#acl LcnGroup:read,write,delete,revert  KhoaNguyen:read,write,delete,revert All:read 

== FreeSurfer Tutorial: Useful recon-all flags. ==

This page extends ReconAllDevTable.
The following flags can be used in conjunction with individual steps or the entire process:

||<bgcolor='#FFFFE0'>'''-autorecon-all'''||<|2-5(bgcolor='#E0E0FF'>either of these flags will work to run the entire recon-all process.||
||<bgcolor='#FFFFE0'>'''-all'''||
##||<bgcolor='#FFFFE0'>'''-legacy'''||<-5(bgcolor='#E0E0FF'>use this flag on data that was previously processed with a different version of freesurfer.  Use this flag THE FIRST TIME only.  It will automatically keep all your prior edits (talairach, control points, white matter etc). ||
||<bgcolor='#FFFFE0'>'''-clean-tal'''||<-5(bgcolor='#E0E0FF'>trashes any manual edits to the talairach, makes talairach.xfm and talairach.auto.xfm the same and runs using the automatically generated talairach.xfm||
||<bgcolor='#FFFFE0'>'''-clean-seed'''||<-5(bgcolor='#E0E0FF'>trashes all saved seed point for the cutting planes and uses the automatically set cutting planes.||
||<bgcolor='#FFFFE0'>'''-clean-cp'''||<-5(bgcolor='#E0E0FF'>trashes control points and runs the normalization without control points.||
||<bgcolor='#FFFFE0'>'''-clean-bm'''||<-5(bgcolor='#E0E0FF'>trashes any manual edits to the brainmask.mgz volume, makes brainmask.mgz and brainmask.auto.mgz the same and runs using the automatically generated brainmask.mgz||
||<bgcolor='#FFFFE0'>'''-clean-wm'''||<-5(bgcolor='#E0E0FF'>trashes any manual edits to the wm.mgz volume and runs using the automatically generated wm.mgz.||
||<bgcolor='#FFFFE0'>'''-clean-aseg'''||<-5(bgcolor='#E0E0FF'>trashes any manual edits to the aseg.mgz and runs using the automatically generated aseg.mgz||
||<bgcolor='#FFFFE0'>'''-clean-cpwm'''||<-5(bgcolor='#E0E0FF'>combination of -clean-cp and -clean-wm.||
||<bgcolor='#FFFFE0'>'''-clean-xopts'''||<-5(bgcolor='#E0E0FF'>delete pre-existing expert options file||
||<bgcolor='#FFFFE0'>'''-clean-cw256'''||<-5(bgcolor='#E0E0FF'>||
||<bgcolor='#FFFFE0'>'''-clean-lta'''||<-5(bgcolor='#E0E0FF'>moves *.lta files to trash ||
||<bgcolor='#FFFFE0'>'''-clean-pfh'''||<-5(bgcolor='#E0E0FF'> trashes preflood height volumes (skullstrip)||
||<bgcolor='#FFFFE0'>'''-clean-bfse'''||<-5(bgcolor='#E0E0FF'> trashes edits to brain.finalsurfs.manedit.mgz ||
||<bgcolor='#FFFFE0'>'''-clean'''||<-5(bgcolor='#E0E0FF'>use this flag to clear all of your manual edits and run it completely fresh.||
||<bgcolor='#FFFFE0'>'''-deface'''||<bgcolor='#E0E0FF'>removes the face from the orig volume to anonymize it.||
||<bgcolor='#FFFFE0'>'''-dontrun'''||<-5(bgcolor='#E0E0FF'>useful for debugging. just prints the commands that will run (does not execute them).||
||<bgcolor='#FFFFE0'>'''-gcut'''||<-5(bgcolor='#E0E0FF'>use this flag when skull strip leaves a little bit of dura behind. In this case, adjusting the watershed parameters won't be as useful and manual edits will take too long. <<BR>>INFO: Care must be taken to thoroughly inspect your data when using -gcut. In particular, inpsect the edges of gm and cerebellum for over-aggressive cutting. Add -segmentation brainmask.gcuts.mgz to tkmedit to view the voxels which gcut has removed. ||
||<bgcolor='#FFFFE0'>'''-mprage'''||<-5(bgcolor='#E0E0FF'>changes some of the assumptions about CNR and SNR, and will use a higher threshold to allow the control points to grow more liberally than in general.||
