Dear all,
I have a few questions regarding wm.mgz edits.
I am very new to this area and have only recently started using Freesurfer so
please excuse me if my questions appear naive or misinformed.
I have managed to make most of the necessary edits needed to fix skullstrip
errors, intensity nor
Dear all Freesurfer users,
I have a few questions regarding wm.mgz edits.
I am very new to this area and have only recently started using Freesurfer so
please excuse me if my questions appear naive or misinformed.
I have managed to make most of the necessary edits needed to fix skullstrip
errors
Hi everyone and happy new year!
I made a couple of manual edits to a wm.mgz file and then relaunched part
of that subject's recon (-autorecon2-wm -autorecon3). After it finished,
however, the wm.mgz had lost its manual edits - even though I had saved the
edited version under the same name, in the
Hi Tudor
Are you doing the editing with tkmedit?
Cheers
Bruce
> On Jan 5, 2014, at 6:20 AM, Tudor Popescu wrote:
>
> Hi everyone and happy new year!
>
> I made a couple of manual edits to a wm.mgz file and then relaunched part of
> that subject's recon (-autorecon2-wm -autorecon3). After it fi
Hi Bruce
Yes I am - sorry to not have mentioned
Tudor
On 5 January 2014 17:00, Bruce Fischl wrote:
> Hi Tudor
> Are you doing the editing with tkmedit?
> Cheers
> Bruce
>
> > On Jan 5, 2014, at 6:20 AM, Tudor Popescu wrote:
> >
> > Hi everyone and happy new year!
> >
> > I made a couple of man
Hello, I have worked quite a bit in the past with fs 5.3 on datasets which
required a fair number of manual edits to the white matter volume in order to
correct defects in the white matter surface. Typically, these edits take the
form of removing voxels in the wm.mgz volume that have been incorr
Hi David
if you upload a subject to our ftp site and give us enough detail to
replicate what you tried we will take a look
cheers
Bruce
On Fri, 10 Mar 2017, David
Semanek wrote:
Hello, I have worked quite a bit in the past with fs 5.3 on datasets which
required a fair number of manual edi
Thanks, I have uploaded the cross and long stream processing from one subject
which requires numerous white matter edits to correct defects in the white
matter surfaces; the file is on the ftp server as dsemanek.zip.
Both of the cross subject folders, s02_t1 and s02_t2 have had edits done to
bo
Hi David,
first I think it makes sense to
- replicate the problem in the regular (cross sectional) stream
- then fix it there (if it exists) or look for it in long.
So you see the problem in the S02_t1 and S02_t2 also, right?
Best, Martin
> On 13 Mar 2017, at 16:55, David Semanek wrote:
>
his further.
best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of David Semanek
Sent: Monday, March 13, 2017 11:55 AM
To: Bruce Fischl; Freesurfer support list
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6
er support list , David Semanek
Cc: Bruce Fischl
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6
Cross and Long Streams
Hi David
Try editing the base wm.mgz first instead of editing the long and cross wm
files. Rerun autorecon2-wm and autorecon3 for the base
OF THE ERROR BY RETURN E-MAIL AND DELETE THIS
MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.
From: "Hoopes, Andrew"
Date: Wednesday, March 15, 2017 at 12:47 PM
To: Freesurfer support list , David Semanek
Cc: Bruce Fischl
Subject: Re: [Freesurfer] wm.mgz Edits Ignored Wi
cooperation.
From: "Hoopes, Andrew"
Date: Monday, March 20, 2017 at 4:54 PM
To: Freesurfer support list , David Semanek
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6
Cross and Long Streams
Hi David,
That is interesting. Sorry to ask you to upload data
day, March 20, 2017 at 4:54 PM
*To: *Freesurfer support list , David
Semanek
*Subject: *Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset
in FS 5.3/6 Cross and Long Streams
Hi David,
That is interesting. Sorry to ask you to upload data again, but if you
could upload this subject
RETURN E-MAIL AND DELETE THIS
MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.
From: Martin Reuter
Date: Tuesday, March 28, 2017 at 1:27 PM
To:
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6
Cross and Long Streams
This is how it should work:
WM edits
.
Thank you for your cooperation.
*From: *Martin Reuter
*Date: *Tuesday, March 28, 2017 at 1:27 PM
*To: *
*Subject: *Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset
in FS 5.3/6 Cross and Long Streams
This is how it should work:
WM edits in the base should affect surfaces in the base
, 2017 at 11:20 AM
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6
Cross and Long Streams
So the way to debug this is to test if we can replicate the problem of WM edits
not taking effect in a regular cross sectional s
ror or from someone who was not authorized to send it to you, you are
> strictly prohibited from reviewing, using, disseminating, distributing or
> copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN
> E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your
&g
YOUR SYSTEM. Thank you for your
> cooperation.
>
> From: Martin Reuter <mailto:mreu...@nmr.mgh.harvard.edu>>
> Date: Tuesday, April 4, 2017 at 11:20 AM
> To: "freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>"
> mailto:freesurfer@nmr.m
SYSTEM. Thank you for your cooperation.
From: Martin Reuter
Date: Wednesday, April 5, 2017 at 2:19 AM
To: David Semanek
Cc: "freesurfer@nmr.mgh.harvard.edu" , "Hoopes,
Andrew"
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6
Cross and Long St
Cc: "freesurfer@nmr.mgh.harvard.edu" , "Hoopes,
Andrew"
Subject: Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6
Cross and Long Streams
Hi David,
so edits are affecting the surfaces in cross, just not as much as you would
like. We need to check i
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