One thing I would like you to please clarify is this: If someone is interested in comparing motion between two dMRI groups what's the best current way?
I followed all the emails and I'm confused. There is no doubt that the newest eddy does a superior job compared to previous versions of the eddy. But what we discuss here is not to verify the correction ability of new eddy.Specifically, I want to show the readers that there is X amount of motion between dMRI of two groups before any correction ( so I have to calculate the amount of motion before correction) and then use new eddy and its outputs to show the readers that although there was X amount of motion before correction, after applying the new eddy, we achieved this amount of motion residuals so new eddy did a great job!
Please correct me if I'm wrong. My understanding is that the *.eddy_parameters gives the motion parameters after all correction applied inside the new eddy. If this is correct, then using the *.eddy_parameters is not meaningful to show the initial motion difference between two groups.
I'm not sure whether or not *.eddy_restricted_movement_rms gives the motion rms values before or after corrections? Although, the motion rms could be used as a motion index, what if someone wants to have a more detailed look at the motion? let's say wants to know what's the difference in motion in a certain direction?
I really appreciate if the experts provide a clear and terminal answer to my questions.
Thank you all!Mahmoud
On Thu, Sep 22, 2016 at 11:49 AM, Jesper Andersson <[log in to unmask]> wrote:
Dear Michael and Thais,
this paper pertains to a method (eddy_correct) that we have recommended against for the last three years. We believe that our current method does a quite good job at estimation movement in the presence of distortions, as can be seen for example in https://www.ncbi.nlm.nih.
gov/pubmed/26549300 (which we didn’t write). You can also have a look at figure 7 in http://www.sciencedirect.com/science/article/pii/ (which we did write).S1053811915009209
As has been discussed earlier on the mailbase there is a particular “problem” with estimating translations in the PE-direction, so these should be treated with some caution. Our current recommendation for assessing overall movement is there for the .eddy_restricted_movement_rms. There are some explanation how to use it in the EDDY wiki pages.
Jesper
Did you acquire multiple Bval=0 scans in the course of each DTI? They'd be less distorted by eddy currents, so give you a handle on overall motion during the series.
On 22 September 2016 at 15:18, Thais Minett <[log in to unmask]> wrote:
Dear FSL experts,
I am submitting my DTI-TBSS analyses paper for publication. One of the reviewers asked me: "The authors should report on some metric describing the level of head motion in each group during the DTI scan.". I have no idea how I should address that. I used ‘eddy’ and not ‘eddy_correct’ for my data processing.
Regards,
Thais Minett
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Tel 07920 113060University of BristolSchool of Experimental Psychology and School of Clinical SciencesMichael John Knight, PhDElizabeth Blackwell Institute Early Career Fellow