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| ||<|2(bgcolor='#FFFFE0'>-gcareg||<bgcolor='#E0E0FF'>brain.mgz||<|2(bgcolor='#E0E0FF'>["mri_em_register"] -mask brain.mgz -p .5 -fsamples fsamples.mgz nu.mgz $FREESURFER_HOME/average/talairach_mixed.gca transforms/talairach.lta||<|2(bgcolor='#E0E0FF'>transforms/talairach.lta||<|16(bgcolor='#FFFFE0'>Use this flag in conjunction with other steps of recon-all and it will default to the old set of atlases. Uses talairach_mixed.gca for the subcortical segmentation, ?h.average.tif for the surface morph, and ?h.atlas2002_simple.gcs for the cortical parcellations.|| | ||<|2(bgcolor='#FFFFE0'>-gcareg||<bgcolor='#E0E0FF'>brain.mgz||<|2(bgcolor='#E0E0FF'>["mri_em_register"] -mask brain.mgz -p .5 -fsamples fsamples.mgz nu.mgz $FREESURFER_HOME/average/talairach_mixed.gca transforms/talairach.lta||<|2(bgcolor='#E0E0FF'>transforms/talairach.lta||<|15(bgcolor='#FFFFE0'>Use this flag in conjunction with other steps of recon-all and it will default to the old set of atlases. Uses talairach_mixed.gca for the subcortical segmentation, ?h.average.tif for the surface morph, and ?h.atlas2002_simple.gcs for the cortical parcellations.|| |
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||<bgcolor='#FFFFE0'>-rerun||<bgcolor='#FFFFE0'>||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>||<bgcolor='#FFFFE0'>|| |
||<bgcolor='#FFFFE0'>-rerun||<bgcolor='#FFFFE0'>||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>||<bgcolor='#FFFFE0'>this flag will re-run your subject with a new version while maintaining all the manual changes you've made.|| |
FreeSurfer Tutorial: Useful recon-all flags.
The following flags can be used in conjunction with individual steps or the entire process:
recon-all flag |
Used with step |
Input |
Command Line |
Output |
Description |
-usecontrolpoints |
-normalization |
nu.mgz |
["mri_normalize"] -f $SUBJECTS_DIR/subjid/tmp/control.dat nu.mgz T1.mgz |
T1.mgz |
uses control points, saved to tmp/control.dat to modify the normalization |
-keepwmedits |
-segmentation |
brain.mgz |
["mri_segment"] -keep brain.mgz wm.mgz |
wm.mgz |
preserves any previous edits to wm volume |
-cc-xyz <X Y Z> |
-fill |
wm.mgz |
["mri_fill"] -a ../scripts/ponscc.cut.log -C X Y Z -xform transforms/talairach.xfm wm.mgz filled.mgz |
filled.mgz |
manually sets the corpus callosum seed point |
-pons-xyz <X Y Z> |
-fill |
wm.mgz |
["mri_fill"] -a ../scripts/ponscc.cut.log -P X Y Z -xform transforms/talairach.xfm wm.mgz filled.mgz |
filled.mgz |
manually sets the pons seed point |
-rh-xyz <X Y Z> |
-fill |
wm.mgz |
["mri_fill"] -a ../scripts/ponscc.cut.log -rh X Y Z -xform transforms/talairach.xfm wm.mgz filled.mgz |
filled.mgz |
manually sets the right hemisphere seed point |
-lh-xyz <X Y Z> |
-fill |
wm.mgz |
["mri_fill"] -a ../scripts/ponscc.cut.log -lh X Y Z -xform transforms/talairach.xfm wm.mgz filled.mgz |
filled.mgz |
manually sets the left hemisphere seed point |
-old-atlas |
|||||
