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

[Gavin Winston]

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. 
  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