Mishkin,
It looks like a copy-and-paste error.
Add this to your ASegStatsLUT.txt file in your $FREESURFER_HOME:
63 Right-choroid-plexus0 200 2210
then run:
recon-all -s -segstats
Nick
On Fri, 2007-12-14 at 18:02 -0500, Mishkin Derakhshan wrote:
> Hi,
> Is the
Hi,
Is there any reason why aseg.stats only has a label for the
left-choroid-plexus (id 31) and none for the right?
I am using freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.1
thanks,
mishkin
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you could also use:
mri_convert with the -rl (reslice like) option to change the volume back to
the scanner template
On Fri, 14 Dec 2007, Nick Schmansky wrote:
On Fri, 2007-12-14 at 15:57 -0500, Mishkin Derakhshan wrote:
Thanks.
It didn't quite work as I'm guessing the step sizes in origina
On Fri, 2007-12-14 at 15:57 -0500, Mishkin Derakhshan wrote:
> Thanks.
> It didn't quite work as I'm guessing the step sizes in original.mnc
> are negative, but I am able to reshape the minc file afterwards to get
> it exactly the same.
>
> From my (limited) understanding of mri_vol2vol, when you
or use the -noaseg flag with -fill, that is:
recon-all -s -fill -noaseg
use the -noaseg flag just with the -fill flag, and not with other flags,
as you will want aseg.mgz used with the other commands that make use of
it.
On Fri, 2007-12-14 at 16:49 -0500, Bruce Fischl wrote:
> this is a know
this is a known bug. We'll have a fix soon. You can change the mri_fill
call in recon-all to use aseg.auto.mgz as a quick fix.
On Fri,
14 Dec 2007, Michael Harms wrote:
Hello,
Just a brief addendum:
Our previous experience with -autorecon2 has been primarily with v3.0.5
(and thus v3.0.5 ase
Hello,
Just a brief addendum:
Our previous experience with -autorecon2 has been primarily with v3.0.5
(and thus v3.0.5 asegs, not 4.0.1 asegs as Matt initially indicated)
where we have never encountered this "nbrs" error during mri_fill. We
have just started processing some new brains through -au
Dear FreeSurfer folks,
We recently had an error occur while processing two brains in recon2. We
are using FreeSurfer version 4.0.1 for these subjects. The error message
in both cases mentions that mri_fill could not find points where lh and rh
wm were "nbrs" (I assume this is short for neighbors).
Thanks.
It didn't quite work as I'm guessing the step sizes in original.mnc
are negative, but I am able to reshape the minc file afterwards to get
it exactly the same.
>From my (limited) understanding of mri_vol2vol, when you invoke it
with the --regheader is it taking the ras to voxel transform a
Good to know.
So, if we ever encounter a problem with a pial, white, or orig surface
crossing the midline, we should first run -autorecon3 (if not already
run, so as to generate the ?h.aparc.annot) and then reprocess from -
finalsurfs onward, but without the -noaparc flag in the command for
mris_m
Hi Mike,
if noaparc is not given, mris_make_surfaces will look for ?h.aparc.annot
and read it in to determine what regions it should disable the deformation
in to avoid crossing the midline.
cheers,
Bruce
On Fri, 14 Dec 2007,
Michael Harms wrote:
Hello,
What is the role of the -noaparc
Hello,
What is the role of the -noaparc flag in 'mris_make_surfaces' of FS v4?
thanks,
Mike H.
--
Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department
So it looks like you have Fedora Core 4 installed. You need to install
from the FC4 distribution the compat-libstdc++-33 package/RPM
http://rpm.pbone.net/index.php3/stat/4/idpl/1981813/com/compat-libstdc++-33-3.2.3-47.fc4.i386.rpm.html
On Sat, 15 Dec 2007, Feng-Xian Yan wrote:
Hi,
I do that
Feng-Xian,
Sorry for the late reply. You have two options:
1) install libstdc++.so.5 (aka compat-libstdc++-33)
or
2) wait until next week when v4.0.2 of freesurfer is released. this
next version contains mni tools that are built against libstdc++.so.6
instead of libstdc++.so.5.
Also, I m
Hi,
I do that you type, but it is also error.
And, I find "libstdc++.so.6", not"libstd++.so.6". What is difference
between them?
And, what can I do next??
Iteration 1 Thu Dec 13 11:49:43 CST 2007
nu_correct -clobber ./tmp.mri_nu_correct.mni.4568/nu0.mnc
./tmp.mri_nu_correct.mni.4568/nu1.mnc
[EMA
yes, with the current version it seems to almost never fail.
On Fri, 14 Dec
2007, Nick Schmansky wrote:
Simon or Martin,
If you have a chance, can you try the -multistrip option of recon-all
with a subject that you know fails the default fs skullstrip? That
option launches eight instances o
Simon or Martin,
If you have a chance, can you try the -multistrip option of recon-all
with a subject that you know fails the default fs skullstrip? That
option launches eight instances of mri_watershed all with different
parameter combos, and the best one is selected. If all of those fail,
can
Juergen,
Freesurfer doesnt automatically handle input images with a FOV > 256, so
you must add this to your recon-all command:
-cropsize256
You would add that to the -autorecon1 stage, that is, start recon-all
from the start with the -cropsize256 flag.
Nick
On Fri, 2007-12-14 at 08:42 +010
I've found it varies. A couple of brains that didn't go through with
the FS brain extraction tool went through with BET. Maybe recon-all
could include an option to try BET? Obviously have the most reliable
tool as default but allow the user to easily test an alternative tool
before start
Hi -
Does anyone have any advice/experience on converting/creating DICOMS from
arbitrary image formats like png or jpg?
Basically I have a set of post-processed png images that were derived from a
set of DICOMS. I'd like to convert these png images back into DICOM again.
Many thanks
-=R
--
that's good to know, maybe we should try it in general. Do you do this
in addition to N3? Before? After?
On Fri, 14 Dec 2007, Martin Kavec wrote:
In my experience, the FreeSurfer's brain extraction works better than the
BET. Although, now with an option of iterative BET in the latest FSL, the
In my experience, the FreeSurfer's brain extraction works better than the
BET. Although, now with an option of iterative BET in the latest FSL, the
outcomes are much better than before. In cases where brain extraction
failed in my analysis, I found that it was the bias field correction which
di
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