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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. < DGREVE@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:
External Email - Use CautionDear 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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