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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