mriconvert: ordering of diffusion / non-diffusion volumes

[Roman Fleysher]

Dear Jolinda,
Dear All,

I thought mcverter outputs images in order determined by some DICOM flags. This is important because I could use the same mechanism to extract other dicom parameters and match with the output of the mcverter. This is how I get time of volume acquisition in fMRI scan, for example.

I always urge people to split the functionality of software for clarity. In this case, bval file is output by mcverter and can be used for sorting of any kind, moving b-value=0 images to front of the file or back. This image sorter is a separate routine with its own options. This is in fact what I have and do. 

In other words, keep the sorting mechanism as it was (defined by DICOM tags) and external sorters with their options can do the sorting job. Different projects may prefer different order: sometimes you want magnitude images first, imaginary phases second, ordered by time within each; sometimes, order by time first, then magnitude/phase. If external sorter needs additional info  it should either use text files provided by the mcverter or reach out to the original DICOM and use the same DICOM-tag mechanism as in mcverter to match the volumes.

Thank you,

Roman

________________________________________
From: mriconvert-bounces at lists.uoregon.edu [mriconvert-bounces at lists.uoregon.edu] on behalf of Jolinda Smith [jolinda at uoregon.edu]
Sent: Wednesday, August 07, 2013 12:57 PM
To: mriconvert at lists.uoregon.edu; Andreas Bartsch
Subject: Re: mriconvert: ordering of diffusion / non-diffusion volumes

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
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