mriconvert: ordering of diffusion / non-diffusion volumes

[Jolinda Smith]

Very good point Andreas. It should be simple enough to order by time instead. Is there any benefit to having an option to put them at the front? I don't want to have unnecessary options, but I don't want to fix it for some and break it for others.

Jolinda

On Wed, 07 Aug 2013 07:39:06 -0700, Andreas Bartsch <bartsch at radvisory.net> wrote:

> 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
>
>
>
>


-- 
Jolinda Smith, Ph.D.
MR Physicist
Interim Director of Operations
Lewis Center for Neuroimaging
University of Oregon
Eugene, OR USA