Hi Antonin
yes, the -mprage flag is likely to be at least one source of the
differences. It makes the normalization more aggressive (since mprage
trades higher CNR for lower SNR). I'm surprised removing it didn't help. I
think that changing things like wlo could also help depending on how wrong
the normalization is. Upload a subject and I'll take a look
cheers
Bruce
On Thu, 20 Apr 2017,
Antonin Skoch wrote:
Dear David,
thank you for the feedback; I saw your posts concerning edits and responded
to them, see
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52549.html
Just my case is not concerning poor response to the edits (which I believe
is not systematically different between 5.3 and 6.0), my concern is that the
data processed by v6.0 need much more wm.mgz edits than data processed by
v5.3.
I think that my issue lies in -normalization2 step of recon-all. One of the
difference between v5.3 and v6.0 is that by default the -mprage flag is
passed to mri_normalize. This affects several parameters inside
mri_normalize. I tried to reprocess my subjects using v6.0 with -no-mprage,
but unfortunately this did not help.
See the example screenshots processed by v5.3 and v6.0 with -no-mprage:
The brain.mgz is still more aggressively filtered in v6.0 and there is much
more prominent leak of ?h.white outside brain, which is probably caused by
extended filtration which affects GM/WM contrast.
Looking at the source code of mri_normalize.c I did not comprehend where the
basis of the issue lies, but in any case there are big differences in
mri_normalize.c code between versions.
Antonin
From: David Semanek <seman...@nyspi.columbia.edu>
To: Antonin Skoch <a...@ikem.cz>, "freesurfer@nmr.mgh.harvard.edu"
<freesurfer@nmr.mgh.harvard.edu>
Sent: 4/20/2017 3:41 PM
Subject: Re: [Freesurfer] Worse determination of ?h.white with v6.0 in
comparison to v5.3 - worse GM/WM contrast
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 potential issues
before pursuing further work with 6.0.
Best,
David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885
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From: Antonin Skoch <a...@ikem.cz>
Date: Wednesday, April 19, 2017 at 5:23 PM
To: <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Worse determination of ?h.white with v6.0 in
comparison to v5.3 - worse GM/WM contrast
Dear experts,
I am sending just one more example to illustrate issue with white
surface estimation in v6.0. See the attached screenshots: In v6.0
there seems to be insufficient contrast in brain.finalsurfs.mgz, so
the white surface is leaking at three spots dramatically outwards
towards pial surface. The white surface in v5.3 looks much more
anatomically relevant in the same spot.
Could you please comment on how to avoid such issues in v.6.0?
Regards,
Antonin Skoch
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