Not sure it's helpful.
The simplest way I can think of is to directly edit WM.mgz. You can load
wm.mgz into matlab, it's basically a 3D matrix. You can directly set
values for wm matrix, for instance
wm(wm(:)>200)=110;
Then you save the new wm matrix into wm.mgz.
On 9/5/16 10:54 AM, 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
<mailto: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
<mailto:benjamin.s.ba...@gmail.com>>
An: freesurfer@nmr.mgh.harvard.edu
<mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<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
<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 <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<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
<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.
