Re: [Freesurfer] Head Motion -- was: surface reconstruction and quality control

[Harms, Michael]

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  63110 Email: mha...@wustl.edu From: Martin Reuter <mreu...@nmr.mgh.harvard.edu> Reply-To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, August 5, 2015 6:55 PM To: "freesurfer@nmr.mgh.harvard.edu" <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  63110 Email: mha...@wustl.edu From: Emma Thompson <vonecono...@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, August 5, 2015 4:34 PM To: Freesurfer support list <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> 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! _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://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 but does not contain patient information, please contact the sender and properly dispose of the e-mail.   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.eduhttps://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   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. 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