I forgot to mention, we used the QC protocol described here:
http://cbs.fas.harvard.edu/science/core-facilities/neuroimaging/information-investigators/qc
with a manual of examples:
http://cbs.fas.harvard.edu/usr/mcmains/CBS_MRI_Qualitative_Quality_Control_Manual.pdf
where Fig. 6 in our paper shows the results when removing the 'fail'
cases, so fail is basically everything > 7mm/sec and some cases below that.
The "warn" category is more heterogeneous and has a range of low and
medium motion cases.
Best, Martin
On 08/05/2015 08:25 PM, Martin Reuter wrote:
Yes, I wanted to make those images available, but this was not in the
consent forms and I don't think it will be possible to re-consent the
subjects. I pushed that a little a while ago, will try again.
Martin
On 08/05/2015 08:17 PM, Harms, Michael wrote:
Hi Martin,
I totally agree that we need robust approaches to either correct for
motion during the structurals in real time (as you guys have been
working on with your vNav sequence), or start at least quantifying
motion during structural imaging (e.g,. again by using the same vNav
sequence, but just using it to estimate the motion).
It seems challenging to me though, and potentially somewhat arbitrary
(i.e., variable across investigators), to start making decisions to
exclude scans with moderate to mild movement related ringing, which
is such a common problem. At least not without a better
understanding of how a given degree of ringing translates to your
quantitative X mm/min of motion measurement. Along those lines, do
you guys have any illustrations of what X mm/min of motion looks like
in the actual structurals for varying values of X? It would be
really helpful for contextualizing your paper if a set of images were
available showing that mapping.
cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110Email: mha...@wustl.edu
From: Martin Reuter <mreu...@nmr.mgh.harvard.edu
<mailto:mreu...@nmr.mgh.harvard.edu>>
Reply-To: "freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>"
<freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, August 5, 2015 6:55 PM
To: "freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>"
<freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Head Motion -- was: surface reconstruction and
quality control
Hi Michael,
we showed that motion (even the one that you cannot really see in the
image) produces biased measurements (and not just in FreeSurfer but
also other methods). FS handels all kinds of data, even really crappy
images, and that is exactly the problem, as these measurements can be
severely biased and most users don't even check their images. We
found that 1mm/min of motion reduces gray matter volume by 0.7%. This
is a lot, given that the best still scans in our healthy young adult
test subjects were at 2-3mm/min (that was the no-motion scan). QC was
able to remove scans with above 6 or 7mm/min. So on average even
after QC and removal of scans with motion problems, you end up having
lots of cases with 5 to 7mm/min motion = 3.5% to 5% reduced GM
volume. I think, (maybe someone here knows better), that is the
atrophy of a healthy control in 5 years and probably more than the
yearly loss in an advanced AD or HD patient.
Depending on the study, it may very well be possible that the disease
group moves more than the control group, the older group more than
the younger (unless you have kids, who move a lot) and also
longitudinally that motion increases over time. This will bias your
study.
You are right, that removing single (worst case) images will not cut
it. The problem is far worse. We need a way to either
-correct motion online
-at least quantify motion during structural imaging to use as a
covariate or for filtering severe cases.
That is why I recommended to use fMRI or diffusion close to the
structural to estimate the motion there. That should give you an idea
(of course does not replace manual QC for filtering bad cases). We
need to avoid running drug studies that basically quantify the amount
of reduced motion with an expensive MRI scan.
Anyway, I would say, if in doubt remove it. To at least limit the
influence of motion bias to the 3-5% range (which is still too large).
Cheers, Martin
On 08/05/2015 05:44 PM, Harms, Michael wrote:
Hi Emma, Martin,
I'd like to offer a different perspective. Based on what you
showed, I thought that the motion related ringing wasn't too bad,
and I'd expect that FS would handle that data quite well, which is
what you indicated was indeed the case. If we all started excluding
data of the sort that you showed, then there are going to be a lot
of studies that would have to exclude a chunk of subjects. If that
is the worst motion related artifact in your study, then you've been
very successful at collecting good quality structurals!
cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110Email: mha...@wustl.edu
From: Emma Thompson <vonecono...@gmail.com
<mailto:vonecono...@gmail.com>>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, August 5, 2015 4:34 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] surface reconstruction and quality control
Thanks Martin, I will exclude this subject from my analyses.
On Wed, Aug 5, 2015 at 4:18 PM, Martin Reuter
<mreu...@nmr.mgh.harvard.edu <mailto:mreu...@nmr.mgh.harvard.edu>>
wrote:
Hi Emma,
I'd exclude it and similar images. Or if you have a motion
estimate of those subjects (e.g. via adjacent fMRI or diffusion
scans), you could use motion as a covariate in your statistics.
Motion does bias measurements (smaller cortical GM volume), see
e.g. here:
http://dx.doi.org/10.1016/j.neuroimage.2014.12.006
http://reuter.mit.edu/papers/reuter-motion14.pdf
Best, Martin
On 08/05/2015 02:55 PM, Emma Thompson wrote:
Hi Freesurfers,
I have a question regarding quality control. One of my subjects
has pretty moderate ringing in their mprage image (presumably
due to motion), I was thinking I should be excluding this
subject, however I ran the subject through the pipeline anyway
and I see that the segmentation and surfaces look ok. I'm
wondering if based on this I should go ahead and include this
subject for my analyses. I have attached a screenshot of the
mprage and was hoping someone would take a look and give me
their expert opinion. Thanks for you help!
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--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone:+1-617-724-5652 <tel:%2B1-617-724-5652>
Web :http://reuter.mit.edu
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--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web :http://reuter.mit.edu
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The materials in this message are private and may contain Protected
Healthcare Information or other information of a sensitive nature. If
you are not the intended recipient, be advised that any unauthorized
use, disclosure, copying or the taking of any action in reliance on
the contents of this information is strictly prohibited. If you have
received this email in error, please immediately notify the sender
via telephone or return mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web :http://reuter.mit.edu
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web : http://reuter.mit.edu
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
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