[Mrtrix-discussion] MRview MRTrix 3 CSD

[Robert Smith]

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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