Hi Ruth - Indeed, setting the intensity threshold too low compared to the intensities in your low-b images will lead to underestimating the amount of signal drop-out due to motion.
a.y On Fri, 14 Mar 2014, Ruth Carper wrote:
Thanks Anastasia, I'd looked at the Benner article which didn't give a rationale for the selection of thresholds. I've been testing different T values and am settling on something much higher than the default (~700). With the default value nearly all of our scans wind up with floor values (0 and 1 respectively) for the Benner score and % bad slices. Ruth ____________________________________________________________________________ From: Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> To: Ruth Carper <rcarper...@yahoo.com> Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Sent: Friday, March 14, 2014 4:46 PM Subject: Re: [Freesurfer] dmri_motion Hi Ruth - These parameters are described in Benner 2011 (cited in our paper). The -T threshold is mostly what you might need to change, depending on your scanner. You should look at the low-b images and find a rough lower threshold for the image intensities of brain voxels. It doesn't have to be exact, but it shouldn't be off by an order of magnitude, either. Also, for the purposes of a group study, the most important thing is differences in motion measures between groups or correlation between motion measures and study effects, rather than the absolute values of the motion measures themselves. Hope this helps, a.y On Fri, 14 Mar 2014, Ruth Carper wrote: > Hi, > I've been using dmri_motion to quantify motion in our DTI data. Can you > give any guidance on selecting values for the -D and -T flags? I didn't see > anything in the wiki or in your related papers and it can have a substantial > effect on the outputs. > Thanks. > > > 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.
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