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<DIV>I have a similar question. </DIV>
<DIV>We have dataset of subjects before/after intervention, we have 15 dir DTI and 3D T1 data (GE) with same parameters both times, but orientation not exactly the same (clinical protocol). The brains are not normal at baseline with enlarged ventricles that may have changed minimally (due to treatment, e.g. smaller size). Normalization is not a possibility d/t abnormalities on brain to begin with, we just want to compare before/after. We are investigating the effect on white matter and would like to get best approach to compare basic measurement before/after. We have manual (blinded) ROI showing differences before/after, but want to make sure we are in the exact same ROI. To co-register seems the best way, but tricky as the structure of the brain is not exactly the same. Any suggestions?</DIV>
<DIV> </DIV>
<DIV>1) would it be best to co-register DTI to T1 at both time points and then to co-register T1 in time point A to B followed by change of DTI with same matrix? If so, I assume this would have to be done with DiffeoMap, what would be the steps to do so?</DIV>
<DIV>2) is co-registration to "dangerous" for bias as there is the possibility that the brain is not exactly the same before and after (ventricle size change)<BR></DIV>
<DIV>Thanks,</DIV>
<DIV> </DIV>
<DIV>JMT</DIV>
<DIV><BR>>>> susumu mori <susumu@mri.jhu.edu> 7/28/2010 3:23 PM >>><BR>Usually, we first calculate tensor and then register the tensor maps with proper reorientation, rather than register the raw DWIs with rotated gradient tables.<BR><BR>It is possible to do your approach, but tensor registration would be easier, I think.<BR><BR></DIV>
<DIV class=gmail_quote>On Wed, Jul 28, 2010 at 2:40 PM, Rajagopalan, Venkateswaran <SPAN dir=ltr><<A href="mailto:rajagov2@ccf.org">rajagov2@ccf.org</A>></SPAN> wrote:<BR>
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<DIV><BR>
<P><FONT size=2>Dear All,<BR><BR>We have diffusion data set acquired with 5 trails/repetitions(in single time point/cross sectional) for each and every subject. After eddy current correction i would like to do gradient table rotation. I am registering all the 5 trails to the b0 image. Since after eddy/motion correction i have affine matrix for all the 5 trails i.e i have 13*5 affine matrices so I am wondering which set of affine matrices i.e first 13 affine matrices or affine matrices from second trail/repetition should i use to rotate my gradient table.<BR><BR>Thanks<BR></FONT></P>
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