[Mrtrix-discussion] MRview MRTrix 3 CSD

[Erik Ziegler]

Rob,

Thanks for the information, I suppose it's easiest to recalculate them in
my case.

Erik
On Jun 2, 2014 8:33 AM, "Robert Smith" <robert.smith at florey.edu.au> wrote:

> Hi Erik
>
> Just as FODs calculated using MRtrix 0.2 will appear slightly incorrect
> when viewed in the new version, any metrics derived from them will also be
> slightly incorrect. Furthermore, the nature and severity of the error will
> vary as a function of orientation.
>
> If you have not yet seen it, there's a discussion on this topic on the
> relevant wiki page
> <https://github.com/jdtournier/mrtrix3/wiki/Orthonormal-SH-basis>
> (there's a couple of other pages there that might be worth having a look
> at, and the wiki should hopefully expand over time). If you first run
> shbasis on your data with either the -force_new or -force_native option,
> then the FODs will be interpreted correctly by any command within the new
> software. Note that this does not mean that the FODs will be exactly as
> they would be if they were calculated in the new MRtrix command dwi2fod;
> only that they will be correctly interpreted as they were produced by the
> 0.2 version command.
>
> An important point regarding the shbasis command is that it won't ruin
> your data if you accidentally run it on the same file multiple times; on
> subsequent attempts it will detect that the image data are already stored
> in the new orthonormal basis, and therefore will not modify the data any
> further.
>
> Best regards
> Rob
>
>
> --
>
> *Robert Smith, Ph.D*
> Research Officer, Imaging Division
>
> The Florey Institute of Neuroscience and Mental Health
> Melbourne Brain Centre - Austin Campus
> 245 Burgundy Street
> Heidelberg Vic 3084
> Ph: +61 3 9035 7128
> Fax: +61 3 9035 7301
> www.florey.edu.au
>
>
> On Mon, Jun 2, 2014 at 2:26 AM, Erik Ziegler <erik.ziegler at ulg.ac.be>
> wrote:
>
>>  Hi Donald,
>>
>>  As you've mentioned that the FOD basis is slightly different between
>> versions, I was wondering if it was safe to use fod2metric on FODs from
>> mrtrix 0.2? It is okay if I first use shbasis with -force_new?
>>
>>  Thanks,
>>
>>  Erik
>>
>>
>>
>>
>> On Tue, May 27, 2014 at 9:37 AM, Donald Tournier <jdtournier at gmail.com>
>> wrote:
>>
>>> Hi Ralf,
>>>
>>> Currently it's not possible to view the FODs in volume render mode - I
>>> couldn't think of a way of rendering such a massive amount of information
>>> as a volume render - it's hard enough to absorb all that information in
>>> single-slice mode... The only sensible way to do it would be to render the
>>> FODs on the clip planes, but then it doesn't really add much to the normal
>>> single-slice mode anyway...
>>>
>>> And yes, of course it's possible to display the MRtrix3 generated FODs
>>> in the new viewer - although only in single-slice or ortho view. You can
>>> still display the MRtrix 0.2 FODs, but they will be subtly wrong since the
>>> definition of the SH basis has changed slightly. You really need to watch
>>> out for that, the difference is so subtle that I can't tell which is which
>>> by eye - you need to use the shbasis app for this. Now that I think about
>>> it, I might need to emphasise this more strongly on the wiki...
>>>
>>> Cheers,
>>> Donald
>>>
>>> --
>>> Dr J-Donald Tournier (PhD)
>>>
>>> Senior Lecturer, Biomedical Engineering
>>> Division of Imaging Sciences & Biomedical Engineering
>>> King's College London
>>>
>>> A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St
>>> Thomas' Hospital, London. SE1 7EH
>>> T: +44 (0)20 7188 7118 ext 53613
>>> W:
>>> http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering
>>>
>>>  On 27 May 2014 07:46, "Luetzkendorf, Ralf" <
>>> Ralf.Luetzkendorf at med.ovgu.de> wrote:
>>>
>>>> Hi MRTrix community,
>>>>
>>>> a quick question. Is it possible to show the FODs with MRTrix3 in the
>>>> Volume View?
>>>> I guess with the MRTrix3 calculated CSD it works, but does it work with
>>>> the MRTrix 0.2 calculated CSDs / FODs?
>>>>
>>>> Ralf
>>>>
>>>>
>>>> +++++++++++++++++++++++++++++++++++++++++++++++
>>>> Ralf Lützkendorf
>>>> Department for Biometry and Medical Informatics
>>>> University of Magdeburg, Germany
>>>> phone: +49 391 67 13546
>>>> fax: +49 391 67 13536
>>>> _______________________________________________
>>>> Mrtrix-discussion mailing list
>>>> Mrtrix-discussion at www.nitrc.org
>>>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>>>
>>>
>>> _______________________________________________
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>>>
>>
>
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