||<bgcolor='#FFFFE0'>'''-3T'''|| Enables the two 3T specific options that recon-all supports: nu intensity correction params, and the special schwartz atlas ||
||<bgcolor='#FFFFE0'>'''-multistrip'''||<-5(bgcolor='#E0E0FF'>use this flag on a subject when you would like to get skullstrip results using several different watershed preflood heights simultaneously. Output will be nu, orig, and T1 volumes stripped at these heights:  5, 10, 20, 30. You can change which preflood heights are used by setting this variable first: setenv WATERSHED_PREFLOOD_HEIGHTS '20 30 40 50'. Be sure to use -clean-bm with this flag. ||
||<bgcolor='#FFFFE0'>'''-noaseg'''||<-5(bgcolor='#E0E0FF'>use this flag on subjects that either cannot use an aseg (i.e., baby brains or non-human primates) or for those for which you will never want an aseg.  It skips the subcortical segmentation and will not try and use it (aseg.mgz) in any of the subsequent steps.||
||<bgcolor='#FFFFE0'>'''-norandomness'''||<-5(bgcolor='#E0E0FF'>use this flag on a subject when it is necessary to ensure that results are exactly the same from run to run. it seeds the random number generator used by some algorithms with the same number, removing any variability.||
||<bgcolor='#FFFFE0'>'''-notal-check'''||<-5(bgcolor='#E0E0FF'>use this flag when running a subject after receiving an error about Tailarach Failure Detection and the tailarach transform looks fine after checking it with this command line: tkregister2 --mgz --s <subjid> --fstal ||
||<bgcolor='#FFFFE0'>'''-no-wsgcaatlas'''||<-5(bgcolor='#E0E0FF'>use this flag when you have reason to believe that certain anatomy could be an outlier, and is responsible for causing the skullstripping step to fail or produce poor skullstripping (wsgcaatlas = with skull gaussian classifier array atlas)||
||<bgcolor='#FFFFE0'>'''-time'''||<-5(bgcolor='#E0E0FF'>this flag can be added to report the time each step takes ||
||<bgcolor='#FFFFE0'>'''-canorm-usecps'''||<bgcolor='#E0E0FF'> This flag uses control points to change the aseg. This can be particularly useful when you have an overlabeled putamen (the strategy would be to put the control points in white matter surrounding the putamen. It is advised to do these types of edits first before using control points to edit the surfaces (the default use of control points).||
||<bgcolor='#FFFFE0'>'''-vno_match_check'''||<bgcolor='#E0E0FF'> Confirms that the surface data is out of sync in case an error indicates that there is a size mismatch. Then run from whatever stage that is out of sync.||

||<rowbgcolor='#80FF80'>'''recon-all flag'''||'''Used with step'''||'''Description'''||
||<|2(bgcolor='#FFFFE0'>'''-no-ca-align'''||<bgcolor='#FFFFE0'>-careg||<|2(bgcolor='#E0E0FF'>this flag should be used if the data to be processed comes from the same scanner platform and pulse sequence as the atlas.  With the FreeSurfer RB40 atlas this means MPRAGE on a 1.5T Siemens scanner.||
||<bgcolor='#FFFFE0'>-calabel||
||<|7(bgcolor='#FFFFE0'>'''-subcortseg'''||<bgcolor='#FFFFE0'>-gcareg||<|7(bgcolor='#E0E0FF'>runs the subcortical segmentation and associated statistics||
||<bgcolor='#FFFFE0'>-canorm||
||<bgcolor='#FFFFE0'>-careg||
||<bgcolor='#FFFFE0'>-rmneck||
||<bgcolor='#FFFFE0'>-skull-lta||
||<bgcolor='#FFFFE0'>-calabel||
||<bgcolor='#FFFFE0'>-segstats||
||<bgcolor='#FFFFE0'>'''-cc-crs <c r s>'''||<bgcolor='#FFFFE0'>-fill||<bgcolor='#E0E0FF'>manually sets the corpus callosum seed point||
