris_curvature]] -thresh .999 -n -a 5 -w -distances 10 10 ?h.inflated ||<style="text-align:left" |1>?h.inflated.H ||
||?h.inflated.K ||
||<style="text-align:left" |3>-curvstats ||<style="text-align:left">?h.smoothwm ||<style="text-align:left" |3>mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/?h.curv.stats -F smoothwm <subjid> ?h curv sulc ||<style="text-align:left" |3>stats/?h.curv.stats ||
||<style="text-align:left">?h.curv ||
||<style="text-align:left">?h.sulc ||


||<tablestyle="text-align:left;                    ;text-align:left">'''recon-all step''' ||'''Individual Flag''' ||'''Input''' ||'''Command Line''' ||'''Output''' ||
||<style="text-align:left;" |85>'''[[https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all|recon-all]] -autorecon3 -subjid <subjid>''' ||
||<style="text-align:left" |2>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/sphere|sphere]] ||?h.inflated ||<style="text-align:left" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_sphere|mris_sphere]] ?h.inflated ?h.sphere ||<style="text-align:left" |2>?h.sphere ||
||<style="text-align:left">?h.smoothwm ||
||-[[https://surfer.nmr.mgh.harvard.edu/fswiki/surfreg|surfreg]] ||?h.sphere ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_register|mris_register]] -curv ?h.sphere $FREESURFER_HOME/average/?h.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ?h.sphere.reg ||?h.sphere.reg ||
||<style="text-align:left;" |2>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/jacobian_white|jacobian_white]] ||?h.white.preaparc ||<style="text-align:left;" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_jacobian|mris_jacobian]] ?h.white.preaparc ?h.sphere.reg ?h.jacobian_white ||<style="text-align:left;" |2>?h.jacobian_white ||
||?h.sphere.reg ||
||-[[https://surfer.nmr.mgh.harvard.edu/fswiki/avgcurv|avgcurv]] ||?h.sphere.reg ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mrisp_paint|mrisp_paint]] -a 5 $FREESURFER_HOME/average/?h.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ?h.sphere.reg ?h.avg_curv ||?h.avg_curv ||
||<style="text-align:left;" |3>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/cortparc|cortparc]] ||aseg.presurf.mgz ||<style="text-align:left;" |3>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_ca_label|mris_ca_label]]  -l ../label/?h.cortex.label -aseg mri/aseg.presurf.mgz <subjid>  ?h ?h.sphere.reg  $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs  ?h.aparc.annot ||<style="text-align:left;" |3>label/?h.aparc.annot ||
||<style="text-align:left">?h.cortex.label ||
||?h.sphere.reg ||
||<style="text-align:left;" |8>-pial ||<style="text-align:left;" |1>aseg.presurf.mgz ||<style="text-align:left;" |8>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_make_surfaces|mris_make_surfaces]] -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs <subjid> ?h ||<style="text-align:left" |4>?h.pial ||
||brain.finalsurfs.mgz ||
||wm.mgz ||
||filled.mgz ||
||<style="text-align:left;" |3>?h.orig ||
||?h.curv.pial ||
||<style="text-align:left">?h.area.pial ||
||<style="text-align:left" |1>label/?h.aparc.annot ||?h.thickness ||
||<style="text-align:left;" |17>-T2pial ''or'' <<BR>>-FLAIRpial ''optional'' ||orig/T2raw.mgz ||bbregister --s <subjid> --mov mri/orig/T2raw.mgz --lta mri/transforms/T2raw.lta --init-fsl --T2 ||transforms/T2raw.lta ||
||orig/T2raw.mgz ||<style="text-align:left" |2>mri_convert -odt float -at mri/transforms/T2raw.lta -rt cubic -ns 1 -rl mri/orig.mgz mri/orig/T2raw.mgz mri/T2.prenorm.mgz ||<style="text-align:left" |2>T2.prenorm.mgz ||
||transforms/T2raw.lta ||
||aseg.presurf.mgz ||<style="text-align:left" |3>mri_normalize -sigma 0.5 -nonmax_suppress 0 -min_dist 1 -aseg mri/aseg.presurf.mgz -surface surf/rh.white identity.nofile -surface surf/lh.white identity.nofile mri/T2.prenorm.mgz mri/T2.norm.mgz ||<style="text-align:left" |3>T2.norm.mgz ||
||?h.white ||
||T2.prenorm.mgz ||
||T2.norm.mgz ||<style="text-align:center" |2>mri_mask mri/T2.norm.mgz mri/brainmask.mgz mri/T2.mgz ||<style="text-align:center" |2>T2.mgz ||
||brainmask.mgz ||
