Diff for "AnalyzingData/check_autorecon2" - Meg Wiki
location: Diff for "AnalyzingData/check_autorecon2"
Differences between revisions 8 and 13 (spanning 5 versions)
Revision 8 as of 2010-07-28 17:36:13
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Editor: YaaraErez
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Revision 13 as of 2016-10-25 09:57:42
Size: 1289
Editor: OlafHauk
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Deletions are marked like this. Additions are marked like this.
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   '''tkmedit <mysubjectname> brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white'''  . '''tkmedit <mysubjectname> brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white'''
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Use the "TkMedit Tools" window to scroll through slices ("Slice +/-"), to change the views ("C, H, S") etc. Use the "!TkMedit Tools" window to scroll through slices ("Slice +/-"), to change the views ("C, H, S") etc. If the !TkMedit Tools window is not visible straight away, right click on its icon in the bottom toolbar, choose "Move", and place it wherever you like.
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attachment:checkintensity.jpg {{attachment:checkintensity.jpg}}
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See the [http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints Freesurfer Wiki] on how to fix such a problem. See the [[http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints_freeview|Freesurfer Wiki]] on how to fix such a problem.
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   '''recon-all -subjid <mysubjectname> -autorecon2-cp'''  . '''recon-all -subjid <mysubjectname> -autorecon2-cp'''
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See the [http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits Freesurfer Wiki] on what to do in this case. See the [[http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freeview|Freesurfer Wiki]] on what to do in this case.
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   '''recon-all -subjid <mysubjectname> -autorecon2-wm '''  . '''recon-all -subjid <mysubjectname> -autorecon2-wm '''

Check intensity normalisation

With the following command you can check whether white matter was segmented correctly:

  • tkmedit <mysubjectname> brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white

Use the "TkMedit Tools" window to scroll through slices ("Slice +/-"), to change the views ("C, H, S") etc. If the TkMedit Tools window is not visible straight away, right click on its icon in the bottom toolbar, choose "Move", and place it wherever you like.

This is what you should look out for (rare in our data):

checkintensity.jpg

See the Freesurfer Wiki on how to fix such a problem.

If you made edits (i.e. added control points), run

  • recon-all -subjid <mysubjectname> -autorecon2-cp

Then check again.

Check White Matter

Using the same tkmedit command as above, you can check whether there is white matter not included in the segmentation, or whether voxels are assigned to white matter when they shouldn't.

See the Freesurfer Wiki on what to do in this case.

If you made edits, run

  • recon-all -subjid <mysubjectname> -autorecon2-wm

CbuMeg: AnalyzingData/check_autorecon2 (last edited 2016-10-25 09:57:42 by OlafHauk)