Hi Dr. Mori,<div><br></div><div>I think I have figured out the pipeline now. Two more questions I have are:</div><div><br></div><div>1. I have tested both DTIstudio and ExploreDTI. The second produced occasionally more voxels with FA over 0.25 following motion and eddy current correction. As you have recently coauthored a paper with Dr. Leemans (Diffusion tensor imaging and beyond), I wanted to ask what may be different to cause different results from the same dataset.</div>
<div><br></div><div>2. You mentioned in another email the possibility to use masks (for example, an entire hemisphere) during normalization. I haven't found an option like this in Diffeomap. Is there any such possibility, so that I can possibly avoid using SPM in the pipeline?</div>
<div><br></div><div>Thank you.</div><div>Dorian</div><div><br><br><div class="gmail_quote">2012/12/30 susumu mori <span dir="ltr"><<a href="mailto:susumu@mri.jhu.edu" target="_blank">susumu@mri.jhu.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Dorian,<div><br></div><div>We don't have experience in mixing SPM transformation and MriStudio pipeline. In general, you have to be very careful to mix pipelines from different sources;</div>
<div><br></div><div>1) coordinate systems could be different; right-hand or left-hand coordinates / neurology or radiology orientation. You have to be careful so that the images and transformation matrices are in correct orders.</div>
<div>2) gradient vector re-orientation: If you touch raw diffusion-weighted images, you have to transform the gradient vectors too. This is not difficult when you use linear transformation, but if you are using non-linear transformation, each voxel has to have its own gradient table. The procedure becomes simpler if you transform images after tensor calculation, but if you transform a tensor field, you need to make sure to re-orient the tensor in each voxel.</div>
<div><br></div><div>In general, each software (FSL, SPM, MriStudio) should be already tested for the consistency for these issues in a transparent manner, but once you mix the pipeline, such a consistency may be lost.</div>
<div><br></div><div>Susumu<br><br><div class="gmail_quote"><div><div class="h5">On Wed, Dec 26, 2012 at 12:16 PM, Dorian P. <span dir="ltr"><<a href="mailto:alb.net@gmail.com" target="_blank">alb.net@gmail.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
Hi everybody, and happy holidays,<div><br></div><div>I am using DTIstudio in a complex workflow. </div><div><br></div><div>First, I need to make a nonlinear registration using masks on lesioned data. SPM is doing a good job at this point. To apply the transformation matrix produced by SPM, I must export images from DTI studio (analyze format), apply the deformations in SPM and import the files back to DTIstudio. However I am not sure whether a problem arises with the gradient tables not being the same any more. How can I apply the transformation matrix from SPM? Is there maybe a way to convert .mat files to .vtk and do all transofmrations in DTIstudio/Diffeomap?</div>
<div><br></div><div><br></div><div>Second, having both T1 and b0 images in two different sessions, which one is better in theory for registration, T1s or B0s ? In many examples the b0 has been used for linear (AIR) and nonlinear (LBBDMM) registration. But on the other side a b0 is acquired in a fraction of the time of a T1, so may be less stable to artifacts (or with fat artifacts?).</div>
<div><br></div><div>Thank you.</div><div>Dorian</div><div>TJU</div>
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