Hi Xiaoqian
it's pretty hard to tell what's going on from these images. If you tar/gzip
your whole subject dir and upload it with an email telling us the specific
voxel coords that you want us to examine
cheers
Bruce
On Wed, 16 Oct 2019, Xiaoqian Yan wrote:
External Email - Use Caution
Dear Douglas,
Thanks for your reply. I double checked my results. It was true that the
rh.orig.nofix and rh.orig did not overlap over the region that I was
interested in. I re-edit the wm, and only ran 'recon-all -autorecon2-wm
-subjid patientname' to check the results, but the rh.orig.nofix and rh.orig
were still not overlapped. Do you mind helping me check my wm edits? For me,
the thermal lesion is a black hole that big enough to confuse the
segmentation. Maybe there is a way to mark that region or add a label,
before I run the recon-all?
P.S. in the attached figures, pial is in green, rh.orig.nofix in red, and
rh.orig in yellow.
Thanks and have a nice day,
Xiaoqian
On Fri, 11 Oct 2019 at 00:47, Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu> wrote:
I think that the wm edits should have worked. Can you load the
rh.orig.nofix and rh.orig to see if they encompass your edits?
If not, then maybe your did not re-run it properly.
On 10/8/2019 12:22 PM, Xiaoqian Yan wrote:
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Dear Freesurfer experts,
I am trying to do the segmentation on a patient's T1 image. I
did not get error messages running the 'recon-all' (recon-all -i
T1.nii -subjid PatientName -all), but the segmentation over the
right occipital lobe was imperfect, which caused failures to map
the functional activations in this region onto the surface.
I tried to manually edit the wm.mgz several times, but the
output did not change a lot (please see the attached image). The
patient had depth EEG electrodes implanted in this region
before, so there is a thermal lesion which I thought could have
caused the bad segmentation. Do you have any ideas about what I
can do next, or it is possible for you to help me editing the
data?
Thanks in advance, best wishes
Xiaoqian
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