||?h.pial ||cp -v surf/?h.pial surf/?h.woT2.pial ||?h.woT2.pial ||
||aseg.presurf.mgz ||<style="text-align:left" |9>[[mris_make_surfaces]] -orig_white white -orig_pial woT2.pial -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs -T2 ../mri/T2 -nsigma_above 2 -nsigma_below 5 <subjid> ?h ||<style="text-align:left" |3>?h.pial ||
||brain.finalsurfs.mgz ||
||wm.mgz ||
||filled.mgz ||<style="text-align:left" |2>?h.curv.pial ||
||?h.white ||
||<style="text-align:left" |1>label/?h.aparc.annot ||<style="text-align:left" |1>?h.area.pial ||
||<style="text-align:left" |1>T2.mgz ||<style="text-align:left" |3>?h.thickness ||
||?h.woT2.pial ||
|| ||
||<style="text-align:left;" |3>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/cortribbon|cortribbon]] ||aseg.presurf.mgz ||<style="text-align:left" |3>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_volmask|mris_volmask]] --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon <subjid> ||<style="text-align:left;" |2>?h.ribbon.mgz ||
||?h.white ||
||?h.pial ||<style="text-align:left" |1>ribbon.mgz ||
||<style="text-align:left" |5>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/parcstats|parcstats]] ||<style="text-align:left" |1>label/?h.aparc.annot ||<style="text-align:left" |5>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_anatomical_stats|mris_anatomical_stats]]  -th3 -mgz -cortex ../label/?h.cortex.label -f stats/?h.aparc.stats -b  -a label/?h.aparc.annot -c label/aparc.annot.ctab <subjid> ?h <white or pial> ||stats/?h.aparc.stats ||
||<style="text-align:left" |1>wm.mgz, ribbon.mgz ||<style="text-align:left" |4>label/aparc.annot.ctab ||
||?h.white ||
||?h.pial ||
||?h.thickness ||
||<style="text-align:left;" |3>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/cortparc|cortparc2]] ||aseg.presurf.mgz ||<style="text-align:left;" |3>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_ca_label|mris_ca_label]]  -l ../label/?h.cortex.label -aseg aseg.presurf.mgz <subjid> ?h  ?h.sphere.reg  $FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs  label/?h.aparc.a2009s.annot ||<style="text-align:left;" |3>label/?h.aparc.a2009s.annot ||
||?h.sphere.reg ||
||label/?h.cortex.label ||
||<style="text-align:left" |5>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/parcstats|parcstats2]] ||<style="text-align:left" |1>label/?h.aparc.a2009s.annot ||<style="text-align:left" |5>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_anatomical_stats|mris_anatomical_stats]]  -th3 -mgz -cortex ../label/?h.cortex.label -f  stats/?h.aparc.a2009s.stats -b -a label/?h.aparc.a2009s.annot -c  label/aparc.annot.a2009s.ctab <subjid> ?h ||stats/?h.aparc.a2009s.stats ||
||<style="text-align:left" |1>wm.mgz, ribbon.mgz ||<style="text-align:left" |4>label/aparc.annot.a2009s.ctab ||
||?h.white ||
||?h.pial ||
||?h.thickness ||
||<style="text-align:left;" |3>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/cortparc|cortparc3]] ||aseg.presurf.mgz ||<style="text-align:left;" |3>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_ca_label|mris_ca_label]]   -l ../label/?h.cortex.label -aseg aseg.presurf.mgz <subjid> ?h  ?h.sphere.reg $FREESURFER_HOME/average/?h.DKTatlas.2016-03-20.gcs  ../label/?h.aparc.DKTatlas.annot ||<style="text-align:left;" |3>label/?h.aparc.DKTatlas.annot ||
||?h.sphere.reg ||
||label/?h.cortex.label ||
||<style="text-align:left" |5>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/parcstats|parcstats3]] ||<style="text-align:left" |1>label/?h.aparc.DKTatlas.annot ||<style="text-align:left" |5>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_anatomical_stats|mris_anatomical_stats]]  -th3 -mgz -cortex ../label/?h.cortex.label -f  stats/?h.aparc.DKTatlas.stats -b -a label/?h.aparc.DKTatlas.annot -c  label/aparc.annot.DKTatlas.ctab <subjid> ?h ||stats/?h.aparc.DKTatlas.stats ||
||<style="text-align:left" |1>wm.mgz, ribbon.mgz ||<style="text-align:left" |4>label/aparc.annot.DKTatlas.ctab ||
||?h.white ||
||?h.pial ||
||?h.thickness ||
