On Mon, Oct 16, 2017 at 1:08 PM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

I don't know what coordinates those are. Can you give indices? indices are non-neg
On 10/16/17 12:59 PM, Nicholas Goh wrote:
An example of the aparc+aseg not covering all that it needs to can be found around [-7, 114, 133]
On Mon, Oct 16, 2017 at 12:47 PM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:
what is the index (ie, col, row, slice) where you are seeing a problem?
On 10/16/17 11:44 AM, Nicholas Goh wrote:
Hi,

I am not sure if this email got lost in the process or is still awaiting approval, but I was asked to tar and gzip the images that I was having no luck with fixing the white matter for.

Any help would be appreciated.

Thank you,

Nicholas Goh

---------- Forwarded message ----------
From: Nicholas Goh <ngoh95@gmail.com>
Date: Mon, Oct 2, 2017 at 12:33 PM
Subject: Re: [Freesurfer] Adding control points to aparc+aseg
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>

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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