mriconvert: ordering of diffusion / non-diffusion volumes

Wed Aug 7 10:44:14 PDT 2013

The order would still be defined by DICOM tags, it's just a matter which tags are used to sort. Since the time information is not not (I think!) included in the NIFTI file, this is actually a good argument for changing it away from B0 first -- you can always resort it to put them first after the fact, using the bval file. Or am I wrong, and it's simple to sort by time afterwards too?

Jolinda

On Wed, 07 Aug 2013 10:31:56 -0700, Roman Fleysher <roman.fleysher at einstein.yu.edu> wrote:

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