External Email - Use Caution 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> 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 <fis...@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 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: > > > > 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 > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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