Hi Ben
sorry, but I don't know how to fix it automatically. You have voxels that
look just like wm in the gm - that's going to be tough to avoid. You could
try messing with some of the mris_make_surfaces options, but I don't have
much confidence that it will help.
Any idea why you are getting the bright voxels in the first place?
Bruce
On Mon, 5 Sep 2016, Benjamin
Baird wrote:
Hi Bruce and Clara,
Many thanks for your comments. Indeed the bright points are segmented as WM
in wm.mgz, however these errors do not occur only in a few places but in
many slices throughout the brain so manual edits will be very extensive,
which is why we wanted to double check that there is no parameter tweak to
recon that might at least help some of these errors. But sounds like there's
no way to adjust the parameters of recon to mitigate this type of error? If
not we will move forward with manual edits to wm.mgz as you suggest. Also
I'm wondering if this is a common issue with GE scanners, as I've never
encountered it before on Siemens, and I recently saw a post to the FS group
from someone else encountering the same issue on GE
Best regards,
Ben
On Fri, Sep 2, 2016 at 8:36 AM, Clara Kühn <cku...@cbs.mpg.de> wrote:
Hello Ben,
I am no expert, I can only talk from my experience.
I've had similar images in my data. Those might be blood vessels
or dura that were included in the surface. If they are included
in the surface on more than 5 slices and pretty well visible you
could delete those voxels from the brainmask. From the looks of
the attached screenshots however I wouldn't worry about the
brainmask but rather remove a few voxels from the wm.mgz. Then
you rerun the subject with the -wm flag and check again. If it
is only on one or two slices, though, I wouldn't edit it at all.
The surfaces are just not going to be perfect.
Hope I could help.
Clara
----- Ursprüngliche Mail -----
Von: "Benjamin Baird" <benjamin.s.ba...@gmail.com>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Donnerstag, 1. September 2016 21:56:58
Betreff: [Freesurfer] white matter errors due to inhomogeneities
(bright spots) in cortex
Dear Freesurfer experts,
We are currently working with some scans that were collected on
a GE 3T scanner. The goal is to analyze cortical thickness. The
scans seem to be relatively high quality with the exception that
there are what appear to be inhomogeneities in the intensity of
the gray matter (appears too bright in places), which is causing
the WM to extend/jump into cortex (see attached image). We're
wondering if there are any parameter adjustments to recon that
might help with this as the errors occur frequently enough that
fixing them all manually will be fairly cumbersome. This type of
error doesn’t seem to be discussed very much in the available
information on freesurfer quality control as far as we’ve seen.
Thanks in advance for any advice you might be able to offer.
Best regards,
Ben
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person
to whom it is
addressed. If you believe this e-mail was sent to you in error
and the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent
to you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person
to whom it is
addressed. If you believe this e-mail was sent to you in error
and the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent
to you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
