Hi again,
> Really appreciate the quick response!
>
> Just to confirm, the acquisition should be:
>
> 1) blip-down b0 (just 1 volume)
> 2) 96 direction 3000 bvalue blip-up scan (first volume is b0 => 97 total volumes)
> 3) 96 direction 2500 bvalue blip-up scan (first volume is b0 => 97 total volumes)
> 4) 96 direction 2000 bvalue blip-up scan (first volume is b0 => 97 total volumes)
> 5) 96 direction 1500 bvalue blip-up scan (first volume is b0 => 97 total volumes)
> 6) 96 direction 1000 bvalue blip-up scan (first volume is b0 => 97 total volumes)
>
> I'm a little confused as to what the inputs to topup/eddy should be:
>
> ---
> 1)
>
> all_b0s = [blip-down b0, blip-up b0 (from bvalue = 3000), blip-up b0 (from bvalue = 2500), blip-up b0 (from bvalue = 2000), blip-up b0 (from bvalue = 1500), blip-up b0 (from bvalue = 1000)] ?
>
The first thing I would do would be to carefully check the b0 from the b=3000 series to make sure that is hasn’t been affected by intra-volume (slice-to-vol) movement. If that is the case I would do
my_b0s = [blip-up b0 (from bvalue = 3000) blip-down b0]
and run topup with that pair. In practice there is little gain from using the additional b0 scans.
I would then do
all_dwmri = [scan 2); scan 3); scan 4); scan 5); scan 6]; (total length = 5*96)
and
index = [1 1 1 1 ... 1 1 1]
The latest version of eddy has changed so that it now starts with an alignment of the b0s and then interpolates the movement estimates for those as starting estimates for position of the dwis. That means that the original motivation for using multiple b0 in topup has gone.
Let us say when inspecting the b0 from the b=3000 I found it to be broken (by slice-to-vol movement). I would then instead do
my_b0s = [blip-up b0 (from bvalue = 2000) blip-down b0]
all_dwmri = [scan 3); scan 2); scan 4); scan 5); scan 6]; (total length = 5*96)
I also recommend acquiring not one blip-down b0, but maybe three. That way you can inspect also the blip-down b0 for intra-volume movement and make sure you pick a non-broken one. You are otherwise putting all your eggs in the one b0 basket.
Jesper
> and
>
> all_dwmri = [scan 2); scan 3); scan 4); scan 5); scan 6]; (total length = 5*96)
> index = [2...2 3...3 4...4 5...5 6...6]; (total length = 5*96)
>
> (or is it ok to keep the blip-down b0 in the all_dwmri and add a 1 to the front of "index"?)
>
> OR
>
> 2)
>
> all_b0s = [blip-up b0 (from bvalue = 3000), blip-down b0, blip-up b0 (from bvalue = 2500), blip-up b0 (from bvalue = 2000), blip-up b0 (from bvalue = 1500), blip-up b0 (from bvalue = 1000)] ?
>
> all_dwmri = [scan 2); scan 3); scan 4); scan 5); scan 6];
> index = [1...1 3...3 4...4 5...5 6...6]; (total length = 5*96)
> ---
>
> I was under the impression that the first b0 in topup needs to correspond to the first b0 in eddy? Is that incorrect?
>
> The only requirement is that the first b0 in topup needs to be collected close in time to the first dwmri volume given to eddy?
>
> Thanks!
>
> -Justin
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