[Mrtrix-discussion] Question about the gradient direction table used in Mrtrix

Sun Apr 7 20:40:34 PDT 2013

Dear Dr J-Donald Tournier，

Thank you for your help. And I have another question. I have a dataset from GE scanner. I get one of the gradient directions is '-0.002, 1.000, 0.000' with the command 'dicominfo' in Matlab. The gradient direction achieved with the command 'mrinfo' in Mrtrix is '-0.00650699, -0.998944, -0.0454892 ', and the transform matrix achieved with 'mrinfo ' is [0.9951 0.004517 0.09862 -136.6; -0 0.9989 -0.04591 -104.6; -0.09873 0.04569 0.9941 -50.04; 0 0 0 1]. Can I transform the direction  '-0.002, 1.000, 0.000' to '-0.00650699, -0.998944, -0.0454892 ' with the transform matrix. No matter flipping the sign of z component or not, I cannot get '-0.00650699, -0.998944, -0.0454892 ' from '-0.002, 1.000, 0.000'. Are there other steps for the transfromation to get  '-0.00650699, -0.998944, -0.0454892 ' .

Thanks.

Regards,
Sangma Xie

Sangma Xie , Master  
Brainnetome Center 
National Laboratory of Pattern Recognition (NLPR)
Institute of Automation, Chinese Academy of Sciences (CASIA)
95 Zhong Guan Cun East Road, Hai Dian District, Beijing 100190, P.R.China

From: Donald Tournier
Date: 2013-04-03 11:26
To: smxie
CC: mrtrix-discussion
Subject: Re: [Mrtrix-discussion] Question about the gradient direction table used in Mrtrix
Hi Sangma,

OK, there's quite a few issues at play here. First off, the convention used in MRtrix is that the gradients are specified with respect to the DICOM patient coordinate system. This is essentially the same convention as for DICOM images produced on Siemens and Philips scanners, and the newer standard DICOM tags recently introduced, with one notable exception: the DICOM patient-centered coordinate system has its x-axis running right-to-left and its y-axis running anterior-posterior, whereas MRtrix assumes these axes run in the opposite direction (as per the NIfTI standard). So MRtrix will flip the x & y components to account for this. 

For Siemens & Philips images, that's essentially all that happens to the DW gradients. For GE images, it's a little different, since in this case the gradients are (or at least, used to be) stored with respect to the images axes. This means that to convert to MRtrix convention, they must be re-oriented back into the patient-centered coordinate system. This is what the rotate_DW_scheme flag specifies: when the DW gradient information was read from a GE-specific tag, this is set to true and the gradients are then rotated according to the direction of the images axes. In this case, the z component is inverted, since flipping the x & y is essentially the same as flipping z, given the symmetry of diffusion.

As far as I know, dcm2nii provides the DW directions with respect to the image axes (in the NIfTI coordinate system). To convert these back to MRtrix convention, the same transformation as you highlighted is needed, but without the negative sign. The transform you highlighted also accounts for differences in the directions of these axes due to the different conventions used for DICOM versus NifTI/MRtrix, so is not appropriate as-is to do convert a dcm2nii-supplied gradient table into one suitable for MRtrix. This is because the dcm2nii gradient table is provided with respect to the image axes in NIfTI coordinate space, and in MRtrix they are provided with respect to the original axes, also in NIfTI coordinate space. 

To get back to your question, what do you mean when you say 'the original gradient table'? The one supplied by dcm2nii (in which case converting using the highlighted section of code would not work, as explained above), or the actual ones as read directly from the DICOM headers? If the latter, then unless your images were acquired on a GE scanner, then that also would not work, since that section of code would only be used for GE images. If you are trying to convert non-GE DW directions read directly from the DICOM headers, then all you need to do is flip the sign of the x & y components. 

Basically, it's really hard to keep track of all the possible conventions and what each step in the processing pipeline might have done to the DW gradients. Hopefully the above will help you figure out where the problem might be...

Hope this helps.
Cheers,

Donald.

On 3 April 2013 12:57, smxie_nlpr <smxie at nlpr.ia.ac.cn> wrote:

Hi,

I have a question about the gradient direction table used in Mrtrix. The gradient direction table achieved from the DICOM images with dcm2nii is different from the table achieved with the command 'mrinfo DICOMDIR -grad encoding.b'. I checked the source code of Mrtrix and found the following codes '
if(rotate_DW_scheme)
{
G(n,0) = image_transform(0,0) * d[0] + image_transform(0,1) * d[1] - image_transform(0,2) * d[2];
G(n,1) = image_transform(1,0) * d[0] + image_transform(1,1) * d[1] - image_transform(1,2) * d[2];
G(n,2) = image_transform(2,0) * d[0] + image_transform(2,1) * d[1] - image_transform(2,2) * d[2];
}' in image.cpp.
I transformed the original gradient table with similar code in Matlab, but the result is not equal to the table achieved with mrinfo. So I want to know the procedure of transforming the original gradients to the gradients achieved with mrinfo. And why is it 'G(n,0) = image_transform(0,0) * d[0] + image_transform(0,1) * d[1] - image_transform(0,2) * d[2];' rather than 'G(n,0) = image_transform(0,0) * d[0] + image_transform(0,1) * d[1] + image_transform(0,2) * d[2];' ?

Thanks.

Sangma Xie

Sangma Xie , Master  
Brainnetome Center 
National Laboratory of Pattern Recognition (NLPR)
Institute of Automation, Chinese Academy of Sciences (CASIA)
95 Zhong Guan Cun East Road, Hai Dian District, Beijing 100190, P.R.China

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-- 
Dr Jacques-Donald Tournier

Research Fellow

The Florey Institute of Neuroscience and Mental Health
Melbourne Brain Centre - Austin Campus
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