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Dear Bruce,
Thanks for the reply. I have uploaded my data through the Martinos Center FileDrop, here is the link: + Data_Xiaoqian.zip (169.46 MiB) < http://gate.nmr.mgh.harvard.edu/filedrop2/?p=6wbctqzrzh1%3E
I explained my problems in that link, but still copy and past here:
'' I am having troubles doing a good segmentation in the right occipital lobe in a patient's brain. There is a thermal lesion in that region, a black whole, that could make the segmentations go wrong. I tried to edit the wm, but the results were not ideal.
The thermal lesion can be clearly seen from the axial slices 108 - 115, e.g. in RAS coordinate [40,-50,-4] on the axial slice 112. The bad segmentation (wm and pial surface) can be seen from the coronal slices 54 - 62, e.g. in coordinate [42, -52, -10] on the coronal slice 57. The wrong segmentation made it impossible to overlap the functional activations in the OFA (occipital face area) region on the surface.
In my uploaded data directory, I already edited the wm and brainmask, and I only reran 'recon-all -autorecon2-wm -subjid name' to save time. ''
Thanks in advance, and best wishes,
Xiaoqian
On Wed, 16 Oct 2019 at 15:07, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
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 CautionDear 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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