||<bgcolor='#FFFFE0'>'''-pons-crs <c r s>'''||<bgcolor='#FFFFE0'>-fill||<bgcolor='#E0E0FF'>manually sets the pons seed point||
||<bgcolor='#FFFFE0'>'''-rh-crs <c r s>'''||<bgcolor='#FFFFE0'>-fill||<bgcolor='#E0E0FF'>manually sets the right hemisphere seed point||
||<bgcolor='#FFFFE0'>'''-lh-crs <c r s>'''||<bgcolor='#FFFFE0'>-fill||<bgcolor='#E0E0FF'>manually sets the left hemisphere seed point||
||<bgcolor='#FFFFE0'>'''-jacobian_dist0'''||<bgcolor='#FFFFE0'> ||<bgcolor='#E0E0FF'>Computes how much an individual surface must be distorted in order to perfectly match the atlas (ie, distance contraints are turned off). ||

The following flags can be used after certain manual intervention to regenerate accurate volumes and surfaces (if a data set has or needs spherical morphing, add the -autorecon3 flag):


||<tablestyle="text-align:left;        ;text-align:left">'''recon-all step''' ||'''Individual Flag''' ||'''Input''' ||'''Command Line''' ||'''Output''' ||
||<style="text-align:left;" |50>'''[[recon-all]] -autorecon2-wm -subjid subj '''(use this after doing manual wm edits.  This flag will regenerate all necessary volumes and surfaces) ||
||<style="text-align:left;" |3>-[[normalization2]] ||brainmask.mgz ||<style="text-align:left;" |3>[[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>-[[maskbfs]] ||brain.mgz ||<style="text-align:left;" |2>[[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>-[[segmentation]] ||brain.mgz ||[[mri_segment]] -mprage brain.mgz wm.seg.mgz ||wm.seg.mgz ||
||wm.seg.mgz ||<style="text-align:left;" |3>[[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>[[mri_pretess]] wm.asegedit.mgz wm norm.mgz wm.mgz ||<style="text-align:left;" |2>wm.mgz ||
||norm.mgz ||
||<style="text-align:left;" |3>-[[fill]] ||wm.mgz ||<style="text-align:left;" |3>[[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>-[[tessellate]] ||filled.mgz ||<style="text-align:left;" |2>[[mri_pretess]] filled.mgz 255 norm.mgz filled-pretess255.mgz ||<style="text-align:left;" |2>filled-pretess255.mgz ||
||norm.mgz ||
||filled-pretess255.mgz ||[[mri_tessellate]] filled-pretess255.mgz 255 lh.orig.nofix ||lh.orig.nofix ||
||filled.mgz ||<style="text-align:left;" |2>[[mri_pretess]] filled.mgz 127 norm.mgz filled-pretess127.mgz ||<style="text-align:left;" |2>filled-pretess127.mgz ||
||norm.mgz ||
||filled-pretess127.mgz ||[[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 || ||
||-[[smooth|smooth1]] ||?h.orig.nofix ||[[mris_smooth]] -nw ?h.orig.nofix ?h.smoothwm.nofix ||?h.smoothwm.nofix ||
||-[[inflate|inflate1]] ||?h.smoothwm.nofix ||[[mris_inflate]] -no-save-sulc ?h.smoothwm.nofix ?h.inflated.nofix ||?h.inflated.nofix ||
||-[[qsphere]] ||?h.inflated.nofix ||[[mris_sphere]] -q ?h.inflated.nofix ?h.qsphere.nofix ||?h.qsphere.nofix ||
||<style="text-align:left;" |6>-[[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 ||[[mris_fix_topology]] -mgz -sphere qsphere.nofix -ga <subjid> ?h ||?h.orig ||
||?h.orig ||[[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>[[mris_make_surfaces]] -aseg ../mri/aseg.presurf -whiteonly -noaparc -mgz -T1 brain.finalsurfs <subjid> ?h ||<style="text-align:left" |4>?h.white ||
||<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 ||
||-[[smooth|smooth2]] ||?h.white ||[[mris_smooth]] -n 3 -nw ?h.white ?h.smoothwm ||?h.smoothwm ||
||<style="text-align:left" |2>-[[inflate|inflate2]] ||<style="text-align:left" |2>?h.smoothwm ||<style="text-align:left" |2>[[mris_inflate]] ?h.smoothwm ?h.inflated ||?h.inflated ||
