Hi Markus,
You can try running mri_gcut with a slightly higher T value, default is
0.4.
command would be something like (running from within subject's mri dir):
mri_gcut -T 0.5 T1.mgz brainmask.gcuts.T-0.5.mgz
Carefully inspect the output, overlaid as a heatmap on the T1 and/or
previous brainmask.mgz. You might have to clone back in some brain
voxels.
-Louis
On Fri, 11 Apr 2014, Markus Gschwind wrote:
Dear Louis (and Bruce),
So I have run
recon-all -skullstrip -clean-bm -gcut -subjid <subjid>
on my subjects where remaining pieces of dura after a normal recon-all got
included into pial surface. I am having a look at the result before
continuing with autorecon2 etc.
Results are not yet satisfactory as there is still several centimeters of
dura included in the brainmask, mostly on the convex part of central regions
Is there a possibility to make graph-cut slightly more agressive?
Thank you for help!
Markus
2014-04-07 22:40 GMT+02:00 Louis Nicholas Vinke
<vi...@nmr.mgh.harvard.edu>:
Hi Markus,
It will only skullstrip the T1 and generate a new
brainmask.mgz. So you'll need to run autorecon2 and
3 afterwards.
-Louis
On Mon, 7 Apr 2014, Markus Gschwind wrote:
Dear Louis!
Thank you for the link.
It says I should use
recon-all -skullstrip -clean-bm -gcut
-subjid <subjid>
My question is if this command only
skullstrips and then stops and I would
have to resume with
autorecon2 etc. or if it continues until
the end and overwrites the whole
processing (I'd like to
know before I mess up with te subject
and have a further 16 hours processing
for nothing... ;-)
Thanks!
Markus
2014-04-07 20:01 GMT+02:00 Louis
Nicholas Vinke
<vi...@nmr.mgh.harvard.edu>:
Hi Markus,
Instructions for using gcut within
recon-all can be found on this wiki
page, near the
bottom.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview
-Louis
On Mon, 7 Apr 2014, Bruce Fischl
wrote:
Hi Markus
that looks pretty blurry and
low contrast, although it's hard to tell
without windowing it. Does
the intensity normalization remove the
contrast?
If so, you can try making it
less aggressive with the -gentle flag or
playing with individual
parameters (like -b).
I can't remember the graph
cuts stuff. Hopefully Nick or Zeke or
someone
will point you in the right
direction
Bruce
On Mon, 7 Apr 2014, Markus
Gschwind wrote:
Dear Bruce,
Thanks for your
detailed answer!
> it's tough to
tell for sure on just a single slice,
particularly if it is
the intensity normalized one that
removes a lot of
the contrast if it is (as you suspect)
doing the wrong thing.
What does the orig look like? We try
pretty hard to
avoid including deep, highly myelinated
gray matter inside the
white matter surface, but of course if
the contrast is
low enough we can fail. If you scroll
backwards and forward
a few slices does or look in a different
orientation does
it look different/better? Sometimes the
surface is curving
sharply and this kind of thing will show
up on a single
slice, but actually isn't a significant
inaccuracy.
Yes, when scrolling
throug the slides it really appears
consistent across
several slides (actually the attached
screenshots
showed Freeview in
coronal, sagittal and axial perspective
of
the same region). Here
is the orig attached together with the
wm,
pial and white.
So how should I treat
it?
> As for the
dura, that certainly looks like a
problem for
thickness estimates.
Have you tried using the graph cuts
skull stripping?
That is more aggressive than
mri_watershed. You can
also play with the watershed parameters
to try
to get more dura
removed. Finally, if you have a T2-space
FLAIR scan we can use
that to properly reposition the
surfaces (or
less ideally, a T2-space scan without a
FLAIR
inversion).
No, unfortunately
there are no other images at
disposition.
How would one go with
the graph cuts ?
I found "mri_gcut
[-110| -mult <filename> |-T <value>]
in_filename
out_filename",
but how is it run
within recon-all in order to repair (FS
version 5.3)?
Thank you so much!
Markus
2014-04-07 14:47
GMT+02:00 Bruce Fischl
<fis...@nmr.mgh.harvard.edu>:
Hi Markus
it's tough to
tell for sure on just a single slice,
particularly if it is
the intensity normalized one that
removes
a lot of the
contrast if it is (as you suspect) doing
the
wrong thing. What does
the orig look like? We try pretty
hard to avoid
including deep, highly myelinated gray
matter inside the
white matter surface, but of course if
the
contrast is low
enough we can fail. If you scroll
backwards and forward
a few slices does or look in a different
orientation does
it look different/better? Sometimes the
surface is curving
sharply and this kind of thing will show
up on a single
slice, but actually isn't a significant
inaccuracy.
As for the dura,
that certainly looks like a problem for
thickness estimates.
Have you tried using the graph cuts
skull stripping?
That is more aggressive than
mri_watershed. You can
also play with the watershed parameters
to try
to get more dura
removed. Finally, if you have a T2-space
FLAIR scan we can use
that to properly reposition the
surfaces (or
less ideally, a T2-space scan without a
FLAIR
inversion).
cheers
Bruce
On Mon, 7 Apr
2014, Markus Gschwind wrote:
Dear all,
I would
like to show some very frequent and
typical
cases of segmentation
problems
in my bunch of data of normal subjects
(after recon-all), of
which
I couldn't
find a description in the
wiki(http://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorking
With
Data/FreeviewEditingaRecon).
I am
therefore not sure if these types of
error are
serious and will
affect
later
results like thickness, curvature, GWR,
etc.
Here are
the examples (c.f. attached screenshots
from Freeview)
1) In the
primary sensory-motor cortex it
frequently
happens that the
"?h.white"
line lies several mm within the wm
border
(c.f. yellow arrow), I
did not
observe this behavior in other places.
>>Would I
need to edit that?
2)
Sometimes the "?h.pial" line includes
also dura
or parts of the skull
(green
arrow).
>>Is it
necessary to edit that as well?
3) Another
question concerns the yellow parts of
the
wm which sometimes are
much
larger than the ventricles and also
include
both caudate nuclei
(not
shown).
>>Is this
a problem?
Thanks in
advance!!
Markus
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