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| == Recon-all steps and stages == | = ReconAll Table = The !ReconAll Table lists the inputs, outputs, and commands used for each processing step in {{{recon-all -all}}}. This can be a helpful resource when trying to figure out how to modify a particular part of the processing stream or how to rerun a few of the steps. |
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| ||<rowbgcolor='#80FF80'>'''recon-all step'''||'''Individual Flag'''||'''Input'''||'''Command Line'''||'''Output'''|| ||<bgcolor='#FFFFE0'>none||<bgcolor='#FFFFE0'>none||<bgcolor='#E0E0FF'>file.dcm||<bgcolor='#E0E0FF'>["mri_convert"] file.dcm orig/001.mgz||<bgcolor='#E0E0FF'>orig/001.mgz|| ||<|10(bgcolor='#FFFFE0'>["recon-all"] -autorecon1 -subjid subj|| ||<|2(bgcolor='#FFFFE0'>-motioncor||<bgcolor='#E0E0FF'>orig/001.mgz||<|2(bgcolor='#E0E0FF'>["mri_motion_correct2"] -i orig/001.mgz -i orig/002.mgz -o rawavg.mgz||<|2(bgcolor='#E0E0FF'>rawavg.mgz|| ||<rowbgcolor='#E0E0FF'>orig/002.mgz|| |
These tables list the generic steps that come from running the different versions of !FreeSurfer downloaded from our website. To most accurately know what commands were run on one of your datasets, you should look at the recon-all.log found in the scripts directory of that subject. This will list the exact commands and flags used as well as the appropriate hemi and file names. The tables list ?h to show it is done on each hemisphere separately and also make certain assumptions about the directory from which the command is being run. |
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||<rowbgcolor='#E0E0FF'>rawavg.mgz||["mri_convert"] rawavg.mgz orig.mgz --conform||orig.mgz|| ||<rowbgcolor='#E0E0FF'>orig.mgz||["mri_convert"] orig.mgz orig.mnc||orig.mnc|| ||<rowbgcolor='#E0E0FF'>orig.mnc||(4 iterations of) ["nu_correct"] -clobber nu0.mnc nu1.mnc||nu4.mnc|| ||<rowbgcolor='#E0E0FF'>nu4.mnc||["mri_convert"] nu4.mnc nu.mgz||nu.mgz|| ||<rowbgcolor='#E0E0FF'>nu.mgz||["talairach2"] subjid -mgz||transforms/talairach.xfm|| ||<rowbgcolor='#E0E0FF'>nu.mgz||["mri_normalize"] nu.mgz T1.mgz||T1.mgz|| ||<rowbgcolor='#E0E0FF'>T1.mgz||["mri_watershed"] T1.mgz brain.mgz||brain.mgz|| ||<-4(rowbgcolor='#FF8080'>Check skullstrip (brain.mgz), talairach (transforms/talairach.xfm), and normalization (brain.mgz or T1.mgz - mean wm voxel value = 110)|| ||<|35(bgcolor='#FFFFE0'>["recon-all"] -autorecon2 -subjid subj|| ||<rowbgcolor='#E0E0FF'>brain.mgz||<|2(>["mri_em_register"] -mask brain.mgz -p .5 -fsamples fsamples.mgz nu.mgz $GCA transforms/talairach.lta||<|2(>transforms/talairach.lta|| ||<rowbgcolor='#E0E0FF'>nu.mgz|| ||<rowbgcolor='#E0E0FF'>brain.mgz||<|3(>["mri_ca_normalize"] -mask brain.mgz nu.mgz $GCA transforms/talairach.lta norm.mgz||<|3(>norm.mgz|| ||<rowbgcolor='#E0E0FF'>nu.mgz|| ||<rowbgcolor='#E0E0FF'>transforms/talairach.lta|| ||<rowbgcolor='#E0E0FF'>brain.mgz||<|3(>["mri_ca_register"] -cross-sequence -mask brain.mgz -T transforms/talairach.lta norm.mgz $GCA transforms/talairach.m3z||<|3(>transforms/talairach.m3z|| ||<rowbgcolor='#E0E0FF'>transforms/talairach.lta|| ||<rowbgcolor='#E0E0FF'>norm.mgz|| ||<rowbgcolor='#E0E0FF'>norm.mgz||<|2(>["mri_ca_label"] -cross-sequence norm.mgz transforms/talairach.m3z $GCA aseg.mgz||<|2(>aseg.mgz|| ||<rowbgcolor='#E0E0FF'>transforms/talairach.m3z|| ||<rowbgcolor='#E0E0FF'>brain.mgz||<|2(>["mri_normalize"] -mask brain.mgz nu.mgz T1.mgz||<|2(>T1.mgz|| ||<rowbgcolor='#E0E0FF'>nu.mgz|| ||<rowbgcolor='#E0E0FF'>T1.mgz||<|2(>["mri_mask"] T1.mgz brain.mgz brain.mgz||<|2(>brain.mgz|| ||<rowbgcolor='#E0E0FF'>brain.mgz|| ||<rowbgcolor='#E0E0FF'>brain.mgz||["mri_segment"] brain.mgz wm.mgz||wm.mgz|| ||<rowbgcolor='#E0E0FF'>wm.mgz||<|2(>["mri_edit_wm_with_aseg"] wm.mgz aseg.mgz wm.mgz||<|2(>wm.mgz|| ||<rowbgcolor='#E0E0FF'>aseg.mgz|| ||<rowbgcolor='#E0E0FF'>wm.mgz||<|2(>["mri_fill"] -a ../scripts/ponscc.cut.log -xform transforms/talairach.xfm -segmentation aseg.mgz wm.mgz filled.mgz||filled.mgz|| ||<rowbgcolor='#E0E0FF'>aseg.mgz||../scripts/ponscc.cut.log|| ||<|2(rowbgcolor='#E0E0FF'>filled.mgz||["mri_tessellate"] filled.mgz 255 ../surf/lh.orig||lh.orig|| ||<rowbgcolor='#E0E0FF'>["mri_tessellate"] filled.mgz 128 ../surf/rh.orig||rh.orig|| ||<rowbgcolor='#E0E0FF'>?h.orig||["mris_smooth"] ?h.orig ?h.smoothwm||?h.smoothwm|| ||<rowbgcolor='#E0E0FF'>?h.smoothwm||["mris_inflate"] ?h.smoothwm ?h.inflated||?h.inflated|| ||<rowbgcolor='#E0E0FF'>?h.inflated||["mris_sphere"] -w 0 -inflate -in 200 -q ?h.inflated ?h.qsphere||?h.qsphere|| ||<rowbgcolor='#E0E0FF'>?h.qsphere||["mris_fix_topology"] subj ?h||?h.orig|| ||<rowbgcolor='#E0E0FF'>?h.orig||["mris_euler_number"] ?h.orig||?h.orig.euler|| ||<rowbgcolor='#E0E0FF'>?h.orig||["mris_smooth"] ?h.orig ?h.smoothwm||?h.smoothwm|| ||<rowbgcolor='#E0E0FF'>?h.smoothwm||["mris_inflate"] ?h.smoothwm ?h.inflated||?h.inflated|| ||<rowbgcolor='#E0E0FF'>brain.mgz||<|3(>["mris_make_surfaces"] -w 0 subj ?h||?h.white|| ||<|2(rowbgcolor='#E0E0FF'>?h.orig||?h.pial|| ||<rowbgcolor='#E0E0FF'>?h.thickness|| ||<rowbgcolor='#E0E0FF'>orig.mgz||<rowspan=3>["mri_surf2vol"] --mkmask --hemi ?h --fillribbon --template orig.mgz --volregidentity subj --outvol ?h.ribbon.mgz||<rowspan=3>?h.ribbon.mgz|| ||<rowbgcolor='#E0E0FF'>?h.white|| ||<rowbgcolor='#E0E0FF'>?h.pial|| ||<-4(rowbgcolor='#FF8080'>Check final surfaces '''["tkmedit]" subj wm.mgz ?h.white brain.mgz'''|| ||<|8(bgcolor='#FFFFE0'>["recon-all"] -autorecon3 -subjid subj|| ||<rowbgcolor='#E0E0FF'>?h.inflated||["mris_sphere"] -w 0 ?h.inflated ?h.sphere||?h.sphere|| ||<rowbgcolor='#E0E0FF'>?h.sphere||["mris_register"] -w 0 -curv ?h.sphere $AvgTif ?h.sphere.reg||?h.sphere.reg|| ||<rowbgcolor='#E0E0FF'>rh.sphere||["mris_register"] -w 0 -curv -reverse rh.sphere $AvgTif rh.lh.sphere.reg||rh.lh.sphere.reg|| ||<rowbgcolor='#E0E0FF'>lh.sphere||["mris_register"] -w 0 -curv -reverse lh.sphere $AvgTif lh.rh.sphere.reg||lh.rh.sphere.reg|| ||<rowbgcolor='#E0E0FF'>?h.sphere.reg||["mrisp_paint"] -a 5 $AvgTif#6 ?h.sphere.reg ?h.avg_curv||?h.avg_curv|| ||<rowbgcolor='#E0E0FF'>?h.sphere.reg||["mris_ca_label"] -t $CPAnnotTable subj ?h sphere.reg $CPAtlas ?h.aparc.annot||label/?h.aparc.annot|| ||<rowbgcolor='#E0E0FF'>?h.aparc.annot||["mris_anatomical_stats"] -f scripts/?h.aparc.stats -b -a label/?h.aparc.annot subj ?h||scripts/?h.aparc.stats|| |
Here is a list of tables we have: * ReconAllDevTable - this table is updated as changes are made during ongoing development of !FreeSurfer * OtherUsefulFlags - lists flags and processing stage shortcuts which are useful when editing a recon * [[ReconAllTableStableV6.0]] * [[ReconAllTableStableV5.3]] * [[ReconAllTableStableV5.1]] * [[ReconAllTableStableV5]] * [[ReconAllStableTablev4]] |
ReconAll Table
The ReconAll Table lists the inputs, outputs, and commands used for each processing step in recon-all -all. This can be a helpful resource when trying to figure out how to modify a particular part of the processing stream or how to rerun a few of the steps.
These tables list the generic steps that come from running the different versions of FreeSurfer downloaded from our website. To most accurately know what commands were run on one of your datasets, you should look at the recon-all.log found in the scripts directory of that subject. This will list the exact commands and flags used as well as the appropriate hemi and file names. The tables list ?h to show it is done on each hemisphere separately and also make certain assumptions about the directory from which the command is being run.
Here is a list of tables we have:
ReconAllDevTable - this table is updated as changes are made during ongoing development of FreeSurfer
OtherUsefulFlags - lists flags and processing stage shortcuts which are useful when editing a recon