Hi,
I am attempting to run an fMRI data set through the freesurfer workflow and
the skullstripping step seems to be delayed.
It has been stuck on the following command line for an inordinate amount of
time.
First Search limited to translation only.
using real data threshold=28.0
Found translat
check the talairach to see if it is value, and also make sure that the
T1.mgz white matter intensities are close to 110 almost everywhere.
On Mon, 31 Jul 2006 [EMAIL PROTECTED] wrote:
I keep getting this error when trying to skullstrip a scan...
*WATERSHED*
---Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Paul Schauer
Sent: Tuesday, June 30, 2015 7:03 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Skullstrip problems
Hi all,
I ran the normal recon-all -i... -s... -all on
gt; [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Paul
> Schauer
> Sent: Tuesday, June 30, 2015 7:03 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] Skullstrip problems
>
> Hi all,
>
> I ran the normal recon-all -i... -s... -all on a couple o
ehalf Of Paul Schauer
Sent: Tuesday, June 30, 2015 7:49 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Skullstrip problems
Hi Jennifer,
thank you for your speedy answer.:-)
Unfortunately I didn't understand all of it. The problems with the skullstrip
did not (!) affect any of th
Hi Paul,
As long as your surfaces are unaffected (no brain is missing), the dura
does not matter. Ideally, the brainmask.mgz should be /only/ brain.
-Ani
On 06/30/2015 08:03 AM, Paul Schauer wrote:
Hi all,
I ran the normal recon-all -i... -s... -all on a couple of subjects
and I realized t
ra
>>> volume as well, it's not going to affect your brain volume measure.
>>
>> Best regards,
>> Jennifer Kriegel
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.ed
Hi Ani,
thank you,too. This is exactly what I wanted to know!:-)
Have a nice day!
Best,
Paul
Zitat von Ani Varjabedian :
> Hi Paul,
>
> As long as your surfaces are unaffected (no brain is missing), the
> dura does not matter. Ideally, the brainmask.mgz should be /only/
> brain.
>
> -Ani
Hello experts,
I am getting skull strip issues with FreeSurfer recon-all runs in every data.
I ran recon-all on my T1-data and noticed that the skullstrip is not so good.
Almost in every subjects there were dura included, so I tried the suggestion
of using the flags -skullstrip and -Clean–bm an
Hannah, are you trying to run fMRI data through the anatomical
processing stream? That will certainly not work ...
doug
Riskin-Jones, Hannah wrote:
> Hi,
>
> I am attempting to run an fMRI data set through the freesurfer
> workflow and the skullstripping step seems to be delayed.
>
> It has
are you really trying to run an fMRI dataset through? recon-all will only
work with T1-weighted anatomicals.
cheers
Bruce
On Fri, 2 Jul 2010, Riskin-Jones, Hannah
wrote:
> Hi,
>
> I am attempting to run an fMRI data set through the freesurfer workflow and
> the skullstripping step seems to be d
Hi Rashmi
getting rid of all the dura without removing any problem is exceedingly
difficult (if not impossible). Usually we live with some remaining dura
as it doesn't affect the surface placement much.
cheers
Bruce
On Tue, 2 Oct 2012, Rashmi
Singh wrote:
Hello experts,
I am getting skul
Thank you Bruce,
I certainly understand your point. In my study I am trying to use whole
brain volume to normalize my volumetrics data. Due to the inclusion of the
dura into brain, I may get variation in the whole brain volume across
subjects.
In addition the current issue is affecting the grayma
Hi Rashmi,
I assume you've read the skullstrip wiki page, but I've included it below
just in case.
Have you tried different watershed thresholds? Also, you do not need to
include the -clean-bm flag every time. You can run the skullstrip step
once with the -clean-bm to start from scratch, and
Dear experts,
I recently finished processing a subject for whom I had performed a skullstrip
on the brainmask volume. I decreased the watershed parameter and re-examined
the brainmask and the portion of the skull was gone, although some dura was
left over. I did a recon-all using the following
Hi
I did autorecon1 on T1 structural brain images acquired by
GE magnet. However, a small piece of skull with dura
still remained on brainmask.mgz (around the occiput), even after adjustment
of watershed threshold to 10. (Some brain would loss
when threshold was lowered to 7 or 5). I wondered if I
Hi Arsenije,
-autorecon-pial should not recreate the brainmask. Is the brainmask.mgz
currently correct?
Bruce
On Tue, 21 Nov 2017, Arsenije Subotic wrote:
Dear experts,
I recently finished processing a subject for whom I had performed a skullstrip
on the brainmask
volume. I decreased t
Hi Wei-Ta
if the remaining skull and dura don't affect the pial surface then it
doesn't matter. Run it all the way through recon-all and you'll probably
find it doesn't matter.
cheers
Bruce
On Fri, 19 Aug
2011, Wei-Ta Chen wrote:
Hi
I did autorecon1 on T1 structural brain images acqu
Hi Freesurfers,
I have problems with the troubleshoot of a scan that didn't run at all
within autorecon (while the scan actually looks good).
So I ran the skullstrip manually and came across the following
phenomenon:
-when using waterthreshold 25 it gives me an error message and no
brainmask.mgz
Hi Bruce,
I performed the -autorecon-pial as a means of regenerating the surfaces as
instructed on the Freesurfer skull strip tutorial. The brainmask.mgz file does
not have the skull but it has some dura left over. The issue I had before was
that the skull would re-appear after the subject fin
Hi Anne,
What's the error message when you are running waterthreshold 25
Sita
On Wed, 23 May 2012, Anne Uhlmann wrote:
> Hi Freesurfers,
>
> I have problems with the troubleshoot of a scan that didn't run at all
> within autorecon (while the scan actually looks good).
> So I ran the skullstri
Hello,
I see that the new 5.1 version may be available soon.
Thererfore, I was wondering if the brainmask.mgz file that contains the manual
editing (using tkmedit from FS 5.0) will be compatible with the forthcoming FS
5.1 version. I am planning to use the 5.1 version for the longitudinal
pro
yes, it should be compatible.
cheers
Bruce
On Thu, 17 Feb 2011, Hyunwoo Lee wrote:
> Hello,
>
> I see that the new 5.1 version may be available soon.
>
> Thererfore, I was wondering if the brainmask.mgz file that contains the
> manual editing (using tkmedit from FS 5.0) will be compatible with
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