that is in ventricle, so you don't need to edit it (unless it is
creating such a big topological defect that FS is crashing or taking a
really long time)
On 9/4/2021 1:05 PM, halil ibrahim AKÇAY wrote:
External Email - Use Caution
Hi
My name is Halil Ibrahim akçay. I am a neurologist
External Email - Use Caution
Hi
My name is Halil Ibrahim akçay. I am a neurologist.
I have been used FreeSurfer for a while. And I cannot understand some part of
troubleshooting process. I am sending a screenshot of my question. How can I
understand whether gray zone as marked
no, probably not, but it is something we will need to fix as they should
be conseistent. If you run mris_euler_number on e.g. rh.white and
rh.inflated and they have the same number of edges/vertices/faces then you
are all set.
cheers
Bruce
On Sun, 3 Aug 2014, angela.fav...@unipd.it wrote:
>
Hi Bruce, hi Maria,
thank you for your suggestions!
However, the message
WARN: time for rh.white is older than rh.inflated
WARN: lh.rh.sphere.reg is empty/missing
WARN: time for lh.white is older than lh.inflated
appears for all subjects I checked.
I tried with the command:
recon-all -s -sd -m
Hi Angela,
Use mris_euler_number on the pial surface, but the probability that there will
be any defect is indeed relatively low. Have you carefully checked your white
and pial surface slice by slice overlaid on the T1? Sometimes a small region
where the surfaces are "wrinkled" is responsible
Hi Angela
1. if recon-all has completed successfully there shouldn't be any
topological defects. You can run mris_euler_number on lh.pial and rh.pial.
The Euler number for a closed surface with no defects should be 2.
2. This means something has been rerun but not to completion. You should be
Hi all,
I am running lgi analyses in 5.3 FS version (lion OSX)
one of my subjects failed with a typical message:
lGI for vertex number 39901 of the outer mesh is 1.8067
... remeasuring lGI value for vertex iV = 40001. It may take a few minutes.
WARNING -- Problem for vertex iV = 40001, lGI value
Martin,
One thing to try is to make sure that your volumes look ok. There is a
tutorial here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData
You don't need to download the tutorial data to follow it, just
substitute the subject 'bert' which is distributed in the
freesurfer/subjec
On Monday 09 June 2008 21:57:36 Bruce Fischl wrote:
> I guess it's possible but the -make switch is designed to prevent this. Are
> the surfaces topologically incorrect? What is the euler number for them?
Bruce, this depends on at which point the topology fixing was interrupted. For
this thread I
I guess it's possible but the -make switch is designed to prevent this. Are
the surfaces topologically incorrect? What is the euler number for them?
On Mon, 9 Jun 2008, Martin Kavec wrote:
On Monday 09 June 2008 21:14:35 Michael Harms wrote:
No, I don't have any examples (although we haven't
On Monday 09 June 2008 21:14:35 Michael Harms wrote:
> No, I don't have any examples (although we haven't been looking either).
> However, Martin's email regarding problems he is encountering on the LGI
> computation seems premised on having surfaces with topological problems
> even under v4 -- hen
No, I don't have any examples (although we haven't been looking either).
However, Martin's email regarding problems he is encountering on the LGI
computation seems premised on having surfaces with topological problems
even under v4 -- hence my question Am I mis-reading your situation
Martin?
Hi Mike,
I think it is the case. Sorry, I haven't been following this thread. Do
you find situations in which the corrected surfaces have the wrong
topology?
Bruce
On Mon, 9 Jun 2008, Michael Harms wrote:
Hello,
Here is a related question prompted by this thread, perhaps based on a
misco
Hello,
Here is a related question prompted by this thread, perhaps based on a
misconception on my part:
I was under the impression that you are guaranteed to get surfaces with
an euler number of 2 under the "new" topology fixer of version 4 (which
runs by default if the "old" fixer does not initi
Hi Maria,
On Monday 09 June 2008 15:00:10 Marie Schaer wrote:
> Martin,
>
> Which version of freesurfer did you use to generate the surfaces?
with the latest one, 4.0.4
> Because the number of topological defects in your surface (64) is very
> high. You may have to relaunch the surfaces (orig an
Martin,
Which version of freesurfer did you use to generate the surfaces?
Because the number of topological defects in your surface (64) is very
high. You may have to relaunch the surfaces (orig and pial) to get
better surfaces (i.e. 0 defect).
Lgi often fail if there are defects, someti
Hi,
I get the following warning followed by error in LGI calculation:
... remeasuring lGI value for vertex iV = 6301. It may take a few minutes.
WARNING -- Problem for vertex iV = 6301, lGI value is aberrantly high
(lGI=48.6447)...
...lGI
Hi Juergen,
why are you getting large defects? The time goes as the square of the
convex hull of the defect, so it is *slow* for large defects (and fast
for small ones). Where are your defects?
Bruce
On Tue, 15 May 2007, Juergen Haenggi wrote:
Dear Freesurfer users
Is there any rule of th
Dear Freesurfer users
Is there any rule of thumb with respect to the size of topological defects?
Sometimes large defects (involving more than 1 or 2 vertices) occur
and the topological correction for these defects runs more than 48 hours and
sometimes failed to correct them. How long shou
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