Hi Dan
it depends what your goal is. I think you could get a decent quality recon
with an hour two of work, but I'm not sure I would trust thickness
estimates from a scan of that quality
cheers
Bruce
On Fri, 12 May 2017, Weisholtz, Daniel
S.,M.D. wrote:
Dear Bruce,
Thank you for your help. I was able to view the defects. It does seem to be
an extensive defect—possibly retained dura? I’m not sure of any other way to
fix it. Do you think that the poor quality of the source image makes it
impossible to generate any kind of surface using free surfer?
Best,
Dan
On May 11, 2017, at 12:00 PM,
freesurfer-requ...@nmr.mgh.harvard.edu wrote:
Message: 9
Date: Thu, 11 May 2017 11:38:42 -0400 (EDT)
From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer Digest, Vol 159, Issue 12
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.lrh.2.20.1705111132360.28...@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-7"
Hi Dan
that's a pretty low-contrast, severely motion-corrupted scan. We did
pretty
well given the input I think. To visualize the defects you can cd into
the
subject's mri dir and run:
fv -v brain.mgz wm.mgz:colormap=heat -f \
../surf/lh.orig.nofix:overlay=../surf/lh.defect_labels:overlay_threshold=1,
100 \
../surf/lh.inflated.nofix:overlay=../surf/lh.defect_labels:overlay_threshol
d=1,100
then click the "use overlay color" button for the lh.orig.nofix
surface.
You can also change the display paramters in "configure overlay" to
find a
specific defect by setting the min/max to a narrow range around the
one you
are interested in (this will put it in the middle of the range and
color it
orange)
cheers
Bruce
On Thu, 11 May 2017, Weisholtz, Daniel S.,M.D. wrote:
Dear Bruce,
Thank you so much for your suggestions. Unfortunately, I
was not able to
open lh.defect_labels in freeview. ?When I try, Freeview
crashes. ?There are
no rh surfaces in the surf folder, so I presume this means
the problem
occurred in the left hemisphere. I was able to view the
inflated.nofix and
orig.nofix but I?m still not exactly sure what the problem
is, and I would
be grateful if you could take a look at the subject
folder. I will upload it
to the ftp site. It is called s117.
Thank you!
Best,
Dan
On May 10, 2017, at 10:43 AM,
freesurfer-requ...@nmr.mgh.harvard.edu wrote:
Message: 9
Date: Tue, 9 May 2017 15:54:12 -0400 (EDT)
From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all freezes while
CORRECTING DEFECT 60
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.lrh.2.20.1705091553090.16...@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-15"
Hi Daniel
you can load the ?h.defect_labels as an overlay on either
the?
inflated.nofix or orig.nofix surface and use it to find
the location
of?
that defect. Usually this means something big is wrong -
it should be?
obvious looking at the inflated.nofix I would think. If
you can't find
it,?
upload the subject to our ftp site and I'll take a look
Bruce
On Tue, 9 May 2017, Weisholtz, Daniel S.,M.D. wrote:
Hello Freesurfer Developers,
I am trying to run recon-all -all and the procedure
is
freezing while trying
to correct what appears to be a large defect
(vertices=36706). The source T1
image is not great quality due to rippling artifact,
but I
have inspected
brainmask.mgz, wm.mgz, and aseg.mgz and I cannot
identify
a large defect.
The dura was not completely removed, and I tried
improving
this by using
various watershed thresholds as well as using gcut. I
also
tried manually
removing the remaining dura, but none of this was
helpful.
?I also tried
using -T2FLAIR, but this did not seem helpful
either.?
I am attaching the recon-all.log. This does not
include
the edits I made to
brainmask.mgz. That was done on a separate attempt.
This
does include the
-T2FLAIR, as you can see in the recon-all.log file.
1) FreeSurfer
version:?freesurfer-Darwin-lion-stable-pub-v5.3.0
2) Platform: OS X Yosemite 10.10.5
3) recon-all.log attached
I very much appreciate any assistance you can
provide.
Happy to send any of
the data if it would be helpful.
Sincerely,
Dan Weisholtz
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