Hi Ruth - It expects the output format of eddy_correct. It then computes
the transforms between consecutive frames from the transforms between each
frame and the reference frame.
Best,
a.y
On Sun, 29 Nov 2015, Ruth Carper wrote:
Hi,
I'm hoping to use the dmri_motion tool to quantify motion for some diffusion
data that did not use the eddy_correct tool. We
have registration matrices that we've successfully reformatted, but I've been
scanning the FreeSurfer forum and see some
conflicting information about whether the input to dmri_motion should reflect
registration of each time point to a single
reference orregistration of each time point to the preceding time point. i.e.
t0-t1, t0-t2, t0-t3, ....
vs.
t0-t1, t1-t2, t2-t3, ...
What input does dmri_motion expect? I think it's the former but the confusion
arises from this post:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg41541.html
5/28/15
...
Of our 4 motion measures, the rotation and translation are computed from
the output of the eddy correction (which
computes relative displacement from one volume to the next), and the
intensity drop-out measures are computed
from the raw uncorrected images (because the subsequent corrections will
introduce some blurring and might lead
to underestimation of the drop-out in each slice). So all measures are
computed prior to B0 correction.
Hope this helps, a.y
But, the contents of the “eddy_correct” command appears to register each time
point to a single reference time point. We’re
using timepoint 1, i.e. b=0.
From the text of Yendiki et al., 2013, I suspect that dmri_motion takes an
input that is each timepoint to a single reference
timepoint, but outputs a summary that is based on each timepoint to the
immediately preceding timepoint?
Can you clarify what input does dmri_motion expect?
Thanks!
Ruth Carper, PhD
Research Assistant Professor, SDSU
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