New subject: Fwd: Adding control points to aparc+aseg

2 Oct 2017

      I have still been having trouble with fixing the white matter of the
aparc+aseg.mgz file for a subject.
I have tried using
recon-all -autorecon2-cp -autorecon3 -subjid XXXX
recon-all -autorecon2-wm -subjid XXXX
recon-all -autorecon2-wm -autorecon3 -subjid XXXX
None of these have solved the issue, and I was hoping for help in finding a
way to fix this? There are other more extreme examples, but this one seems
to have an error at [-7, 114, 133]
Thank you for the help,
Nicholas Goh
On Thu, Sep 28, 2017 at 5:34 PM, Nicholas Goh ngoh95@gmail.com wrote:
...
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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