e to local variations which is
what makes it robust, but also makes it more difficult to modify. I'll take
a look and think about how to make it easier
cheers
Bruce
On Thu, 20 Apr 2017, David Semanek
wrote:
>
> Thank you for looking into th
IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS
MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.
From: Antonin Skoch
Date: Thursday, April 20, 2017 at 10:25 AM
To: David Semanek ,
"freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] Worse determination o
Agreed. A validated protocol run on a very large group of subjects in 5.3 was
attempted with similar data in 6.0 and not only was the longitudinal edit
stream nearly non-functional for white matter edits, cross edit performance was
disappointing.
I am currently waiting on a response to these po
In my experience, OSX has weird issues with things in system and Application
directories. My guess would be your files have inherited some permission flags
from the Linux environment and OSX is having trouble making them properly
available.
The first thing I would try would be to copy them to a
Hi John,
Yes understanding how freesurfer deals with edits can be a bit confusing. I
have a lot of experience doing edits to the wm.mgz and brainmask.mgz for cross
sectional data in Freesurfer 5.3 so perhaps I can help.
Recon-all is basically a script which runs a series of about 25 or so
proc
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
hat Andrew can take a look at that.
Best, Martin
On 04/04/2017 05:03 PM, David Semanek wrote:
I used –uselongbasewmedits only as a test to see if I could get some condition
under which the wm edits would be taken into account when the surfaces were
generated.
I did not use that flag for
recommended. It copies WM
edits from base to the long and that is only meaningful if there is very little
longitudinal change.
Best, Martin
On 03/23/2017 04:12 PM, David Semanek wrote:
Thanks for taking another look at our data.
I have uploaded another subject in the archive dsemanek2.zip . For
Yes, I have this exact same problem. I have uploaded two rounds of data for
review to the ftp service a week or so ago and I believe they are being
reviewed.
After several days of testing on my end with various permutations of flags and
cross and long runs and intervention points I didn’t see a
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
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
ake 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 edits to the white matter volume in order
> to correct defec
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
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