||?h.sulc ||
||<style="text-align:left" |4>-curvHK ||<style="text-align:left" |2>?h.white ||<style="text-align:left" |2>[[mris_curvature]] -w ?h.white ||<style="text-align:left" |1>?h.white.H ||
||?h.white.K ||
||<style="text-align:left" |2>?h.inflated ||<style="text-align:left" |2>[[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;" |50>'''[[recon-all]] -autorecon2-noaseg -subjid subj '''(use this after doing aseg edits.  This flag will regenerate all necessary volumes and surfaces) ||
||<style="text-align:left;" |3>-[[normalization2]] ||brainmask.mgz ||<style="text-align:left;" |3>[[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>-[[maskbfs]] ||brain.mgz ||<style="text-align:left;" |2>[[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>-[[segmentation]] ||brain.mgz ||[[mri_segment]] -mprage brain.mgz wm.seg.mgz ||wm.seg.mgz ||
||wm.seg.mgz ||<style="text-align:left;" |3>[[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>[[mri_pretess]] wm.asegedit.mgz wm norm.mgz wm.mgz ||<style="text-align:left;" |2>wm.mgz ||
||norm.mgz ||
||<style="text-align:left;" |3>-[[fill]] ||wm.mgz ||<style="text-align:left;" |3>[[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>-[[tessellate]] ||filled.mgz ||<style="text-align:left;" |2>[[mri_pretess]] filled.mgz 255 norm.mgz filled-pretess255.mgz ||<style="text-align:left;" |2>filled-pretess255.mgz ||
||norm.mgz ||
||filled-pretess255.mgz ||[[mri_tessellate]] filled-pretess255.mgz 255 lh.orig.nofix ||lh.orig.nofix ||
||filled.mgz ||<style="text-align:left;" |2>[[mri_pretess]] filled.mgz 127 norm.mgz filled-pretess127.mgz ||<style="text-align:left;" |2>filled-pretess127.mgz ||
||norm.mgz ||
||filled-pretess127.mgz ||[[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 || ||
||-[[smooth|smooth1]] ||?h.orig.nofix ||[[mris_smooth]] -nw ?h.orig.nofix ?h.smoothwm.nofix ||?h.smoothwm.nofix ||
||-[[inflate|inflate1]] ||?h.smoothwm.nofix ||[[mris_inflate]] -no-save-sulc ?h.smoothwm.nofix ?h.inflated.nofix ||?h.inflated.nofix ||
||-[[qsphere]] ||?h.inflated.nofix ||[[mris_sphere]] -q ?h.inflated.nofix ?h.qsphere.nofix ||?h.qsphere.nofix ||
||<style="text-align:left;" |6>-[[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 ||[[mris_fix_topology]] -mgz -sphere qsphere.nofix -ga <subjid> ?h ||?h.orig ||
||?h.orig ||[[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>[[mris_make_surfaces]] -aseg ../mri/aseg.presurf -whiteonly -noaparc -mgz -T1 brain.finalsurfs <subjid> ?h ||<style="text-align:left" |4>?h.white ||
||<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 ||
||-[[smooth|smooth2]] ||?h.white ||[[mris_smooth]] -n 3 -nw ?h.white ?h.smoothwm ||?h.smoothwm ||
||<style="text-align:left" |2>-[[inflate|inflate2]] ||<style="text-align:left" |2>?h.smoothwm ||<style="text-align:left" |2>[[mris_inflate]] ?h.smoothwm ?h.inflated ||?h.inflated ||
||?h.sulc ||
||<style="text-align:left" |4>-curvHK ||<style="text-align:left" |2>?h.white ||<style="text-align:left" |2>[[mris_curvature]] -w ?h.white ||<style="text-align:left" |1>?h.white.H ||
||?h.white.K ||
||<style="text-align:left" |2>?h.inflated ||<style="text-align:left" |2>[[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;" |100>'''[[recon-all]] -autorecon-pial -subjid subj ''' (use this after editing brainmask.mgz or brain.finalsurfs.mgz to alter pial surface. This flag will regenerate all final surfaces)<<BR>>**note** this flag includes all the steps in -autorecon3 therefore it is not necessary to pass the -autorecon3 flag after this||