-gcareg |
brain.mgz |
["mri_em_register"] -mask brain.mgz -p .5 -fsamples fsamples.mgz nu.mgz $FREESURFER_HOME/average/talairach_mixed.gca transforms/talairach.lta |
transforms/talairach.lta |
Use this flag in conjunction with other steps of recon-all and it will default to the old set of atlases. Uses talairach_mixed.gca for the subcortical segmentation, ?h.average.tif for the surface morph, and ?h.atlas2002_simple.gcs for the cortical parcellations. |
|
nu.mgz |
|||||
-canorm |
brain.mgz |
["mri_ca_normalize"] -mask brain.mgz nu.mgz $FREESURFER_HOME/average/talairach_mixed.gca transforms/talairach.lta norm.mgz |
norm.mgz |
||
nu.mgz |
|||||
transforms/talairach.lta |
|||||
-careg |
brain.mgz |
["mri_ca_register"] -cross-sequence -mask brain.mgz -T transforms/talairach.lta norm.mgz $FREESURFER_HOME/average/talairach_mixed.gca transforms/talairach.m3z |
transforms/talairach.m3z |
||
transforms/talairach.lta |
|||||
norm.mgz |
|||||
-calabel |
norm.mgz |
["mri_ca_label"] -cross-sequence norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/talairach_mixed.gca aseg.mgz |
aseg.mgz |
||
transforms/talairach.m3z |
|||||
-surfreg |
?h.sphere |
["mris_register"] -w 0 -curv ?h.sphere $FREESURFER_HOME/average?h.average.tif ?h.sphere.reg |
?h.sphere.reg |
||
-contrasurfreg |
rh.sphere |
["mris_register"] -w 0 -curv -reverse rh.sphere $FREESURFER_HOME/average?h.average.tif rh.lh.sphere.reg |
rh.lh.sphere.reg |
||
lh.sphere |
["mris_register"] -w 0 -curv -reverse lh.sphere $FREESURFER_HOME/average?h.average.tif lh.rh.sphere.reg |
lh.rh.sphere.reg |
|||
-avgcurv |
?h.sphere.reg |
["mrisp_paint"] -a 5 $FREESURFER_HOME/average?h.average.tif ?h.sphere.reg ?h.avg_curv |
?h.avg_curv |
||
-cortparc |
?h.sphere.reg |
["mris_ca_label"] -t $CPAnnotTable subj ?h sphere.reg $FREESURFER_HOME/average/?h.atlas2002_simple.gcs ?h.aparc.annot |
label/?h.aparc.annot |
||
-rerun |
this flag will re-run your subject with a new version while maintaining all the manual changes you've made. |
The following flags can be used after certain manual intervention to regenerate accurate volumes and surfaces:
recon-all step |
Individual Flag |
Input |
Command Line |
Output |
["recon-all"] -autorecon2-cp -subjid subj (use this after setting control points. This flag will preserve your wm.mgz edits and remake all necessary volumes and surfaces) |
||||
-normalization2 |
brain.mgz |
["mri_normalize"] -f $SUBJECTS_DIR/subjid/tmp/control.dat -mask brain.mgz nu.mgz T1.mgz |
T1.mgz |
|
nu.mgz |
||||
T1.mgz |
["mri_mask"] T1.mgz brain.mgz brain.mgz |
brain.mgz |
||
brain.mgz |
||||
-segmentation |
brain.mgz |
["mri_segment"] -keep brain.mgz wm.mgz |
wm.mgz |
|
-edit_wm_with_aseg |
wm.mgz |
["mri_edit_wm_with_aseg"] wm.mgz aseg.mgz wm.mgz |
wm.mgz |
|
aseg.mgz |
||||
-fill |
wm.mgz |
["mri_fill"] -a ../scripts/ponscc.cut.log -xform transforms/talairach.xfm -segmentation aseg.mgz wm.mgz filled.mgz |
filled.mgz |
|
aseg.mgz |
../scripts/ponscc.cut.log |
|||
-tessellate |
