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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). 'Edits' is the term that describes manual interventions 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.

Edits are treated as permanent change
s, in the sense that once an edit is made, it is saved to a file (either a voxel change in a volume, or a text file listing points), and it is automatically re-used by recon-all when recon-all is run. This is in contrast to the host of possible recon-all flags that could be added 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 an alternative watershed threshold for the skullstrip operation is an example of a 'non-persistent' edit (one which is not saved to disk).
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). 'Edits' is the term that describes manual interventions 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' edits means these edits, once made, are treated as permanent changes, in the sense that once an edit is made, it is saved to a file (either a voxel change in a volume, or a text file listing points or commands), and it is automatically re-used by recon-all when recon-all is run. Persistent edits are removed via '-clean' options to recon-all. A 'persistent' edit is in contrast to the host of possible recon-all flags that could be added 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).
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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.

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). 'Edits' is the term that describes manual interventions 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' edits means these edits, once made, are treated as permanent changes, in the sense that once an edit is made, it is saved to a file (either a voxel change in a volume, or a text file listing points or commands), and it is automatically re-used by recon-all when recon-all is run. Persistent edits are removed via '-clean' options to recon-all. A 'persistent' edit is in contrast to the host of possible recon-all flags that could be added 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).

All of the 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.


control points

user intervention

See troubleshooting.

recon-all handling


talairach.xfm

user intervention

recon-all handling


brainmask.mgz

user intervention

recon-all handling


aseg.mgz

user intervention

recon-all handling


brain.finalsurfs.mgz

user intervention

recon-all handling


wm.mgz

user intervention

recon-all handling


seed points

user intervention

recon-all handling


cw256

user intervention

recon-all handling


expert options

user intervention

recon-all handling

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