[Mrtrix-discussion] Exporting diffusion data from Bruker systems

[Counsell, Serena]

Many thanks Donald.

I will have a go with the Bruker raw data and let you know how I get on.

best wishes
serena


________________________________
From: Donald Tournier [d.tournier at brain.org.au]
Sent: Thursday, May 16, 2013 2:34 AM
To: Counsell, Serena
Cc: mrtrix-discussion at www.nitrc.org
Subject: Re: [Mrtrix-discussion] Exporting diffusion data from Bruker systems

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<mailto: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<mailto: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
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