Hi Markus
I'm not really sure. I'll cc Mike Chee whose lab the graph cuts stuff was
developed in
Bruce
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/FreeviewWorkingWith
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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