[Mristudio-users] b-matrix from dicom header and from techs

[Hangyi Jiang]

hi, Jeff,

if the files are in Mosaic format, DtiDtudio can get the gradients from the header.  
below, I attached the email I sent to Venkat for your reference.

regards,

hangyi


>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Hi Venkat,

this is one of the most confusions to deal with DICOM files.

according the DICOM standard and Siemens documentation, the gradients (bvec as you mentioned) in DICOM header should be defined in patient space (or image matrix space), so the one from dcm2nii should be correct for your dataset.

the 1st one (from your MR techs) seems that it is the original definition based on scanner's coordinate system. this one should be adjusted dynamically during scanning according to patient position and orientation.  by the way, we usually named it as gradient table, not b-matrix. b-matrix has 6 components for each of DWIs. b-matrix can be calculated from the gradient table.

as a matter of fact, Siemens also saves adjusted b-matrix in the DICOM header. if you like, you can also use the adjusted b-matrix from the header for tensor calculation. in fact, using adjusted b-matrix is recommended by Siemens since it also considered other factors (like gradient cross-over effects) for image acquisition.

hope it helps.

hangyi
>>>>>>>>>>>>>>>>>>>>>>>>>>>>



________________________________________
From: mristudio-users-bounces at mristudio.org [mristudio-users-bounces at mristudio.org] On Behalf Of Jeff Sadino [jsadino.queens at gmail.com]
Sent: Saturday, July 10, 2010 10:51 PM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; rajagov2 at ccf.org
Subject: Re: [Mristudio-users] b-matrix from dicom header and from techs

Hi Venkat,

We had the same question on our Siemens VA25A DTIs.  The Siemen's tech support recommended a program called MRIConvert (http://lcni.uoregon.edu/~jolinda/MRIConvert/) to extract the gradients.  I don't have our tables in front of me, but the .8, 0, and .4 values seem pretty close to what I remember.  Siemens said that they suspected the 1, 0, .5 values were in the scanner direction and the .8, 0, .4 values were in the patient direction, since I think Siemens automatically adjusts for that.  Just be careful when using the MRIConvert program to extract gradients, since it flips the y sign for FSL purposes.

Cheers,
Jeff

On Fri, Jul 9, 2010 at 9:33 AM, Rajagopalan, Venkateswaran <rajagov2 at ccf.org<mailto:rajagov2 at ccf.org>> wrote:


Dear All,

we collect our data from Siemens scanner. I got b-matrix from our MR techs for software version VA25A b matrix is as follows

 0: 0.000, 0.000, 0.000
 1: 1.000, 0.000, 0.500
 2: 0.000, 0.500, 1.000
 3: 0.500, 1.000, 0.000
 4: 1.000, 0.500, 0.000
 5: 0.000, 1.000, 0.500
 6: 0.500, 0.000, 1.000
 7: 1.000, 0.000, -0.500
 8: 0.000, -0.500, 1.000
 9: -0.500, 1.000, 0.000
 10: 1.000, -0.500, 0.000
 11: 0.000, 1.000, -0.500
 12: -0.500, 0.000, 1.000

I used dcm2nii software (to convert hem into nifti file for soem other purpose  i also gives me bvec and bval files) which gives me the following matrix from the dicom header file

0       0       0
0.89    0       -0.45
0       0.45    -0.89
0.45    0.89    0
0.89    0.45    0
0       0.89    -0.45
0.45    0       -0.89
0.89    0       0.45
0       -0.45   -0.89
-0.45   0.89    0
0.89    -0.45   0
0       0.89    0.45
-0.45   0       -0.89

Since not only the values are different but +/- signs are also different in DW directions. So I am wondering whether any one could tell me which is the correct table to go with.

Thanks

Venkat


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