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* <ngo...@gmail.com <mailto:ngo...@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
<mailto: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 <ngo...@gmail.com
<mailto:ngo...@gmail.com>> wrote:
Ping, is this okay to do? I Think it is but wanted to check
before sending
---------- Forwarded message ----------
From: *Bruce Fischl* <fis...@nmr.mgh.harvard.edu
<mailto:fis...@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
<mailto: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
<fk...@medschl.cam.ac.uk <mailto:fk...@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
(ngo...@gmail.com <mailto: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
<mailto: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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