Hi all,<br><br>For Siemens users, now a new function to extract a gradient table from Mosaic file header is available. The extracted gradient table is usually different from the generic gradient table provided by Siemens from the following points;<br>
<br>> X/Y/Z gradient signs (+/-) are dynamically changed based on image protocol (e.g. axial/sagittal/coronal). The extracted tables have correct signs.<br>> The extracted table is more exact because it includes not only the diffusion-weighing gradients but also a small contribution of imaging gradients.<br>
<br>The are some mixed information about whether we need to reorient gradient tables when oblique imaging is used (whether we need to check "rotate if applicable" option or not). We are testing it but with the scanner we tested last time (VB17 operating system), we needed to check to this option. <br>
<br>We will follow up this issue soon but we strongly recommend you to test your scanner. It can be easily tested by scanning a person twice. Once with a regular axial and one with a strong oblique (30-45 degree). If you are not sure about your results, you can send us your results for check.<br>
<br>Susumu<br><br><div class="gmail_quote">On Mon, Jul 12, 2010 at 9:56 AM, Hangyi Jiang <span dir="ltr"><<a href="mailto:hjiang@jhmi.edu">hjiang@jhmi.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
hi, Jeff,<br>
<br>
if the files are in Mosaic format, DtiDtudio can get the gradients from the header.<br>
below, I attached the email I sent to Venkat for your reference.<br>
<br>
regards,<br>
<br>
hangyi<br>
<br>
<br>
>>>>>>>>>>>>>>>>>>>>>>>>>>>><br>
Hi Venkat,<br>
<br>
this is one of the most confusions to deal with DICOM files.<br>
<br>
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.<br>
<br>
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.<br>
<br>
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.<br>
<br>
hope it helps.<br>
<br>
hangyi<br>
>>>>>>>>>>>>>>>>>>>>>>>>>>>><br>
<br>
<br>
<br>
________________________________________<br>
From: <a href="mailto:mristudio-users-bounces@mristudio.org">mristudio-users-bounces@mristudio.org</a> [<a href="mailto:mristudio-users-bounces@mristudio.org">mristudio-users-bounces@mristudio.org</a>] On Behalf Of Jeff Sadino [<a href="mailto:jsadino.queens@gmail.com">jsadino.queens@gmail.com</a>]<br>
Sent: Saturday, July 10, 2010 10:51 PM<br>
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support; <a href="mailto:rajagov2@ccf.org">rajagov2@ccf.org</a><br>
Subject: Re: [Mristudio-users] b-matrix from dicom header and from techs<br>
<div class="im"><br>
Hi Venkat,<br>
<br>
We had the same question on our Siemens VA25A DTIs. The Siemen's tech support recommended a program called MRIConvert (<a href="http://lcni.uoregon.edu/%7Ejolinda/MRIConvert/" target="_blank">http://lcni.uoregon.edu/~jolinda/MRIConvert/</a>) 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.<br>
<br>
Cheers,<br>
Jeff<br>
<br>
</div><div><div></div><div class="h5">On Fri, Jul 9, 2010 at 9:33 AM, Rajagopalan, Venkateswaran <<a href="mailto:rajagov2@ccf.org">rajagov2@ccf.org</a><mailto:<a href="mailto:rajagov2@ccf.org">rajagov2@ccf.org</a>>> wrote:<br>
<br>
<br>
Dear All,<br>
<br>
we collect our data from Siemens scanner. I got b-matrix from our MR techs for software version VA25A b matrix is as follows<br>
<br>
0: 0.000, 0.000, 0.000<br>
1: 1.000, 0.000, 0.500<br>
2: 0.000, 0.500, 1.000<br>
3: 0.500, 1.000, 0.000<br>
4: 1.000, 0.500, 0.000<br>
5: 0.000, 1.000, 0.500<br>
6: 0.500, 0.000, 1.000<br>
7: 1.000, 0.000, -0.500<br>
8: 0.000, -0.500, 1.000<br>
9: -0.500, 1.000, 0.000<br>
10: 1.000, -0.500, 0.000<br>
11: 0.000, 1.000, -0.500<br>
12: -0.500, 0.000, 1.000<br>
<br>
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<br>
<br>
0 0 0<br>
0.89 0 -0.45<br>
0 0.45 -0.89<br>
0.45 0.89 0<br>
0.89 0.45 0<br>
0 0.89 -0.45<br>
0.45 0 -0.89<br>
0.89 0 0.45<br>
0 -0.45 -0.89<br>
-0.45 0.89 0<br>
0.89 -0.45 0<br>
0 0.89 0.45<br>
-0.45 0 -0.89<br>
<br>
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.<br>
<br>
Thanks<br>
<br>
Venkat<br>
<br>
<br>
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