Dear All,
I wanted to know if there is any take on the issue of white matter edits
(specifically deleting unwanted voxels from wm.mgz). I sent a subject a
week ago for your review. It seems this is a problem that I had with
several scans, and by the message list, I am not the only one.
Recent user
yes, I think that's what V6 does I think
On Thu, 21 Apr 2016, dgw wrote:
Hi,
I solved it (with help from a colleague) by just calling the
individual mri_make_surfaces command separately (adjusting the
nowhite), and
the subsequent ones through the flair pial command. I am now running
-make all,
Hi,
I solved it (with help from a colleague) by just calling the
individual mri_make_surfaces command separately (adjusting the
nowhite), and
the subsequent ones through the flair pial command. I am now running
-make all, to finish the rest (note it did miss one step in the
re-start: it didn't re-
Hi Mike
yes, I think it is fixed. Daniel: can you try out dev and see if it fixes
this for you?
Bruce
On Thu, 21 Apr 2016, Harms, Michael wrote:
That looks very similar in principle to something I posted back in Oct.
2014 (“pial surface crossing white”).
I think some of the subsequent ba
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 wrote:
>
> Hi,
>
> I followed the advice, and the White Matter surface looks much better;
> however, now the pial surfac
That looks very similar in principle to something I posted back in Oct.
2014 (“pial surface crossing white”).
I think some of the subsequent back-and-forth with Bruce and Nick was off
the list, so I’ve included the key email (where Bruce diagnosed the
problem) below.
Has this been fixed in the f
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
Hi Bruce,
Thanks! I'll give it a whirl.
d
On Tue, Apr 19, 2016 at 5:24 PM, Bruce Fischl
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
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 ase
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
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
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