I am having trouble with one of my skull strips, and getting very
extreme results. When I re-run the skullstrip using different watershed
values, anything at 56% or below takes 75%+ of the brain out, and as
soon as I jump to 57% or higher, it leaves on almost all of the skull,
except for maybe 5%
First have a look at the troubleshooting wiki pages at:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData
In particular, Subject 1 has a skull strip problem, and the fix info is
here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix
I'm guessing you have
I am currently in the process of manual editing...just curious though,
what exatly does adding an atlas do to the skullstrip process?
Quoting Nick Schmansky <[EMAIL PROTECTED]>:
> First have a look at the troubleshooting wiki pages at:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tro
it helps detect cases in which the deformation is too big (e.g. when the
surface deforms all the way into the cerebellum), and can thus recover from
e.g. cerebellum chopping.
On
Wed, 28 Jun 2006 [EMAIL PROTECTED] wrote:
I am currently in the process of manual editing...just curious though,
Hi Sebastian,I installed compat-libstdc++-33-3.2.3-47.fc4.i386 and recon-all worked just fine and exited with no errors. It did take 25 hrs though. Thanks a lot.Anil Roy.
On 6/25/06, Sebastian Moeller <[EMAIL PROTECTED]
> wrote:
Hi Anil,On 26. Jun 2006, at 00:08 Uhr, [EMAIL PROTECTED]
wrote:> Mess
I just finished my 4 hour manual editing...went to file>save volume
as...then saved it to where it defaulted me, which was the mri folder of
this subject. When i pull up my brainmask, it is giving me the same one
that it had before i made any changes. I hope i didnt do something
wrong and lost al
Hello All,
How do we obtain the total volumes(gray+white) of certain regions. In ?.aparc.stats, I can find the gray matter volumes but not total volumes. Is this in some other file?
Thanks,
Aju.
**
Mr.Ajith Kumar U
Junior Research Fellow,
The brainmask.mgz file is the one that should be edited (and saved), so
select that filename to save. Then just continue with autorecon2 (and
it will use your brainmask.mgz). It will not overwrite your
brainmask.mgz unless you specify the aptly named '-clean-bm' flag to
recon-all.
On Wed, 2006-
what would the white matter volume of a cortical region mean?
On Wed, 28 Jun
2006, Ajith Kumar U wrote:
Hello All,
How do we obtain the total volumes(gray+white) of certain regions. In
?.aparc.stats, I can find the gray matter volumes but not total volumes. Is
this in some other file?
Than
sounds like you saved it in COR format, which is what will happen if you
specify a destination folder instead of a file name (e.g. brainmask.mgz).
Try loading that in tkmedit to make sure it's got your edits, then you can
convert it to .mgz with mri_convert.
On Wed, 28 Jun 2006 [EMAIL PROTECTE
but you'll need to convert the COR file you saved to brainmask.mgz if you
want to recover your edits (4 hours of manual editing!).
Bruce
On Wed, 28 Jun
2006, Nick Schmansky wrote:
The brainmask.mgz file is the one that should be edited (and saved), so
select that filename to save. Then jus
What I mean is, for example, the total volume of Heschl's Gyrus. This includes its gray matter and the underlying white matter. I understand that the wm boundary would be difficult to compute but even some estimates would work.
Aju.
On Thu, 29 Jun 2006 Bruce Fischl wrote :
>what would the whi
Hi Everyone,
Is there a way to process the minc files I have and only obtain the
anatomical stats without the entire recon-all process. I have a large
number of brains and it would take a couple of weeks if I was to take
every minc file and run recon-all.
Thanks - Anil.
_
Doug put together a white matter parcellation that does this kind of
thing, but I'm not sure what the status of it is. Doug?
On Wed, 28 Jun 2006,
Ajith Kumar U wrote:
What I mean is, for example, the total volume of Heschl's Gyrus. This includes
its gray matter and the underlying white matter
Hi,
Does anybody have any idea what the scale bar shows in Tksurfer? I have
heard that the scalebar is 10mm for the human brain. I am working with the
monkey brain. Is the length of the scale bar 1cm for the monkey brain as
well?
Thanks,
Reza
Reza Rajimehr, MD
N
We are still evaluating it, but it should be ready by our next stable
release.
doug
Bruce Fischl wrote:
Doug put together a white matter parcellation that does this kind of
thing, but I'm not sure what the status of it is. Doug?
On Wed, 28 Jun 2006, Ajith Kumar U wrote:
What I mean is,
it should be, unless you've "fooled" mri_convert into thinking the voxel
dimensions are different than what they are, which is a standard trick
with the monkey data. In that case its 10 of whatever your original voxel
dimensions were.
cheers,
Bruce
On Wed, 28 Jun 2006, Reza Rajimehr wrote:
Thank you for the response. I may be overly forthcoming here, but when will the next stable release be available.
Aju
On Thu, 29 Jun 2006 Doug Greve wrote :
>
>We are still evaluating it, but it should be ready by our next stable release.
>
>doug
>
>
>
>Bruce Fischl wrote:
>
>>Doug put toge
Not sure, but probably Aug or Sept (that'd be 6mo after the prev
stable).
doug
Ajith Kumar U wrote:
Thank you for the response. I may be overly forthcoming here, but
when will the next stable release be available.
Aju
On Thu, 29 Jun 2006 Doug Greve wrote :
>
>We are still evalu
Hi Bruce,
Thanks for your email. Just to make sure: the original voxel size is 0.35
um isotropic. so in my case, the scale bar would be 3.5 mm, right?
Thanks,
Reza
> it should be, unless you've "fooled" mri_convert into thinking the voxel
> dimensions are different than what they are, which is
The dev build is not posted on the web anymore, rather, bug fixes and
tested minor enhancements get folded into the stable build and released
periodically (so far, it seems about every six weeks).
A new stable release (v3.0.4) will be forthcoming, and I'll make sure
that the --conform flag of mr
I think so.
On Wed, 28 Jun 2006, Reza Rajimehr wrote:
Hi Bruce,
Thanks for your email. Just to make sure: the original voxel size is 0.35
um isotropic. so in my case, the scale bar would be 3.5 mm, right?
Thanks,
Reza
it should be, unless you've "fooled" mri_convert into thinking the voxel
Hi,
during retinotopic mapping,
still at the beginning, when I run the analysis (with the command
sfa-sess), I get the error:
ERROR: meanimg for mean image failed
meanimg -i rtopy/eccen/h-offset -i rtopy/polar/h-offset -o rtopy/h-offset
and I have h.bdhr and omnibus in my eccen and polar folder
Can you send the full terminal output of sfa-sess?
Nurunisa Neyzi wrote:
Hi,
during retinotopic mapping,
still at the beginning, when I run the analysis (with the command
sfa-sess), I get the error:
ERROR: meanimg for mean image failed
meanimg -i rtopy/eccen/h-offset -i rtopy/polar/h-offset
Hi Nick, hi Bruce,
On 29. Jun 2006, at 00:39 Uhr, Nick Schmansky wrote:
The dev build is not posted on the web anymore, rather, bug fixes and
tested minor enhancements get folded into the stable build and released
periodically (so far, it seems about every six weeks).
Which, I might add, is re
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