Can you send me an example of an image that has slices with drop-out, and for which the number of bad slices from dmi_motion is 0?
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Buckless, Colleen" <Buckless@kennedykrieger.orgmailto:Buckless@kennedykrieger.org> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, July 19, 2017 at 9:48 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] dmri_motion -T threshold
We want to match on dropout as well which would require us to change the threshold. How should the threshold value be determined in order for us to match on dropout?
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Wednesday, July 19, 2017 9:31 AM To: Freesurfer support list Subject: Re: [Freesurfer] dmri_motion -T threshold
If neither of your groups has bad slices (which you should confirm by looking at the images), then they are matched in that respect. You can then check for differences in the rotational and translational motion to see if any further matching is needed.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Buckless, Colleen" <Buckless@kennedykrieger.orgmailto:Buckless@kennedykrieger.org> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, July 19, 2017 at 9:14 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] dmri_motion -T threshold
Hi Anastasia, We are trying to match our groups on motion and can’t match them if our scans have the floor values. We are not sure how to determine what the threshold value should be in order to make the dropout score no longer floor out. Any suggestions on how to better match on motion? Thanks, Colleen
From:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Tuesday, July 18, 2017 6:46 PM To: Freesurfer support list Subject: Re: [Freesurfer] dmri_motion -T threshold
Hi Colleen - Do the DWIs of your subjects have any slices that are in the brain but look very dark, almost like the background? That's what those measures capture, and not all subjects have that. If your subjects don't have that, then there's nothing to be concerned about!
Best,
a.y ________________________________ From:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Buckless, Colleen [Buckless@kennedykrieger.orgmailto:Buckless@kennedykrieger.org] Sent: Friday, July 14, 2017 3:35 PM To: 'freesurfer@nmr.mgh.harvard.edumailto:'freesurfer@nmr.mgh.harvard.edu' Subject: [Freesurfer] dmri_motion -T threshold Hi All, I've been using dmri_motion to quantify motion in our DTI data. We are uncertain how to determine what the –T threshold should be. We have read through the wiki and the related papers and are confused what this number represents, how it effects the output, and the rational for selecting a specific threshold value. We have tried the default (100) and almost all of our scans have the floor values (0 and 1) for percent bad slices and average dropout score, and we are concerned that this value is most likely inappropriate for our data. We have tried other values but are unsure what a suitable threshold value should be for our data. We are concerned that this number effects the output, and want to make sure we are using an appropriate value. What is the best way to select the –T threshold and the rational for selecting one value versus another? Thanks, Colleen Buckless Research Assistant Center for Neurodevelopmental and Imaging Research Kennedy Krieger Institute 443-923-2747 Buckless@kennedykrieger.orgmailto:Buckless@kennedykrieger.org
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