Hi Nicholas,

In such situations, I have learned that autorecon2-wm after adding WM voxels 
seems to work pretty well. Hope that helps. 

Best Wishes,
Elijah

On 27 September 2017 at 16:46:43, Nicholas Goh (ngo...@gmail.com) wrote:

Bruce,

Thank you for the response. Attempting to use this method has not produced 
results, and I am unsure how to proceed or if I had performed it improperly. I 
have attached an example of the control points being placed, if that helps any.
Thank you,

Nicholas Goh

On Wed, Sep 27, 2017 at 11:04 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> 
wrote:
Hi Nicholas

yes, possibly, depending on why you are missing chunks. If the white matter in 
the regions you are missing has intensity values significantly < 110 then what 
you are doing should help. The control.dat file must be place in the 
subject/tmp dir for us to find it.

cheers
Bruce
On Wed, 27 Sep 2017, Nicholas Goh wrote:

I am attempting to fix the aparc+aseg.mgz file for an image, and wanted to 
check to see if I am
doing it correctly.What I was doing which seemed to be ineffective was 
1)create a new point set of control points labelled control.dat
2)place control points along what should be white matter
3)save point set
4)run recon-all -autorecon2-cp -autorecon3 -subjid XXXX

Is this the correct way to go about fixing aparc+aseg files that are missing 
chunks of the brain? Is
there a better way to go about this?
Thanks for the help,

Nicholas Goh


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