Hi Darren and Jeff,<div><br></div><div>What Jeff said is correct. DtiStudio provides some handy functions such as extracting gradient information from DICOM/Mosaic and apply rotation based on the oblique angles. However, these functions are activated by users and it is users who have to find out what is the correct way to get a gradient table.</div>
<div><br></div><div>As I mentioned before, for self-defense, I recommend to perform a couple of imaging with severe oblique angles. For us, it is difficult to comment differences with third party programs (we don't have experience with them), but following are some important points to know;</div>
<div><br></div><div>1) The generic gradient tables provided by manufacturers may need to be modified for x/y/z permutation and +/- definition.</div><div>2) The gradient table extracted from DICOM files may be used as is, but that may not be the case for old DICOM formats.</div>
<div>3) We should be always careful when we use oblique angles.</div><div>4) The gradient table extracted from Siemens DICOM (Mosaic) could be different from the generic table because it contains a small amount of contributions from imaging gradient.</div>
<div>5) As Jeff mentioned, to see the effect of the table recalculation based on the oblique-angles, you need to close the window and reopen the initial data input window. There, it remembers the results of the previous gradient table calculation.</div>
<div><br></div><div>Our past experience says that the generic Siemens gradient table and the one extracted from Mosaic are very close. The difference is usually within +/- definition and the small image gradient contribution. The table remains unchanged regardless of oblique angles (within the difference due to small image gradient contribution). </div>
<div><br></div><div>Please don't hesitate to further discuss this issue because there could be something we are missing.</div><div><br><div class="gmail_quote">On Mon, Dec 27, 2010 at 5:44 PM, Jeff Sadino <span dir="ltr"><<a href="mailto:jsadino.queens@gmail.com">jsadino.queens@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hi Darren,<div><br></div><div>I also spent some time on this recently on our Siemens VB17 software. DTIStudio does not rotate the gradients until after you click "OK" to visualize your images. So regardless of whether or not you select "rotate gradients if applicable", the gradient table that you will see DTIStudio pull will be identical. To see the modified table, visualize your data, then close that window, then when you load up your next subject, you will see the rotated table.</div>
<div><br></div><div>As far as I can tell, DTIStudio pulls whatever is written in the DICOM header, without any modifications, unless you tell it to.</div><div><br></div><div>In the DICOM header, there is a tag called ImageOrientationPatient. DTIStudio uses this tag to "know" whether or not a rotation is necessary.</div>
<div><br></div><div>I'm not sure about those specific third party programs, but I think some of them flip the y direction so that they are more compatible with FSL</div><div><br></div><div>Hope it helps,</div><div>Jeff<div>
<div></div><div class="h5"><br>
<br><div class="gmail_quote">On Sun, Dec 26, 2010 at 3:18 PM, Darren Gitelman <span dir="ltr"><<a href="mailto:d-gitelman@northwestern.edu" target="_blank">d-gitelman@northwestern.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi<br>
<br>
I know the issue of gradient directions has been brought up many<br>
times, but I am struggling with what the correct gradient directions<br>
should be. It's not that I doubt dtistudio, but I am puzzled by why<br>
the gradients end up different depending on how one converts the dicom<br>
data. I have spent some time plotting the gradient directions on a<br>
unit sphere and this is what i found (see below). I also have some<br>
questions about how dtistudio "knows" whether or not to rotate the<br>
gradients.<br>
<br>
I am using Siemens data acquired on a scanner with b17 software.<br>
<br>
If I click "get gradient from dicom file header" the values entered by<br>
DTIstudio don't seem to change whether or not I also click rotate<br>
gradients if applicable.<br>
<br>
Is DTIstudio automatically rotating the gradients when it gets them<br>
from the Siemens header?<br>
<br>
Clearly these gradients are different than if I pasted in the default<br>
Siemens gradients. How does DTIstudio know whether or not the<br>
gradients need rotating when I click the OK button? Here is what I<br>
mean- let's say I get the gradients from the Dicom image and I save<br>
these in a text file. Now I try 2 different ways of importing the DTI<br>
data: 1) in one case I paste the default Siemens gradients and in the<br>
other 2) I paste the gradients I obtained from the Dicom image. If I<br>
click rotate gradients if applicable, will DTIstudio know to rotate<br>
the gradients in case 1 (default Siemens directions) but not in case 2<br>
(acquired from Dicom file)?<br>
<br>
Is there any way to get the final gradients that DTIstudio is applying<br>
to the data?<br>
<br>
The whole process of obtaining the gradients seems to be somewhat of a<br>
mystery (to me anyway) and it's hard to know what is correct (at least<br>
for Siemens data). I also notice that the gradients obtained from the<br>
Dicom file are not the same as the gradients one obtains when<br>
converting the data via either dcm2nii<br>
(<a href="http://www.cabiatl.com/mricro/mricron/dcm2nii.html" target="_blank">http://www.cabiatl.com/mricro/mricron/dcm2nii.html</a>) or via mriconvert<br>
(<a href="http://lcni.uoregon.edu/~jolinda/MRIConvert/" target="_blank">http://lcni.uoregon.edu/~jolinda/MRIConvert/</a>). The gradients from<br>
these conversions are flipped by -1 in the y direction from dtistudio.<br>
(In fact the gradients from mriconvert are nearly the same as<br>
dtistudio after accounting for this y-flip, while the gradients form<br>
dcm2nii are off by 4-6 degrees rotation after accounting for the<br>
y-flip).<br>
<br>
Any advice about the gradient directions and how to be sure what is<br>
correct would be appreciated.<br>
<br>
Thanks,<br>
Darren<br>
--<br>
Darren Gitelman, MD<br>
710 N. Lake Shore Dr., 1122<br>
Chicago, IL 60611<br>
Ph: (312) 908-8614<br>
Fax: (312) 908-5073<br>
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