External Email - Use Caution Hi Bram,
Thanks very much for the detailed explanation. I understand that I have to edit the wm first, and only work on the brain.finalsurfs if wm edit does not help. I tried the command you suggested (recon-all -s <subject_id> -white -smooth2 -inflate2 -curvHK -curvstats -autorecon3), with the new brain.finalsurfs and wm files, but the results were not ok (same as I got before). Instead I had to run (recon-all -autorecon2-wm -autorecon3 -subjid <subject>) to get the similar results as you showed in the last email. I don't understand why we get different results. Best wishes, Xiaoqian On Mon, 21 Oct 2019 at 16:33, Diamond, Bram Ryder <brdiam...@mgh.harvard.edu> wrote: > Hi Xiaoquian, > > That's correct -- although I did it in a slightly different order because > I wasn't sure what was causing your issue. I first edited the wm.mgz using > the 'recon edit' option (changing wm lesion voxels to 255) in FreeView, > because I was hoping that would fix the surfaces. When that didn't work, I > instead edited the brain.finalsurfs.mgz with the 'voxel edit' tool and > changed the voxel values within the wm lesion to 110. As you can see in the > attached images, that seemed to do the trick. The latest run-through > applied both the wm and brain.finalsurfs edits -- but it's likely that the > surfaces would have improve with *only* the brain.finalsurfs edits. You > can test that out for yourself. > > Instead of running recon-all between each test, I used the ' > mris_make_surfaces > <https://surfer.nmr.mgh.harvard.edu/fswiki/mris_make_surfaces>' command > exactly how recon-all would call it, but only for the rh (the hemisphere > with the lesion and manual edits). The command can be found in the > ReconAllTableStableV6.0 > <https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0> > table: mris_make_surfaces -aseg ../mri/aseg.presurf -whiteonly -noaparc > -mgz -T1 brain.finalsurfs <subjid> ?h . Once I saw that the new edits > worked, I ran recon-all with the remainder of autorecon2 (-white -smooth2 > -inflate2 -curvHK -curvstats) and all of autorecon3 (-autorecon3). > > If you are not seeing the same surface improvements, make sure you've > replaced your wm.mgz and brain.finalsurfs.mgz with the edited version I > sent you last week. You can save copies of your original files, but rename > them wm_old.mgz and brain.finalsurfs_old.mgz so that FreeSurfer doesn't > accidentally apply them to your new recon-all. > > Going forward, if you have a similar issue, I would first suggest editing > the wm.mgz. If that doesn't work, move to the brain.finalsurfs.mgz. > > Let me know if you're still having trouble or would like more detail. > > Best, > Bram > > ___________________ > Bram R. Diamond, BSc > Sr. Clinical Research Coordinator > Laboratory for Computational Neuroimaging (LCN) > Laboratory for NeuroImaging of Coma and Consciousness (NICC) > Massachusetts General Hospital > (p): 617-726-6598 > > LCN: https://www.martinos.org/lab/lcn > NICC: https://www.massgeneral.org/nicc > > ------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Xiaoqian Yan < > yanxq...@gmail.com> > *Sent:* Friday, October 18, 2019 4:17 PM > *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] imperfect segmentation in the occipital lobe > in epilepsy patient > > > External Email - Use Caution > > Dear Bram, > > Thanks very much for your help. If I am understanding correctly, you first > filled the lesions in the wm (brain.finalsurfs.mgz) in freeview with 'voxel > edit', brush value = 110. Then you recreated a new wm.mgz, with which > commands? I might run into similar situations in the future, as I am > working on a project with epilepsy patients that will have depth electrodes > implanted in their brain (causing thermal lesions). When that happens > again, I want to be able to fix that by myself. > > Thanks again, best wishes > > Xiaoqian > > On Fri, 18 Oct 2019 at 20:48, Diamond, Bram Ryder < > brdiam...@mgh.harvard.edu> wrote: > > Hi Xiaoqian, > > We don't typically recommend this, but it looks like you will need to edit > your brain.finalsurfs.mgz to account for the wm lesion. I tested this out > by filling in the lesion with 110 and recreating the wm surface -- it seems > to work quite well. > > Once that is done, you can run the following command to finish your > recon-all. I'm running it now to make sure the output is okay: > recon-all -s <subject_id> -white -smooth2 -inflate2 -curvHK -curvstats > -autorecon3 > > I also made some edits to the wm.mgz, but I'm not sure they were > necessary. I'll send you copies of the edited files in a private email. > > Best, > Bram > > ___________________ > Bram R. Diamond, BSc > Sr. Clinical Research Coordinator > Laboratory for Computational Neuroimaging (LCN) > Laboratory for NeuroImaging of Coma and Consciousness (NICC) > Massachusetts General Hospital > (p): 617-726-6598 > > LCN: https://www.martinos.org/lab/lcn > NICC: https://www.massgeneral.org/nicc > > ------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Xiaoqian Yan < > yanxq...@gmail.com> > *Sent:* Wednesday, October 16, 2019 12:11 PM > *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] imperfect segmentation in the occipital lobe > in epilepsy patient > > > 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 > > _______________________________________________ > 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
