Well, if you could show me the image, I may be able to help you better, but one thing I can tell now is, when you transform a WMPM, you need to use "nearest neighbor". Each ROI in the WMPM contains artificially assigned numbers; say, ROI-A is 12 and adjacent ROI-B is 20. If you transform this map using trilinear, it would generate the number "16" right in the middle of the region A and B, but the number 16 may be assigned to a totally unrelated ROI.<div>
<br></div><div>So, please try nearest neighbor and see how it goes.<br><br><div class="gmail_quote">On Tue, Oct 11, 2011 at 9:33 PM, manoj sarma <span dir="ltr"><<a href="mailto:mksarma@gmail.com">mksarma@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div>Hello DTI Experts,</div><div><br></div><div>I am trying to do an atlas based analysis using LDDMM. My goal is to do an anlysis on my FA/MD map such as done in <a href="http://www.ncbi.nlm.nih.gov/pubmed?term=20570617" target="_blank">http://www.ncbi.nlm.nih.gov/pubmed?term=20570617</a> (paper by Zhang). Therefore, I have used the steps described in <a href="https://www.mristudio.org/wiki/user_manual/diffeomap" target="_blank">https://www.mristudio.org/wiki/user_manual/diffeomap</a>.</div>
<div><br></div><div>I first processed the DTI data using 'DTI-Studio' and then skull stripped. To obtain the AIR and LDDMM transformation matrices I co-registered my skull stripped FA/MD/B0 map with 'JHU_MNI_SS_b0_ss' template using AIR and then used 'FA + b0 dual-contrast LDDMM' with 'JHU_MNI_SS_b0_ss' and 'JHU_MNI_SS_FA_ss' templates. </div>
<div><br></div><div>After obtaining the LDDMM matrix, I apply the Hmap to the 'JHU_MNI_SS_WMPM_TypeII' template. But it looks to me the image I got is having some problem. I am not sure if doing some mistakes. I used trilinear interpolation for Hmap.</div>
<div><br></div><div>Can anyone please tell me if I am following the correct procedure? Where I may go wrong?</div><div><br></div><div>Thanks in advance,</div><div>Manoj</div>
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