Hi Yang
the problem is that the white matter of the parahippocampal gyrus is so
dark that the surface deforms into hippocampus, which creates little holes
in our estimate of what is cortex. You can see this by loading the
lh.cortex.label into tksurfer. You could fix it by filling in the holes in
the cortex label and rerunning the cortical parcellation. Or you could try
editing the brain.finalsurfs.mgz I guess to brighten up those voxels, but
they are *very* dark - barely any contrast there at all with the GM.
Depending on what you are planning to do with this data I would guess it's
not something to worry about at all. It just two very small holes that
won't appreciaably change any statistics.
cheers
Bruce
On Tue, 4 Feb 2014, Qingyang
Li wrote:
Hi Bruce,
The data is now on the ftp. The path to the file is
"/transfer/incoming/003.tgz".
Thanks,
Yang
------
Qingyang Li
Balance and focus.
On Tue, Feb 4, 2014 at 8:45 AM, Bruce Fischl <[email protected]> wrote:
Hi Yang
if you go to the freesurfer wiki you'll find instructions on uploading
data. Use the ftp site and tar and gzip the
entire subject directory
cheers
Bruce
On Tue, 4 Feb 2014, Qingyang Li wrote:
Hi Bruce,
Where should I upload the data to?
I forgot to mention that the data that I am working with are from a
longitudinal project. The image I sent is a base image generated
from 2 time
points.
The Freesurfer I am running is
"freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0".
Thanks!
Yang
------
Qingyang Li
Balance and focus.
On Tue, Feb 4, 2014 at 8:30 AM, Bruce Fischl
<[email protected]>
wrote:
Hi Yang
hmmm, that is curious. I don't think those will have much if
any
impact on your results, but if you upload that subject I'll
take
a look. What version are you running?
cheers
Bruce
On Tue, 4 Feb 2014, Qingyang Li wrote:
Dear Freesurfer experts,
I was looking at the results of my data when I found
that there were some
black spots in my parcellation results (Please see
the attached screenshot,
the black spots were indicated by arrows).
I did not see any hole or other errors in the
surfaces generated for this
subject. I hope you can help me with why the black
spots were there? is it a
big deal or something that I can ignore? If they
need to be fixed, what
should I do? Thanks!
I am sorry if this question has been posted here. I
really tried to find the
answer by myself but I did not find anything.
Thanks,
Yang
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