||<style="text-align:left;" |2>-[[maskbfs]] ||brain.mgz ||<style="text-align:left;" |2>[[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;" |8>-white ||<style="text-align:left;" |1>aseg.presurf.mgz ||<style="text-align:left;" |8>[[mris_make_surfaces]] -aseg ../mri/aseg.presurf -whiteonly -noaparc -mgz -T1 brain.finalsurfs <subjid> ?h ||<style="text-align:left" |4>?h.white ||
||<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 ||
||-[[smooth|smooth2]] ||?h.white ||[[mris_smooth]] -n 3 -nw ?h.white ?h.smoothwm ||?h.smoothwm ||
||<style="text-align:left" |2>-[[inflate|inflate2]] ||<style="text-align:left" |2>?h.smoothwm ||<style="text-align:left" |2>[[mris_inflate]] ?h.smoothwm ?h.inflated ||?h.inflated ||
||?h.sulc ||
||<style="text-align:left" |4>-curvHK ||<style="text-align:left" |2>?h.white ||<style="text-align:left" |2>[[mris_curvature]] -w ?h.white ||<style="text-align:left" |1>?h.white.H ||
||?h.white.K ||
||<style="text-align:left" |2>?h.inflated ||<style="text-align:left" |2>[[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 ||
||<style="text-align:left" |2>-[[sphere]] ||?h.inflated ||<style="text-align:left" |2>[[mris_sphere]] ?h.inflated ?h.sphere ||<style="text-align:left" |2>?h.sphere ||
||<style="text-align:left">?h.smoothwm ||
||-[[surfreg]] ||?h.sphere ||[[mris_register]] -curv ?h.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif ?h.sphere.reg ||?h.sphere.reg ||
||<style="text-align:left;" |2>-[[jacobian_white]] ||?h.white ||<style="text-align:left;" |2>[[mris_jacobian]] ?h.white ?h.sphere.reg ?h.jacobian_white ||<style="text-align:left;" |2>?h.jacobian_white ||
||?h.sphere.reg ||
||-[[avgcurv]] ||?h.sphere.reg ||[[mrisp_paint]] -a 5 $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif#6 ?h.sphere.reg ?h.avg_curv ||?h.avg_curv ||
||<style="text-align:left;" |3>-[[cortparc]] ||aseg.presurf.mgz ||<style="text-align:left;" |3>[[mris_ca_label]] -l ../label/lh.cortex.label -aseg mri/aseg.presurf.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.2007-06-20gcs ?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>[[mris_make_surfaces]] -orig_white white -orig_pial white -aseg ../mri/aseg.presurf -nowhite -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;" |3>-[[cortribbon]] ||aseg.presurf.mgz ||<style="text-align:left" |3>[[mris_volmask]] --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>-[[parcstats]] ||<style="text-align:left" |1>label/?h.aparc.annot ||<style="text-align:left" |5>[[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 ||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>-[[cortparc|cortparc2]] ||aseg.presurf.mgz ||<style="text-align:left;" |3>[[mris_ca_label]] -l ../label/lh.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>-[[parcstats|parcstats2]] ||<style="text-align:left" |1>label/?h.aparc.a2009s.annot ||<style="text-align:left" |5>[[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>-[[cortparc|cortparc3]] ||aseg.presurf.mgz ||<style="text-align:left;" |3>[[mris_ca_label]]  ../label/lh.