External Email - Use Caution
Hello Bruce,
thank you very much for your response. I just uploaded a file. It is called 109_Caroline_Chwiesko_8-23-2019.tar.gz. And I uploaded a file with some example coordinates. Thank you very much for taking the time and looking at it!
Best Carolin
On Thu, Aug 22, 2019 at 7:16 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Carolin
yes, there are ways. You can modify the intensity thresholds that mris_make_surfaces auto-detects. Sounds like they are a bit off. If you send us the recon-all.log and the intensity of a few voxels that are included in the ?h.white surface and should not be we can suggest some things to try. Or tar and gzip the whole subject dir and ftp it to us and send us some voxel coords of places you think things should be more accurate.
cheers Bruce
On Thu, 22 Aug 2019, Caroline Chwiesko wrote:
External Email - Use CautionHello Freesurfer experts, I would like to follow up on my previous question. As Doug recommended, I did the manual editing to the wm.mgz by deleting voxels in the wm.mgz
file,
which I thought are gray matter. I rerun recon-all using the command below because I also did edits to the brain mask (removing some skull) and adding control points.
recon-all -s $1 -all -parallel -openmp 10 -hippocampal -subfields-T1
I do find spots where the editing lead to an improvement, but I have
other
spots, which did not improve despite wm editing. And for those spots the new wm.mgz does not label voxels as wm
(according to
my edits), but the ?h.white would still extents beyond those voxels. Or the new wm.mgz does label again non wm voxels as wm.
Is there anything else I can try to fix those spots?
Thank you very much in advance for any help! Carolin
On Tue, Aug 6, 2019 at 8:15 PM Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote: ps, and I meant to say that the non-WM will be labeled as WM.
On 8/6/2019 6:44 PM, Douglas N. Greve wrote: > Then re-run with > recon-all -s subject -autorecon2-wm -autorecon3 > > > On 8/6/19 6:42 PM, Greve, Douglas N.,Ph.D. wrote: >> You should edit the wm.mgz. In these places, the WM will be labeled as >> non-WM. Just erase the mislabeled voxels. >> >> On 8/6/19 6:31 PM, Caroline Chwiesko wrote: >>> External Email - Use Caution >>> >>> Hello Freesurfer experts, >>> >>> I wrote a previous email about my issue that in many of my subjects I >>> have spots where the ? >>> h.white is extending too much into the gray matter after running >>> recon-all. >>> >>> As I understood from a conversation from somebody else, >>> [[Freesurfer] WM surface including too much gray matter], you are >>> currently looking into whether default parameter adjustments in >>> recon-all can fix this problem. Until then, it was recommended to >>> edit those errors manually. >>> >>> My question is what editing technique should I use if I want to >>> manually edit thesis type of errors? Removing the voxels that I think >>> are gray matter from the white matter file using recon edit? >>> I am a little confused about this because I noticed that the ?h.white >>> boundary does not necessarily follow the wm boundary (see attached >>> image), so I am wondering, if changes to the wm will fix the problem >>> that I have. >>> >>> Thank you very much in advance! >>> Carolin >>> >>> Screen Shot 2019-08-06 at 1.32.16 PM.png >>> >>> _______________________________________________ >>> 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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