Diff for "AnalyzingData/check_autorecon2" - Meg Wiki
location: Diff for "AnalyzingData/check_autorecon2"
Differences between revisions 10 and 13 (spanning 3 versions)
Revision 10 as of 2013-03-08 10:02:31
Size: 1275
Editor: localhost
Comment: converted to 1.6 markup
Revision 13 as of 2016-10-25 09:57:42
Size: 1289
Editor: OlafHauk
Comment:
Deletions are marked like this. Additions are marked like this.
Line 2: Line 2:
Line 5: Line 4:
   '''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'''
Line 13: Line 12:
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.
Line 17: Line 16:
   '''recon-all -subjid <mysubjectname> -autorecon2-cp'''  . '''recon-all -subjid <mysubjectname> -autorecon2-cp'''
Line 22: Line 21:
Line 25: Line 23:
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.
Line 29: Line 27:
   '''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)