filled.mgz |
["mri_tessellate"] filled.mgz 255 ../surf/lh.orig |
lh.orig |
|
["mri_tessellate"] filled.mgz 128 ../surf/rh.orig |
rh.orig |
|||
-smooth1 |
?h.orig |
["mris_smooth"] ?h.orig ?h.smoothwm |
?h.smoothwm |
|
-inflate1 |
?h.smoothwm |
["mris_inflate"] ?h.smoothwm ?h.inflated |
?h.inflated |
|
-qsphere |
?h.inflated |
["mris_sphere"] -w 0 -inflate -in 200 -q ?h.inflated ?h.qsphere |
?h.qsphere |
|
-fix |
?h.qsphere |
["mris_fix_topology"] subj ?h |
?h.orig |
|
-euler |
?h.orig |
["mris_euler_number"] ?h.orig |
?h.orig.euler |
|
-smooth2 |
?h.orig |
["mris_smooth"] ?h.orig ?h.smoothwm |
?h.smoothwm |
|
-inflate2 |
?h.smoothwm |
["mris_inflate"] ?h.smoothwm ?h.inflated |
?h.inflated |
|
-finalsurfs |
brain.mgz |
["mris_make_surfaces"] -w 0 subj ?h |
?h.white |
|
?h.orig |
?h.pial |
|||
?h.thickness |
||||
-cortribbon |
orig.mgz |
["mri_surf2vol"] --mkmask --hemi ?h --fillribbon --template orig.mgz --volregidentity subj --outvol ?h.ribbon.mgz |
?h.ribbon.mgz |
|
?h.white |
||||
?h.pial |
recon-all step |
Individual Flag |
Input |
Command Line |
Output |
["recon-all"] -autorecon2-wm -subjid subj (use this after doing manual wm edits. This flag will regenerate all necessary volumes and surfaces) |
||||
-fill |
wm.mgz |
["mri_fill"] -a ../scripts/ponscc.cut.log -xform transforms/talairach.xfm -segmentation aseg.mgz wm.mgz filled.mgz |
filled.mgz |
|
aseg.mgz |
../scripts/ponscc.cut.log |
|||
-tessellate |
filled.mgz |
["mri_tessellate"] filled.mgz 255 ../surf/lh.orig |
lh.orig |
|
["mri_tessellate"] filled.mgz 128 ../surf/rh.orig |
rh.orig |
|||
-smooth1 |
?h.orig |
["mris_smooth"] ?h.orig ?h.smoothwm |
?h.smoothwm |
|
-inflate1 |
?h.smoothwm |
["mris_inflate"] ?h.smoothwm ?h.inflated |
?h.inflated |
|
-qsphere |
?h.inflated |
["mris_sphere"] -w 0 -inflate -in 200 -q ?h.inflated ?h.qsphere |
?h.qsphere |
|
-fix |
?h.qsphere |
["mris_fix_topology"] subj ?h |
?h.orig |
|
-euler |
?h.orig |
["mris_euler_number"] ?h.orig |
?h.orig.euler |
|
-smooth2 |
?h.orig |
["mris_smooth"] ?h.orig ?h.smoothwm |
?h.smoothwm |
|
-inflate2 |
?h.smoothwm |
["mris_inflate"] ?h.smoothwm ?h.inflated |
?h.inflated |
|
-finalsurfs |
brain.mgz |
["mris_make_surfaces"] -w 0 subj ?h |
?h.white |
|
?h.orig |
?h.pial |
|||
?h.thickness |
||||
-cortribbon |
orig.mgz |
["mri_surf2vol"] --mkmask --hemi ?h --fillribbon --template orig.mgz --volregidentity subj --outvol ?h.ribbon.mgz |
?h.ribbon.mgz |
|
?h.white |
||||
?h.pial |
recon-all step |
Individual Flag |
Input |
Command Line |
Output |
["recon-all"] -autorecon2-pial -subjid subj (use this after editing brain.mgz to alter pial surface. This flag will regenerate all final surfaces) |
||||
-finalsurfs |
brain.mgz |
["mris_make_surfaces"] -w 0 subj ?h |
?h.white |
|
?h.orig |
?h.pial |
|||
?h.thickness |
||||
-cortribbon |
orig.mgz |
["mri_surf2vol"] --mkmask --hemi ?h --fillribbon --template orig.mgz --volregidentity subj --outvol ?h.ribbon.mgz |
?h.ribbon.mgz |
|
?h.white |
||||
?h.pial |