Hi Daniel
I'm out if town , can you remind me next week? This is fixed in v6 I think if you want to just run the pial stuff in it Bruce
On Apr 21, 2016, at 10:41 AM, dgw dgwakeman@gmail.com wrote:
Hi,
I followed the advice, and the White Matter surface looks much better; however, now the pial surface is crossing the white matter surface.
I ran the following: /usr/local/freesurfer/stable5_3_0/bin/recon-all -subjid nmr01002 -autorecon2-wm -autorecon3 -openmp 8
for those at Martinos the new subjid should indicate the new path.
I've attached a screenshot. Thank you in advance for any advice you can give.
Thank You, Dan
On Tue, Apr 19, 2016 at 5:29 PM, dgw dgwakeman@gmail.com wrote: Hi Bruce,
Thanks! I'll give it a whirl.
d
On Tue, Apr 19, 2016 at 5:24 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Daniel
the problems isn't that it it's ignoring the wm edits, it is that it starts the orig surface out there, but then retracts to the (same) visible gray/white boundary that it found in the first place. For this type of lesion I think what you should do is also edit those voxels in the aseg.mgz and change them to right-lesion. This should freeze the white surface there I think. If it doesn't, let me know and I'll fix it.
cheers Bruce
On Tue, 19 Apr 2016, dgw wrote:
Here is the log for the most recent -autorecon2-wm call:
Thanks! d
On Tue, Apr 19, 2016 at 4:56 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
can you send us the recon-all.log? I don't see an obvious reason why it wouldn't have worked
On Tue, 19 Apr 2016, dgw wrote:
Just to follow up, I have tried several different options with recon-all to get the white matter edits to stick on this participant, and it doesn't seem to be working:
re-editing wm.mgz and running recon-all -autorecon2-wm re-editing wm.mgz and running recon-all -make all
I can't seem to get any appreciable change in the white matter surface. I have attached a screenshot, for an example.
hth d
> On Mon, Apr 18, 2016 at 10:30 AM, dgw dgwakeman@gmail.com wrote: > Hi, > > I recently edited a brain with a gyral cyst, carefully filling the > cyst with white matter in the wm.mgz. Unfortunately after running: > /usr/local/freesurfer/stable5_3_0/bin/recon-all > -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8 > > none of the edits were incorporated. > > Is the FLAIRpial flag incompatible with autorecon2-wm? > > Is there some other misake? > > I followed this guide > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freevi... > > Thanks, > Dan
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