Hi again,
>
> I ran eddy again without using the --dont_peas flag and this is the restricted_movement_rms output (this is for a different subject; I had forgotten which subject I used for the previous example):
>
> 1.205399761 0
> 1.19112802 0.08727720789
> 1.235261903 0.06911038011
> 1.277014419 0.05746483138
> 1.328220068 0.05477667936
> 1.296719305 0.04289894243
> 1.327527439 0.0412624875
> 1.384597285 0.06626312861
> 1.350374247 0.04722069236
> 1.400096729 0.06878605945
> 1.46171889 0.08696581229
> 1.466817115 0.06251576995
> 1.456599549 0.02974539375
> 1.40419918 0.07714932831
> 1.384612061 0.0722092394
> 1.358525652 0.09499191389
> 1.608377061 0.3220011934
> 1.730152512 0.1255724158
> 1.779978513 0.0663517239
> 1.732995462 0.07131034696
> 1.770106212 0.04114718927
> 2.013462871 0.2567823675
> 2.158575278 0.1549992057
> 2.189835362 0.04574981634
> 2.191276597 0.02450847452
> 2.180996486 0.03353525723
> 2.232785528 0.06891595606
> 2.194390872 0.04046050232
> 2.278158085 0.08599108841
> 2.278868982 0.06179001012
> 2.329275666 0.07354776116
> 2.274778343 0.05658979421
> 0 2.274778343
>
>
> If eddy assumes zero movement between the b0 volume and the first dwi volume, why is the first value in the first column not equal to zero?
>
> Is there any way to make eddy not assume zero movement between b0 and the first dwi image?
when you run it _without_ the --dont_peas flag it means it will do PEAS (i.e. Post Eddy Alignment of Shells) i.e. it will _not_ assume zero movement between the b0 and the first dwi image. The first b0 is used as the reference space, i.e. zero movement. In this case it means it has found a movement of 1.205399761 between the first b0 and the first dwi.
I must say it looks strange though. It implies there has been a very large movement between the last dwi and the b0 that is acquired immediately after. I am not sure I believe that. Did you use the latest pre-release of eddy? I did lots of work on improving the PEAS for that version, so should be more reliable.
Jesper
>
> Thanks again!
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