mriconvert: ordering of diffusion / non-diffusion volumes

[Andreas Bartsch]

Hi,

for diffusion EPIs, MRIConvert seems to put all the B0 images at the
beginning of the 4D nifti file.
While I can see the rationale behind it, recent preprocessing tools may be
better / easier off if you >don't< re-shuffle the ordering in time (see the
FSL thread below).
So you might consider not to put all the B0 volumes at the start in future
versions.
Cheers,
Andreas


Von:  Jesper Andersson <jesper.andersson at NDCN.OX.AC.UK>
Antworten an:  FSL - FMRIB's Software Library <FSL at JISCMAIL.AC.UK>
Datum:  Mittwoch, 7. August 2013 15:14
An:  <FSL at JISCMAIL.AC.UK>
Betreff:  Re: [FSL] eddy question

Hi Andreas, 

> in our diffusion sequence multiple B0 (nodif) acquisitions are interspersed
> into the diffusion weightings.
> MRIConvert puts all the B0 images at the beginning of the 4D nifti file.
> Does this adversely affect the output of eddy, given that the *_movpar.txt
> from topup then suggests that all the motion has happened at the beginning of
> the acquisition?

See the answer to the next question, which I hope will clarify things.


> 
> As a related note, does the acp file used for topup have to be the same like
> the one used in eddy? If I have, lets say, 10 B0 images for blip-up and ­down,
> my --datain for topup needs 20 entries. For eddy, I could just use a file with
> 2 enries for --acqp if my --index is ok.
> So I assume that this won't make any difference (i.e. if --datain of topup and
> --acqp of eddy differ) but I want to make sure that it's ok.

Eddy will anyway need to estimate movement parameters for every diffusion
weighted image. BUT given the correct information it can use the parameters
estimated from topup as starting guesses.

To make this concrete: Imagine we have 9 scans where scan 0, 3 and 6 are b=0
and that topup found mb=0.1 between the first and second b=0 and mb=0.3
between the first and third b=0. Eddy would then start out by guessing the
following mb parameters for the six diffusion weighted images

0 0 0.1 0.1 0.3 0.3

and as eddy executes it will update these such this it might end with for
example

0 0.05 0.11 0.27 0.33 0.45
 
You can use a 20 entry --datain file along with the --index file to make
sure that eddy gets the correct information. In our example case above
(where we have 3 b=0 and hence a three-line --acqp file) we would use the
--acqp file that we used for topup and then the following --index file

1 2 3 1 1 2 2 3 3

Is that clear?

Puss J

> 
> Cheers,
> Andreas



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