Hi Jennifer
sorry for the lack of response - do you want to upload your subject data
(the entire subject directory) and we will take a look?
cheers
Bruce
On Mon, 24 Aug 2015, Kriegel, Jennifer Lynn
Sarai wrote:
Hi,
I apologize for asking this question again, but I’m still not receiving any
answers on what things I might try. I’ve only been using Freesurfer about 3
months, and have basically been working on the same analysis project, so I’m
pretty new to the tool.
Again, I have brain surfaces where the white matter surface gets confused
with the brain surface after control point corrections, and after a
suggestion from another question asker, I deleted control points with zeroes
from the control dat files and reran subject reconstructions, to get the
same results.
What possible trouble-shooting method could I do on this? Should I start the
reconstruction edits over completely (several hours per brain) using only
white matter edits for the white matter surface instead of control points?
Does anyone have any suggestions at all?
Thanks.
Jennifer Kriegel
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Kriegel,
Jennifer Lynn Sarai
Sent: Thursday, August 20, 2015 7:08 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] surface lines in manual edits
Hi Freesurfer experts,
I asked this question yesterday. I ended up seeing that a similar question
had been asked in July, and spoke to the asker of the question, who told me
his problem had been zeroes on the control point dat file, for several
points.
I have attempted to go back through these, and reran several subjects with
such zeroes removed, however – the same problem reoccurs with the white
matter surface being seen as the brain surface. Any help would be welcomed.
Thank you.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Kriegel,
Jennifer Lynn Sarai
Sent: Wednesday, August 19, 2015 10:44 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] surface lines in manual edits
Hi,
I’m hand editing brains to get the most accurate cortical thickness analysis
possible, and ran into a bit of a problem with surface lines. One issue is
with the original structural reconstructions from the hdr files, and the
other deals with the manual edits I’ve made when the recon was re-run.
1. A couple of the volumes initially had the white matter surface as
the pial surface/cortical surface. Initially I tried running g-cut for some
of the suggestions I found on the wiki when the surface lines are off. This
didn’t work on those problem volumes.
2. When editing with control points in order to get the white matter
areas that were not incorporated into the white matter surface included, the
control points have overcoverected and made the same issue that was the
occurrence with the two or three original volumes – the white matter surface
is seen as the brain/pial surface. I was conservative with these as well.
I have been looking on the wiki for a way to adjust the actual surface lines
manually based on the actual white matter/brain surface. I think this would
be most useful, but I’m not sure if it is possible. If so, how could this be
done – and, if not, what possible way of trouble shooting can help deal with
this white matter as pial surface issue?
Best regards,
- Jennifer Lynn Sarai Kriegel
MS in Psychological Sciences, Cognition and Neuroscience Emphasis
Functional Neuroimaging of Memory Lab, Center for Vital Longevity
The University of Texas at Dallas
jlk130...@utdallas.edu
------------------------------------------------------------
I am looking for a lot of men who have an infinite capacity to not know what
can't be done.
- Henry Ford
The important thing is not to stop questioning. Curiosity has its own reason
for existing.
- Albert Einstein
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