[Mrtrix-discussion] Exporting diffusion data from Bruker systems

[Donald Tournier]

Sorry, just noticed the HTML links I'd inserted didn't make it
through. The MRtrix
.mih format is documented
here<http://www.brain.org.au/software/mrtrix/appendix/mrtrix.html>,
and the data layout entry is documented
here<http://www.brain.org.au/software/mrtrix/general/formats.html#dataorder>
.
Cheers,

Donald.



On 16 May 2013 12:26, Donald Tournier <d.tournier at brain.org.au> wrote:

> Hi Serena,
>
> MRtrix can handle NIfTI and Analyse natively, so if you can convert your
> data to these formats, this might be simplest approach. It may or may not
> give you the gradient directions unfortunately, but I'm sure there are ways
> to obtain these by other means.
>
> Otherwise, you can try to import the data into MRtrix's own .mih format,
> which is documented on this page. I don't have much experience with Bruker
> data, but if I recall correctly, they're stored as a single raw data file
> with a separate text header. This actually makes it quite easy to deal
> with. The .mih format is just a plain text header with 'key: value'
> entries. All you'd need to do is create such a file in a text editor, with
> 'mrtrix image' as the first line, and the last line with 'file:
> NAME_OF_RAW_DATA_FILE 0' (edit as appropriate). Other lines will be needed
> to specify the dimensions, voxel size, layout, datatype, and optionally the
> transform and DW directions. If in doubt, you can always convert any
> vaguely similar data that you have to the .mih format, and simply edit the
> resulting .mih file to suit your data (you can then discard the raw data
> .dat file generated by the conversion).
>
> Of the required entries, I expect the layout might be the trickiest to
> figure out. You can find an explanation of this on this page. Essentially,
> it provides enough information to figure out the correspondence between a
> voxel's coordinates and the position of its value in the file (i.e. its
> file offset). I recommend you simply experiment with it until you can
> display a sensible looking image in MRView...
>
> If you can, I'd also recommend you try to figure out the transform, unless
> you know the slices were not oblique. You may also find information related
> to the DW gradient orientations in the Bruker text file header, which you
> can also add in using the DW_scheme entries. In both of these cases, you
> might find that things don't necessarily match up correctly (the transform
> might not be quite right, the DW directions might be inverted, etc), in
> particular for data acquired in a non-transverse orientation and/or using
> oblique slices. This can be tricky to handle, since there are quite a few
> conversions between coordinate systems going on behind the scenes...
>
> If you're having trouble with this, feel free to send me the Bruker header
> file, and I'll try to help out.
>
> Hope this helps,
>
> Cheers,
>
> Donald.
>
>
> On 15 May 2013 23:39, "Counsell, Serena" <serena.counsell at kcl.ac.uk>
> wrote:
>
>>  Dear All
>>
>> I am having trouble exporting diffusion data acquired on a Bruker system
>> in a format that can be used by MRtrix. Does anyone have any experience or
>> tips?
>>
>> Many thanks,
>> serena
>>
>>
>>
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>>
>>


-- 
*Dr Jacques-Donald Tournier
*
Research Fellow

The Florey Institute of Neuroscience and Mental Health
Melbourne Brain Centre - Austin Campus
245 Burgundy Street
Heidelberg  Vic  3084
Ph:  +61 3 9035 7033
Fax:  +61 3 9035 7307
www.florey.edu.au
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