Hi Antonin
it is a pretty significant difference, even visually, and it occurs right
at the start of everything, so the differences propagate forward through
recon-all. I only looked at subject 1, but it is a case where the
intensities are ambiguous between gray and white and a slight increase
creates a connection between brain and dura (which looks like white matter
there) and messes everything up. I'm still running things, but I believe
that turning on cubic removes this issue for at least this subject
cheers
Bruce
On Fri, 21 Apr 2017, Antonin Skoch wrote:
Dear Bruce,
sorry for the confusion with xopts-use and recon-all editing.
I have checked the xopts-use and the reason of this is that I run the
subject 1 and 2 as a part of batch job on large amount of subjects, where I
rerun recon-all to anonymize them. Some of them had expert-options file with
bbregister --init-header from the initial run (these were subjects where
--init-fsl failed). I put -xopts-use to invocation of all subjects (even for
them without expert-option file) to make my life easier.
I did not put -cubic expert-options to any of my subjects.
Concerning editing of my 5.3 version of recon-all: My only modification in
recon-all was -nsigma_above 8 for FLAIRpial and patch with .touch files
recommended here:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41284.html
Otherwise my recon-all corresponds to the 5.3.0-patch version.
It seems that there was change in UseCubic wich 5.3.0-patch. Original
recon-all from 5.3.0 has UseCubic=0, whereas recon-all from 5.3.0-patch has
UseCubic=1:
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/recon-al
l
In my v6.0 recon-all I have UseCubic=0.
I am surprised that mere interpolation could have such profound effect !
I will try your suggestions and let you know.
Antonin
From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
To: Antonin Skoch <a...@ikem.cz>
Cc: <freesurfer@nmr.mgh.harvard.edu>
Sent: 4/21/2017 1:00 AM
Subject: Re: [Freesurfer] Worse determination of ?h.white with v6.0 in
comparison to v5.3 - worse GM/WM contrast
Hi Antonin
Doug points out to me that you edited your copy of recon-all in
5.3, which
makes it really hard for me to track down any differences. For
sure your
recon-all used cubic interpolation for conforming by default,
which
introduces pretty big differences right at the start that I
expect explain
the majority of the differences in wm positioning that you are
seeing. I
guess I would suggest trying 6.0 with cubic on (-cubic) and see
if they
become more similar
cheers
Bruce
On Thu, 20 Apr 2017, Antonin Skoch
wrote:
>
> Dear Bruce,
> I am uploading 3 example subjects processed both by v5.3 and
v6.0 I referred
> to in the screenshots in my previous posts:
> Subj 1 - large leak of white surface outside brain in v6.0,
not present in v
> 5.3. RAS coords -53,-1,75
> Subj 2 - another measurement of identical subject - white
surface is leaking
> at three spots dramatically outwards
> towards pial surface in v6.0. RAS coords -48,-2,64
> Subj 3 - leak of white surface outside brain. Both v5.3 and
v6.0 has error i
> n white surface, but the error is much larger in v6.0. RAS
coords 48,5,78
> The v6.0 version is without removing -mprage. Removing -mprage
in v6.0 cause
> d only very small change in brain.mgz, the filtering is still
much higher th
> an in v5.3 and still causes the white matter surface leak.
> The subjects are in files mri_normalize_v5.3.tar.gz and
mri_normalize_v6.0.t
> ar.gz.
> I would very welcome any suggestions how to:
> 1. Prevent new white surface errors in v6.0 in subjects
previously processed
> and edited by v5.3
> 2. How to make edits to modify white/pial surface location
where wm.mgz edit
> ing is not sufficient.
> I tried workaround of directly editing 001.mgz as I discussed
in thread http
>
://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52549.html
> This is very time consuming.
> Better way is maybe to consider implementation of option for
mris_make_surfa
> ces similar to -overlay option for cases where wm.mgz voxels
have value 1 as
> I discussed here:
>
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52730.html
> Antonin
> 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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