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'''All of the persistent edits made to a subject can be revealed by using the recon-all option {{{-show-edits}}}''' (available in v5.X). '''All persistent edits made to a subject can be revealed by using the recon-all option {{{-show-edits}}}''' (available in v5.X).
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'''Note: all edits can be removed with the option {{{-clean}}}''' '''Note: all persistent edits can be removed with the option {{{-clean}}}'''
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'mri_normalize' and 'mri_ca_normalize' use controls points in the -normalization, -canorm and -normalization2 stages. The -normalization, -canorm and -normalization2 stages use control points if present.
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If the talairach alignment is bad, tkregister2 is used to manually correct it. See [[FsTutorial/Talairach]]. If the talairach alignment is wrong, tkregister2 is used to manually correct it. See [[FsTutorial/Talairach]].
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Skull, dura and blood vessels might interfere with surface formation and need to be erased. See [[FsTutorial/PialEdits]].
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The -skullstrip stage creates the file brainmask.auto.mgz and copies it to brainmask.mgz '''unless the file brainmask.mgz already exists'''. If brainmask.mgz already exists, it is assumed the user has either edited brainmask.mgz, or it exists from a prior run of recon-all. brainmask.mgz is used in the -gcareg, -canorm, -careg, -normalization2, -wmparc, and -aparc+aseg-stats stages.
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{{{-clean-bm}}}

Edits

This page lists the 'persistent' edits that can be made to subject data supported by the recon-all stream (both the default 'cross-sectional' stream, and the longitudinal stream). An 'edit' in this context is a manual intervention by a user necessary when the automated stream (recon-all) does not produce output that is correct or suitable as determined by the user, or if the automated stream fails outright. Manual interventions occur via the volume editing tool tkmedit, tkregister2, or by recon-all command-line options. 'Persistent' in this context means that an edit, once made, is treated as a permanent change: it is saved to a file in some manner (either a voxel change in a volume, or a text file listing points or commands), and it is automatically re-used by recon-all if recon-all is run again.

Persistent edits are removed via '-clean' options to recon-all. A 'persistent' edit is in contrast to the many possible recon-all options available to alter the operation of an executable but are not saved to disk (and not re-used by recon-all, thus necessitating the user to specify the options again on any future run of recon-all if that operation is desired). Specifying gm/wm intensity priors is an example of a 'non-persistent' edit (one which is not saved to disk).

All persistent edits made to a subject can be revealed by using the recon-all option -show-edits (available in v5.X).

Each of the persistent edits is now described. Where/when/how it is used is referenced, along with how recon-all handles it internally, and how it can be removed.

Note: all persistent edits can be removed with the option -clean


control points

user intervention

A control point is added to indicate a white matter voxel. See FsTutorial/ControlPoints.

recon-all handling

The -normalization, -canorm and -normalization2 stages use control points if present.

removal

-clean-cp


talairach.xfm

user intervention

If the talairach alignment is wrong, tkregister2 is used to manually correct it. See FsTutorial/Talairach.

recon-all handling

The -talairach stage creates the file talairach.auto.xfm, and copies it to talairach.xfm unless the file talairach.xfm already exists. If talairach.xfm already exists, it is assumed the user has either edited talairach.xfm, or it exists from a prior run of recon-all.

removal

-clean-tal


brainmask.mgz

user intervention

Skull, dura and blood vessels might interfere with surface formation and need to be erased. See FsTutorial/PialEdits.

recon-all handling

The -skullstrip stage creates the file brainmask.auto.mgz and copies it to brainmask.mgz unless the file brainmask.mgz already exists. If brainmask.mgz already exists, it is assumed the user has either edited brainmask.mgz, or it exists from a prior run of recon-all. brainmask.mgz is used in the -gcareg, -canorm, -careg, -normalization2, -wmparc, and -aparc+aseg-stats stages.

removal

-clean-bm


aseg.mgz

user intervention

recon-all handling

removal


brain.finalsurfs.mgz

user intervention

recon-all handling

removal


wm.mgz

user intervention

recon-all handling

removal


seed points

user intervention

recon-all handling

removal


cw256

user intervention

recon-all handling

removal


expert options

user intervention

recon-all handling

removal

Edits (last edited 2015-04-20 16:48:54 by MartinReuter)