[Mrtrix-discussion] Specifying gradient directions on a GE Signa HDx scanner

[Donald Tournier]

Hi Gavin,

Yes, the fun never ends with DICOM...

MRtrix was actually coded up based on the same wiki information, but I only
implemented support for the latest version, as per the last few entries in
the wiki:

In GE DWI images (software version 12.0)


(0008,1090) LO [SIGNA EXCITE]
(0018,1020) LO [12\LX\MR Software release:12.0_M4_0520.a]

diffusion directions are stored under the following tags:


(0019,10bb) DS [0.430617]
(0019,10bc) DS [-0.804161]
(0019,10bd) DS [-0.420008]


This has worked fine for all the GE data I've had access to (admittedly not
a lot), and it does take care of re-orienting the directions into scanner
coordinates. I guess it would be good to include support for these other
data, especially if this is actually the GE 'standard'. I'd be happy to
have a go if you can send me some data to try it out. It sounds like a
relatively trivial change, I just need to parse the (0021,105A) tag...
Actually, just a dump of the output of "read_dicom -a <DICOM file>" should
be sufficient for me to figure out how it's stored. If you can send me
that, I'll add support for it.

Otherwise, the directions you get from the headers sound like they would be
similar to the FSL bvecs/bvals format. There's been a bit of discussion
about how to convert between FSL & MRtrix formats recently, with a few
people contributing their scripts. A quick google search for MRtrix & bvecs
should give you the info you need.

Finally, I see no reason why you couldn't use the trick of resetting the
transform matrix to identity, unless you actually need to preserve the
original orientation.

Hope this helps.
Cheers,

Donald.


On 15 October 2012 23:08, Gavin Winston <g.winston at ucl.ac.uk> wrote:

> Dear all,
>
> I would like to use MRtrix on DTI data from a GE Signa HDx 3.0T scanner
> (software release 14.0).  My query relates to how to specify the gradient
> directions in the correct reference frame for MRtrix.
>
> The gradient table file on the scanner specifies the three components of
> the diffusion gradients relative to the acquisition (i.e. if you tilt the
> acquisition plane by 10 degrees, the applied gradients also tilt by 10
> degrees).  I think this behaviour differs from Siemens scanners.  If I use
> the gradient table directly in MRtrix and the acquisition is tilted the
> fibre orientations are also incorrectly tilted.  There seem to be several
> ways to approach this so which do people advise?
>
> Firstly, extracting the gradient directions from the DICOM header.  I
> understand from previous posts that GE scanners are a bit funny about how
> they do this.  Using read_dicom on our data seems to suggest that it is
> stored in the fields 0019,10E0 (DTI diffusion directions), 0021,105A
> (diffusion direction), 0043,1039 (b value) as per
> http://wiki.na-mic.org/Wiki/**index.php/NAMIC_Wiki:DTI:**
> DICOM_for_DWI_and_DTI#Private_**vendor:_GE<http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI#Private_vendor:_GE>.
>  However mrinfo does not seem to support this as it just produces a
> gradient table which is entirely zeros.
>
> Secondly, I could reorientate the entries of the gradient table according
> to the transforms from the DICOM file (or the qform/sform once converted to
> Nifti).  Are there are ready-made tools to do this?
>
> Finally, it is possibly to implement a quick fix by modifying the
> qform/sform headers.  If you convert DICOM -> NIFTI, using fslorient as
> below then convert NIFTI -> MIF with mrconvert things work fine.  For
> example on a 1.875x1.875x2.4mm dataset:
>
> fslorient -setqform -1.875 0 0 0 0 1.875 0 0 0 0 2.4 0 0 0 0 1 <file>
> fslorient -setsform -1.875 0 0 0 0 1.875 0 0 0 0 2.4 0 0 0 0 1 <file>
>
> Normally our acquisitions are virtually aligned with the scanner axes so
> the error is small, but I acquired a dataset this morning where the
> acquisition was tilted by 45 degrees to check the above worked.
>
> Many thanks,
>
> Gavin
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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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