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| 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 (which 'edits' the alignment to Talairach space), or by adding explicit command-line arguments. '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 flags 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 specifying them again on the recon-all command string 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 and which must be explicitly included on any future runs of recon-all). | 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). |
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| 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. | 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 edits can be removed with the option {{{-clean}}}''' |
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| See [[FsTutorial/TroubleshootingData|troubleshooting]]. |
A control point is added to indicate a white matter voxel. See [[FsTutorial/ControlPoints]]. |
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| 'mri_normalize' and 'mri_ca_normalize' use controls points in the -normalization, -canorm and -normalization2 stages. === removal === {{{-clean-cp}}} |
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| If the talairach alignment is bad, tkregister2 is used to manually correct it. See [[FsTutorial/Talairach]]. | |
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| 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}}} |
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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 of the persistent edits made to a subject can be revealed by using the -show-edits option of recon-all (available in v5.X):
recon-all -s subjid -show-edits
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 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
'mri_normalize' and 'mri_ca_normalize' use controls points in the -normalization, -canorm and -normalization2 stages.
removal
-clean-cp
talairach.xfm
user intervention
If the talairach alignment is bad, 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
recon-all handling
removal
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