Ping, is this okay to do? I Think it is but wanted to check before sending

---------- Forwarded message ----------
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Date: Thu, Sep 28, 2017 at 5:23 PM
Subject: Re: [Freesurfer] Adding control points to aparc+aseg
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>

Hi Nicholas

why don't you tar, gzip and upload your subject and we will take a look. Make sure to tell us the coordinates of where you are trying to fix things

cheers
Bruce


On Thu, 28 Sep 2017, Nicholas Goh wrote:

I am still having trouble with getting the aparc+aseg to recognize sections
that should be white matter as such. Using the control points paired
withrecon-all -autorecon2-cp -autorecon3 -subjid XXXX

did not work, after 4 or 5 attempts with different control points, and using
recon-all -autorecon2-wm -s XXXX
also did not yield appreciable results. Is there anything else that I might
be able to try to fix this?
Thank you for all the help,

Nicholas Goh

On Wed, Sep 27, 2017 at 12:49 PM, Elijah Mak <fkm24@medschl.cam.ac.uk>
wrote:
      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 (ngoh95@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
<fischl@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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