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:
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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 Caution 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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