||<style="text-align:left;" |4>-pctsurfcon ||rawavg.mgz ||<style="text-align:left;" |4>pctsurfcon --s <subjid> --?h-only ||<style="text-align:left;" |2>?h.w-g.pct.mgh ||
||orig.mgz ||
||?h.cortex.label ||<style="text-align:left" |2>stats/?h.w-g.pct.stats ||
||?h.white ||
||<style="text-align:left" |2>-hyporelabel ||<style="text-align:left" |1>aseg.presurf.mgz ||<style="text-align:left" |2>mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz ||<style="text-align:left" |2>aseg.presurf.hypos.mgz ||
||?h.white ||
||<style="text-align:left;" |12>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/aparc2aseg|aparc2aseg]] ||aseg.presurf.hypos.mgz ||<style="text-align:left;" |4>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_aparc2aseg|mri_aparc2aseg]] --s <subjid> --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt ||<style="text-align:left;" |4>aparc+aseg.mgz ||
||?h.ribbon.mgz ||
||label/?h.aparc.annot ||
||<style="text-align:left">ribbon.mgz ||
||aseg.presurf.hypos.mgz ||<style="text-align:left;" |4>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_aparc2aseg|mri_aparc2aseg]] --s <subjid> --volmask --annot aparc.a2009s --aseg aseg.presurf.hypos --relabel mri/norm.mgz  mri/transforms/talairach.m3z  $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca  mri/aseg.auto_noCCseg.label_intensities.txt ||<style="text-align:left;" |4>aparc.a2009s+aseg.mgz ||
||?h.ribbon.mgz ||
||label/?h.aparc.a2009s.annot ||
||<style="text-align:left">ribbon.mgz ||
||aseg.presurf.hypos.mgz ||<style="text-align:left;" |4>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_aparc2aseg|mri_aparc2aseg]] --s <subjid> --volmask --annot aparc.DKTatlas --aseg aseg.presurf.hypos --relabel mri/norm.mgz  mri/transforms/talairach.m3z  $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca  mri/aseg.auto_noCCseg.label_intensities.txt ||<style="text-align:left;" |4>aparc.DKTatlas+aseg.mgz ||
||?h.ribbon.mgz ||
||label/?h.aparc.DKTatlas.annot ||
||<style="text-align:left">ribbon.mgz ||
||<style="text-align:left;" |1>-apas2aseg ||aparc+aseg.mgz ||<style="text-align:left;" |1>apas2aseg --i aparc+aseg.mgz --o aseg.mgz ||<style="text-align:left;" |1>aseg.mgz ||
||<style="text-align:left" |2>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/segstats|segstats]] ||brainmask.mgz, norm.mgz, aseg.mgz, aseg.presurf.mgz, ribbon.mgz ||<style="text-align:left" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats|mri_segstats]]  --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty  --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0  --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz  --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol  --surf-ctx-vol --totalgray --euler --ctab  $FREESURFER_HOME/ASegStatsLUT.txt --subject <subjid> ||<style="text-align:left" |2>stats/aseg.stats ||
||?h.orig.nofix, ?h.white, ?h.pial ||
||<style="text-align:left;" |2>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/wmparc|wmparc]] ||aparc+aseg.mgz ||<style="text-align:left;" |1>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_aparc2aseg|mri_aparc2aseg]] --s <subjid> --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz ||<style="text-align:left;" |1>wmparc.mgz ||
||talairach.xfm, brainmask.mgz, norm.mgz, ribbon.mgz, wmparc.mgz, aseg.presurf.mgz, ?h.white, ?h.pial ||<style="text-align:left;" |1>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats|mri_segstats]]  --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz  --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz  --in-intensity-name norm --in-intensity-units MR --etiv --subject  <subjid> --surf-wm-vol --ctab  $FREESURFER_HOME/WMParcStatsLUT.txt ||<style="text-align:left;" |1>stats/wmparc.stats ||
||-[[https://surfer.nmr.mgh.harvard.edu/fswiki/BrodmannAreaMaps|balabels]] ||?h.sphere.reg ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_label2label|mri_label2label]]  --srcsubject fsaverage --srclabel fsaverage/label/?h.BA*.label  --trgsubject <subjid> --trglabel ?h.BA*.label --hemi ?h  --regmethod surface ||label/?h.BA*_exvivo.label label/?h.perirhinal_exvivo.label label/?h.entorhinal_exvivo.label ||