To continue, all you need to do is rename the good brainmask (generated with the modified gcuts command) to brainmask.mgz.
-Louis
On Fri, 11 Apr 2014, Markus Gschwind wrote:
Thanks Louis!
Great. It seems I need -T 0.65. That looks fine.
Is it necessary
- to name the modified brainmask.gcuts.T065.mgz?
- and keep both brainmask.mgz and brainmask.gcuts.mgz in the mri folder?
And then continue with
recon-all autorecon2 autorecon3 -s subjectid
Is that correct?
Thank you so much!
Markus
2014-04-11 17:23 GMT+02:00 Louis Nicholas Vinke <vi...@nmr.mgh.harvard.edu>:
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_freevie
w
-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/FreeviewWorkin
g
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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