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| This page lists all the various possible edits that could be made to subject data supported by the recon-all stream (both the default 'cross-sectional' stream, and the longitudinal stream). | 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. |
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| All of the edits made to a subject can be revealed by using the -show-edits option of recon-all (available in v5.X): | 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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| {{{ recon-all -s subjid -show-edits }}} |
'''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 that 'edits' are made only to volumes. There is no such thing as a surface edit. Problems with the surface are corrected by making edits to an appropriate volume (see [[FsTutorial/TroubleshootingData|troubleshooting]]). | 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. |
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| '''Note: all persistent edits can be removed with the option {{{-clean}}}''' ---- |
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| === user intervention === === recon-all handling === |
==== 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}}} ---- |
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| === user intervention === === recon-all handling === |
==== 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}}} ---- |
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| === user intervention === === recon-all handling === |
==== 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}}} ---- |
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| === user intervention === === recon-all handling === |
==== user intervention ==== If the automatic subcortical segmentation does not label a voxel correctly, or to the users satisfaction, they may change the voxel value in aseg.mgz using tkmedit. ==== recon-all handling ==== If both aseg.mgz and aseg.auto.mgz exist, and they are different, then the file aseg.manedit.mgz is created from the differences (and if an aseg.manedit.mgz file also exists, then its contents are merged with the newly created aseg.manedit.mgz). If aseg.manedit.mgz exists, then its contents are merged with aseg.auto.mgz (which is the output of the automatic segmentation program mri_ca_label). The default action, if neither aseg.manedit.mgz nor aseg.mgz exist, is to copy aseg.auto.mgz to aseg.mgz. ==== removal ==== {{{-clean-aseg}}} ---- |
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| === user intervention === === recon-all handling === |
==== user intervention ==== ==== recon-all handling ==== ==== removal ==== {{{-clean-bfse}}} ---- |
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| === user intervention === === recon-all handling === |
==== user intervention ==== ==== recon-all handling ==== ==== removal ==== {{{-clean-wm}}} ---- |
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| === user intervention === === recon-all handling === |
==== user intervention ==== ==== recon-all handling ==== ==== removal ==== {{{-clean-seed}}} ---- == cw256 == ==== user intervention ==== ==== recon-all handling ==== ==== removal ==== {{{-clean-cw256}}} ---- == expert options == ==== user intervention ==== ==== recon-all handling ==== ==== removal ==== {{{-clean-xopts}}} |
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
If the automatic subcortical segmentation does not label a voxel correctly, or to the users satisfaction, they may change the voxel value in aseg.mgz using tkmedit.
recon-all handling
If both aseg.mgz and aseg.auto.mgz exist, and they are different, then the file aseg.manedit.mgz is created from the differences (and if an aseg.manedit.mgz file also exists, then its contents are merged with the newly created aseg.manedit.mgz). If aseg.manedit.mgz exists, then its contents are merged with aseg.auto.mgz (which is the output of the automatic segmentation program mri_ca_label). The default action, if neither aseg.manedit.mgz nor aseg.mgz exist, is to copy aseg.auto.mgz to aseg.mgz.
removal
-clean-aseg
brain.finalsurfs.mgz
user intervention
recon-all handling
removal
-clean-bfse
wm.mgz
user intervention
recon-all handling
removal
-clean-wm
seed points
user intervention
recon-all handling
removal
-clean-seed
cw256
user intervention
recon-all handling
removal
-clean-cw256
expert options
user intervention
recon-all handling
removal
-clean-xopts