Hi Dani,<br><br>This issue has been touched upon several times but because it is very important, I want to re-describe it here.<br><br>> All the users who are using the following conditions do not have to worry anything about gradient coordinate system (magnet frame, patient frame, imaging frame). Based on the patient position and imaging parameters (oblique angles), the gradient table is recalculated within the scanner on-the-fly to assure that gradient table x/y/z correspond to image x/y/z. When [1, 0, 0] is applied, it is along image X axis.<br>
<br>All GE scanners with all operating systems<br>Philips scanners with all operating systems except that "Gradient Overplus = on"<br>Siemens scanners after VB15 operating system<br><br>> The following scanner users have to be worried about gradient coordinates. When oblique plane is used, the gradient table HAS TO BE recalculated because the gradient table is in the magnet x/y/z. <br>
<br>Philips scanners when "Gradient Opverplus = on"<br>Siemens scanners before VB15<br><br>If you are using DICOM or MOSAIC, you have to check "Rotate gradients if applicable" checkbox beneath the gradient table window.<br>
If you are using Philips REC/PAR, please use "DTI_gradient_table _creator" at <a href="http://godzilla.kennedykrieger.org/~jfarrell/software_web.htm">http://godzilla.kennedykrieger.org/~jfarrell/software_web.htm</a> written by Jonathan Farrel.<br>
<br>Susumu<br><br><div class="gmail_quote">On Mon, Jan 25, 2010 at 11:34 AM, Nanz Daniel Dr. <span dir="ltr"><<a href="mailto:Daniel.Nanz@usz.ch">Daniel.Nanz@usz.ch</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi<br>
<br>
I could not find definitions for the coordinate<br>
system within which the diffusion directions are to<br>
be defined for the input into DTI studio?<br>
<br>
E.g., on a Philips system, the diffusion direction<br>
cosines found in the DICOM header (private and public tags)<br>
are independent of slice orientation as well as of<br>
patient orientation. Presumably, the direction cosines<br>
are given in a magnet-fixed coordinate system.<br>
<br>
Is this considered and recalculated for tractograpy<br>
by DTI studio, based on the information in the DICOM<br>
header (slice orientation in patient coordinate system)?<br>
Or is the inter-voxel relation of diffusion<br>
ellipsoid directions neglected altogether by DTI studio?<br>
<br>
Or should the directions be re-calculated before<br>
feeding the data into DTI studio? If so, into what<br>
coordinate system should the directions be transformed?<br>
<br>
With best regards and thanks<br>
Dani Nanz<br>
<br>
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