mriconvert: ordering of diffusion / non-diffusion volumes

[Andreas Bartsch]

Hi Jolinda,

hmm, other than that some people might find it convenient to view the B0s
first and possibly extract them - no, not that I can think of.
The info is all there, and I would just not alter the natural scan order.
Hope all is well!
Best wishes from germany,
Andreas

Am 07.08.13 18:57 schrieb "Jolinda Smith" unter <jolinda at uoregon.edu>:

>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