Hi!
I am trying to work around this now using more control points.
However, I was wondering whether the fixed version of mri_segment for
v4.5 that accepts the -p parameter is still available? Just in case I
need to use a different threshold at some point.
Thanks, Caspar
2013/5/17 Caspar M.
Hi Bruce,
I tried adding control points in the white matter in that region,
however, it does not seem to fix the issue. Also, the brainmask.mgz
does not seem to exclude this part of the brain, so that is not the
problem either.
I am attaching another screenshot (horizontal 119) to illustrate the
Hi Caspar
yes, that might help. There are expert opts for this. Sorry, I have
almost no experience analyzing monkey brains at .5mm, so I'm really not
sure what to advise you. Perhaps one of the other people on list who have
done a bunch can comment?
Bruce
On Fri, 17 May 2013, Caspar M.
Hard to fix if that is the receive field and you don't have another image
like a T2w to remove it with. Perhaps mri_normalize can be tuned to
improve this with expert options as the white matter that is being
correctly segmented appears to be darker as well.
Peace,
Matt.
On 5/17/13 9:30 AM,
When I try to specify a different threshold using -p, mri_segment
reads in the threshold as the input volume.
I tried specifying the input with -i (as explained here:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18826.html),
but now it does not recognize the -i flag.
Caspar
what is your command line? You are probably better off setting gray_hi,
gray_low, wm_hi, wm_low, etc...
Bruce
On Fri, 17 May 2013, Caspar M. Schwiedrzik
wrote:
When I try to specify a different threshold using -p, mri_segment
reads in the threshold as the input volume.
I tried specifying the
mri_segment \
-v \
-fillv \
-fillbg \
-wlo 104 \
-ghi 118 \
-whi 140 \
-n 4 \
-keep \
brain.mgz wm.mgz
The pial surface in the rest of the brain is ok, it is only the
orbitofrontal/piriform cortex that is problematic. I now wanted to add
-p 0.7.
Caspar
2013/5/17 Bruce Fischl
and what happens? Can you send the full screen output?
On Fri, 17 May 2013,
Caspar M. Schwiedrzik wrote:
mri_segment \
-v \
-fillv \
-fillbg \
-wlo 104 \
-ghi 118 \
-whi 140 \
-n 4 \
-keep \
brain.mgz wm.mgz
The pial surface in the rest of the brain is ok, it is only the
filling ventricles
filling basal ganglia
using white lolim = 104.0
using gray hilim = 118.0
using white hilim = 140.0
running border classification 4 times
preserving editing changes in output volume...
using 70% threshold
mri_read(): couldn't determine type of file /.../.700
Hi Caspar
can you include the command line and all the output?
Bruce
On Fri, 17 May 2013,
Caspar M. Schwiedrzik wrote:
filling ventricles
filling basal ganglia
using white lolim = 104.0
using gray hilim = 118.0
using white hilim = 140.0
running border classification 4 times
preserving
set threshold = `echo 7/10 | bc -l`
set segment_options = -v -fillv -fillbg -wlo 104 -ghi 118 -whi 140
-n 4 -p $threshold -keep
mri_segment ${segment_options} \
-i brain.mgz -seg wm.mgz
filling ventricles
filling basal ganglia
using white lolim = 104.0
using gray hilim = 118.0
using white hilim
Your line continuation isn't working for some reason? Type the command
line all on one line and see if that fixes the problem.
Matt.
On 5/17/13 1:37 PM, Caspar M. Schwiedrzik
cschwie...@mail.rockefeller.edu wrote:
set threshold = `echo 7/10 | bc -l`
set segment_options = -v -fillv -fillbg -wlo
Hi Matt and Bruce,
still the same problem. What about the fix that was mentioned in the
earlier discussion? Was that not for version 4.5?
Caspar
2013/5/17 Matt Glasser m...@ma-tea.com:
Your line continuation isn't working for some reason? Type the command
line all on one line and see if that
Try leaving out the -i and -seg
Those are mandatory parameters and don't need hyphens
On May 17, 2013, at 3:11 PM, Caspar M. Schwiedrzik
cschwie...@mail.rockefeller.edu wrote:
Hi Matt and Bruce,
still the same problem. What about the fix that was mentioned in the
earlier discussion? Was that
Hi Bruce,
I only put them in because it was not working without them and that
was the solution in the previous discussion.
To summarize: Once I put in -p 0.7, mri_segment misinterprets 0.7 as
the input file name, no matter whether I use -i or not.
Caspar
2013/5/17 Bruce Fischl
Hi Caspar
it's hard to tell from a single slice. There does seem to be some darkening
there, probably due to B0. Is there wm on the next slice inferior/superior?
If you upload the whole subject dir I'll take a look.
cheers
Bruce
p.s. NHP data?
On Thu, 16 May 2013, Caspar M. Schwiedrzik
Hi Bruce and Matt,
yes, it is primate data. I just dropped an archive on your FTP server
in transfer/incoming.
Thanks!
Caspar
2013/5/16 Matt Glasser m...@ma-tea.com:
Is the brain extraction removing that part of the brain? Do you know
where the OFC ends and olfactory bulb begins?
Peace,
Hi Bruce,
ok.
But in theory, what would you recommend to get around the darkening
issue? Unfortunately, I do not have a field map available for this
data set.
Or should I not expect to get a pial surface in this area since the
white matter is not discernable?
There are five slices without clear
Hi Caspar
if it's primate I don't think I'm going to be able to help - you'll need
someone more familiar with primate anatomy
sorry
Bruce
On Thu, 16 May 2013, Caspar M.
Schwiedrzik wrote:
Hi Bruce and Matt,
yes, it is primate data. I just dropped an archive on your FTP server
in
Hi Caspar
is the closest white matter captured by the white surface? What is the
intensity of voxels there? If 110 you could try putting control points in
them and seeing if that helps (that is, in the closest voxels that are
entirely white matter).
Bruce
On Thu, 16 May 2013, Caspar M.
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