[Mrtrix-discussion] CSD

Wed Jun 18 00:51:51 PDT 2014

Hi Ralf,

Just a word of caution regarding Rob's suggestion of using MRtrix3's
fod2metric: if you do want to use it on existing data processed using the
current stable release (0.2.x), then you'll need to worry about the change
in the SH basis (see for details:
https://github.com/jdtournier/mrtrix3/wiki/Orthonormal-SH-basis).

In general, I'd advise against mixing 0.2.x commands with MRtrix3 commands,
unless you have a very good understanding of what the change in SH basis
means, and you take great care to keep track of which image was generated
using which version.

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 18 Jun 2014 08:32, "Robert Smith" <robert.smith at florey.edu.au> wrote:

> Hi Ralf,
>
>
> 1. A command you definitely want to have a look at in the new MRtrix
> release is fod2metric.
> It performs FOD segmentation as outlined in Appendix 2 of this paper
> <http://www.sciencedirect.com/science/article/pii/S1053811912011615>, and
> can output various statistics on the results (see the help file of the
> command for full details).
> It's also a neat way to familiarise yourself with concepts relating to how
> to deal with multiple fibres per voxel in a context other than
> tractography; for instance, the terminology
> <https://github.com/jdtournier/mrtrix3/wiki/Dixels-and-Fixels> you may
> use in such a context, how to store such data
> <https://github.com/jdtournier/mrtrix3/wiki/MRtrix-Sparse-image-formats-(.msf-.msh)>,
> and how to  perform
> <http://www.sciencedirect.com/science/article/pii/S1053811911012092>
> statistical <http://www.ismrm.org/13/session83.htm>  comparisons
> <http://www.ismrm.org/14/program_files/Session57.htm>...
>
>
> 2. Regarding the image overlay, it's important to understand that the
> viewer does not perform an explicit image registration step between images
> when you load one of them using the overlay tool. If you want the images to
> overlap, then most likely some explicit image registration step will first
> be required. If however we assume that such a registration step has been
> performed, the second important concept to understand is that two images
> can be aligned with one another in *real space*, even if they do not
> possess the same image transform or voxel sizes.
>
> So let's imagine that you've loaded your MPRAGE in mrview; you can think
> of the 'camera' in the viewer being a 2D plane that is 'snapped' to
> whatever alignment the voxel grid of that MPrage happens to have. You then
> load your DWI using the overlay tool. Now the DWI is drawn over the top of
> the MPRAGE, based on the position of the 'camera', and the image transform
> of the DWI. The fact that the DWI doesn't have the same image transform and
> voxel size as the MPRAGE (i.e. the image data have not bee *re-gridded*)
> doesn't matter; it's drawn over the top of the image you're looking at
> using interpolation. This argument still holds even if the 'camera' is not
> locked to the underlying MPRAGE (i.e. you've turned off the 'lock to image
> axes' option), in which case the 'camera' defines a plane through space,
> and *both images* are drawn upon this plane using interpolation.
>
> Now imagine that you have *not* performed an image registration step
> first, and the subject moved significantly between the two acquisitions.
> Now when you overlay the DWI, not only do the image transforms and voxel
> sizes differ, but the actual *position of the brain in real space* also
> differs, i.e. the image information from the two images doesn't overlap, no
> matter how you look at them.
>
> The distinction between image registration, image re-gridding /
> re-sampling, and image overlay, is very important to ensure that such
> questions are interpreted correctly.
>
> 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 Tue, Jun 17, 2014 at 6:27 PM, Luetzkendorf, Ralf <
> Ralf.Luetzkendorf at med.ovgu.de> wrote:
>
>> Hi Donald,
>>
>> thanks for the quick answer.
>>
>> 1. What I meant with 1. was, if I have one ODF in my image, can I get
>> some values for that ODF, like:
>> - how many directions it has and how strong
>> - angle
>> - vector
>> or something. So that I have something for a statistics or to compare to
>> subjects in that voxel or the same subject with different measurment
>> parameters or different MR Scanners.
>>
>> Im not sure if "find_SH_peaks" does that. I will test it.
>>
>> 2. If I open MPRage with MRview and overlay DWI and they have not the
>> same resolution. Does it register the DWI to the MPRage or the MPrage to
>> the DWI?
>>
>> Thanks for the help and sorry for the inexplicit questions,
>>
>> Ralf
>>
>>
>> +++++++++++++++++++++++++++++++++++++++++++++++
>> Ralf Lützkendorf
>> Department for Biometry and Medical Informatics
>> University of Magdeburg, Germany
>> phone: +49 391 67 13546
>> fax: +49 391 67 13536
>>
>> ________________________________
>> Von: Donald Tournier [jdtournier at gmail.com]
>> Gesendet: Montag, 16. Juni 2014 19:29
>> An: Lützkendorf, Ralf
>> Cc: mrtrix mailinglist
>> Betreff: Re: [Mrtrix-discussion] CSD
>>
>>
>> Hi Ralf,
>>
>> I'm assuming you're talking about the stable version of MRtrix (the 0.2.x
>> branch)? If so:
>>
>> > 1. Is there a way to have a selected ODF in values, angles or
>> something? Would be interesting to see or compare!
>> >
>>
>> I'm not sure what you mean by that exactly. You can use find_SH_peaks to
>> get the vectors corresponding to the fODF peaks (scaled by their
>> amplitude), maybe this is what you're after?
>>
>> > 2. What does MRViewer do if you overlay DWI over anatomie? Is it
>> interpolating the DWI or the Anatomie or something in between?
>>
>> Both images are interpolated, unless you  explicitly turn it off AND
>> 'lock to image axes' is on (the default), in which case the main image is
>> not interpolated. The overlay image is always interpolated, but if both
>> images align exactly, then the interpolation has negligible effect.
>>
>> > 3. Is there a way to do the TDI for the Gray matter? I set the
>> thresgold for the FA Map very low, but its not enough I guess!
>>
>> There is no FA threshold with streamtrack unless you use the DT_STREAM
>> algorithm, which isn't recommended for TDI (actually, it isn't recommended
>> under any circumstances). If you set the cutoff sufficiently low, you
>> should be able to track through these regions, although how good the
>> results are will depend very much on how good your data are, these regions
>> are really noisy at best... So not too sure why you would have trouble with
>> that, unless 'setting the FA threshold' is a different operation from what
>> I think it is... ?
>>
>> Cheers,
>> Donald a
>>
>> >
>> >
>> > Thanks for the help,
>> >
>> > 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<mailto:Mrtrix-discussion at www.nitrc.org>
>> > http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
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