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>-[[parcstats|parcstats3]] ||<style="text-align:left" |1>label/?h.aparc.DKTatlas.annot ||<style="text-align:left" |5>[[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>-[[aparc2aseg]] ||aseg.presurf.hypos.mgz ||<style="text-align:left;" |4>[[mri_aparc2aseg]] --s <subjid> --ribbon ||<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>[[mri_aparc2aseg]] --s <subjid> --ribbon --annot aparc.a2009s ||<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>[[mri_aparc2aseg]] --s <subjid> --ribbon --annot aparc.DKTatlas ||<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>-[[segstats]] ||brainmask.mgz, norm.mgz, aseg.mgz, aseg.presurf.mgz, ribbon.mgz ||<style="text-align:left" |2>[[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 --totalgray --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>-[[wmparc]] ||aparc+aseg.mgz ||<style="text-align:left;" |1>[[mri_aparc2aseg]] --s <subjid> --labelwm --hypo-as-wm --rip-unknown --ribbon --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>[[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/FreeSurferColorLUT.txt ||<style="text-align:left;" |1>stats/wmparc.stats ||
||-[[BrodmannAreaMaps|balabels]] ||?h.sphere.reg ||[[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 ||


||<tablestyle="text-align:left;        ;text-align:left">'''recon-all step''' ||'''Individual Flag''' ||'''Input''' ||'''Command Line''' ||'''Output''' ||
||<style="text-align:left;" |50>'''[[recon-all]] -autorecon2-perhemi -subjid subj '''(use this to run only the steps that are run per-hemisphere, in conjunction with the '-hemi' flag.  This is useful if one hemisphere failed and you need to run them separately)||
||<style="text-align:left;" |8>-[[tessellate]] ||filled.mgz ||<style="text-align:left;" |2>[[mri_pretess]] filled.mgz 255 norm.mgz filled-pretess255.mgz ||<style="text-align:left;" |2>filled-pretess255.mgz ||
||norm.mgz ||
||filled-pretess255.mgz ||[[mri_tessellate]] filled-pretess255.mgz 255 lh.orig.nofix ||lh.orig.nofix ||
||filled.mgz ||<style="text-align:left;" |2>[[mri_pretess]] filled.mgz 127 norm.mgz filled-pretess127.mgz ||<style="text-align:left;" |2>filled-pretess127.mgz ||
||norm.mgz ||
||filled-pretess127.mgz ||[[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 || ||
||-[[smooth|smooth1]] ||?h.orig.nofix ||[[mris_smooth]] -nw ?h.orig.nofix ?h.smoothwm.nofix ||?h.smoothwm.nofix ||
||-[[inflate|inflate1]] ||?h.smoothwm.nofix ||[[mris_inflate]] -no-save-sulc ?h.smoothwm.nofix ?h.inflated.nofix ||?h.inflated.nofix ||
||-[[qsphere]] ||?h.inflated.nofix ||[[mris_sphere]] -q ?h.inflated.nofix ?h.qsphere.nofix ||?h.qsphere.nofix ||
||<style="text-align:left;" |6>-[[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 ||[[mris_fix_topology]] -mgz -sphere qsphere.nofix -ga <subjid> ?h ||?h.orig ||
||?h.orig ||[[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>[[mris_make_surfaces]] -aseg ../mri/aseg.presurf -whiteonly -noaparc -mgz -T1 brain.finalsurfs <subjid> ?h ||<style="text-align:left" |4>?h.white ||
||<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 ||
||-[[smooth|smooth2]] ||?h.white ||[[mris_smooth]] -n 3 -nw ?h.white ?h.smoothwm ||?h.smoothwm ||
||<style="text-align:left" |2>-[[inflate|inflate2]] ||<style="text-align:left" |2>?h.smoothwm ||<style="text-align:left" |2>[[mris_inflate]] ?h.smoothwm ?h.inflated ||?h.inflated ||
||?h.sulc ||
||<style="text-align:left" |4>-curvHK ||<style="text-align:left" |2>?h.white ||<style="text-align:left" |2>[[mris_curvature]] -w ?h.white ||<style="text-align:left" |1>?h.white.H ||
||?h.white.K ||
||<style="text-align:left" |2>?h.inflated ||<style="text-align:left" |2>[[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 ||