Hi Brendan
usually defects that are that big don't get corrected properly. I would
look at the wm.mgz and the lh.orig.nofix to understand what is causing the
large defects and correct them manually
cheers
Bruce
On Fri, 9 Aug 2019, Balken, Brendan wrote:
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Bruce,
Oh okay I understand now. This has been very enlightening! So, you think if I
let it keep running it will eventually correct the defects? And then I just
need to double check the result to make sure it corrected them properly? When I
got the overlay to work, I could see two big defects on the left hemisphere (30
and 41) so I guess it'll probably get stuck again on 40. Also, is there
anything I can do to make it faster?
Thanks,
Brendan
-----Original Message-----
From: [email protected]
[mailto:[email protected]] On Behalf Of Bruce Fischl
Sent: Friday, August 9, 2019 11:21 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] CORRECTING DEFECT
CAUTION: External
yes, because that is the total # of defects. The 29th or 30th isn't the last
one, just what it got stuck on. The #30 should look much bigger though (you'll
need to change the overlay thresholds) On Fri, 9 Aug 2019, Balken, Brendan
wrote:
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Bruce,
I just imported lh.defect_labels as an overlay over the lh.inflated.nofix but
the values aren't 1-30 they're 0 - 160 roughly. I'm not sure why...
Thanks!
-----Original Message-----
From: [email protected]
[mailto:[email protected]] On Behalf Of Bruce
Fischl
Sent: Friday, August 9, 2019 11:00 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] CORRECTING DEFECT
CAUTION: External
they are an overlay not a surface. Load the surface first then load them as an
overlay on top of it (e.g. the lh.inflated.nofix) On Fri, 9 Aug 2019, Balken,
Brendan wrote:
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Bruce,
Thanks so much for the quick response! I don't know how to load the defect
labels. When I try to load them as a surface, I get an error. I'm doing this in
freeview gui. Also, I checked the cerebellum and it's not attached.
Thanks,
Brendan
-----Original Message-----
From: [email protected]
[mailto:[email protected]] On Behalf Of Bruce
Fischl
Sent: Friday, August 9, 2019 10:27 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] CORRECTING DEFECT
CAUTION: External
Hi Brendan
the time to correct goes with the square of the size of the defect (actually
the convex hull of the defect) so it can take a very long time for big ones.
More importantly, if the defect is that large it may not be corrected in the
anatomically desired manner. You should take a look at it and see what is
causing it. Is skull left over? Cerebellum attached?
Hemispheres connected? Usually the big ones are due to something dramatic.
Look at the ?h.orig.nofix and the ?h.inflated.nofix. YOu can load the
?h.defect_labels on top of the surfaces and brain.mgz and the wm.mgz to see
which one is 29 (note that they defect_labels file is probably 1-based so you
would need to look for 30 in it).
If you can't sort it out gzip and tar your subject and put it on our
ftp site and we will take a look for you cheers Bruce
On Fri, 9 Aug 2019, Balken, Brendan wrote:
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Hello!
So I am attempting to use freesurfer’s recon-all script but for one
of our subjects I keep getting stuck at this point: “CORRECTING
DEFECT 29 (vertices=19321, convex hull=4029, v0=32423) XL defect
detected...” It has already corrected 28 defects, but they were much
smaller. It has been running for about 48 hours on a very powerful
machine and I’m wondering how long I should wait. Will it eventually
move on? If no, what is my contingency plan for processing this? I’m
using the output anatomy folder in brainstorm for source analysis.
Any guidance or information would be greatly appreciated.
Thanks a million!
Brendan
Here’s what the lh and rh.inflated.nofix look like (is that the defect?):
[IMAGE]
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