Hi Bill,<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div style="color:#000;background-color:#fff;font-family:times new roman,new york,times,serif;font-size:12pt">
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1. In Diffeomap I perform Air Linear Registration in order to align my
data with that of the Template (in my case I use the Talairach atlas).
My images are 256*256*55 and I normalise it with the template of
dimensions 192*192*136. How much does the difference in image size
affect the accuracy and reliability of the subsequent analysis.</div></div></div></div></div></div></blockquote><div><br></div><div>because this is a simple upsampling, I assume that you don't have to worry too much about the accuracy/reliability, but I don't have a definite answer. Practically, I believe the accuracy is much more influenced by the registration accuracy, not by the upsampling. </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div style="color:#000;background-color:#fff;font-family:times new roman,new york,times,serif;font-size:12pt"><div>
<div><div style="color:rgb(0,0,0);font-family:times new roman,new york,times,serif;font-size:12pt;background-color:rgb(255,255,255)"><ul>
<li>As an additional to ensure the best LDDMM result, is the contrast
of the two images the most important in setting up the images before
entering the LDDMM screen?<br>
</li>
</ul><div>
<br></div></div></div></div></div></div></blockquote><div><br></div><div>when you do non-linear normalization, two images must have very similar contrasts. Non-linear normalization aggressively deforms images to find the best match. If the contrasts of the two images are different, the matching becomes a very difficult task. So, please make sure that you use the same contrast images and do intensity (histogram) matching before LDDMM.</div>
<div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div style="color:#000;background-color:#fff;font-family:times new roman,new york,times,serif;font-size:12pt">
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2. When I load the Talairach WMPM from diffeomap as an ROI the regions
of interest are loaded as object 1,2 etc. Is it possible to get the name
of each region of interest? When I perform the intensity measurements
using the WMPM I get the a table listing a the same amount of parts as
the objects i.e. in the case of Talairach 170. I then use the following
paper to find what the abbreviations stand for:<br>
<i><br>
</i><b>Oishi et al,</b><i> Atlas-based whole brain white matter analysis
using large deformation diffeomorphic metric mapping: Application to
normal elderly and Alzheimer’s disease participants</i><br>
euroimage 2009 June ; 46(2): 486–499. (Appendix A part 4)<br>
<br>
Is this the correct approach? Or is it the that the regions of interest
in the ROI objects box contain these parts as can be seen when I choose
the button under Atlas: <i>WMPM of division of defined ROIs</i><br>
<br></div></div></div></div></div></div></blockquote><div><br></div><div>If you load an ROI map (like WMPM) in the RoiEditor format, it loads the ROI names too. If you load an ROI map in the binary format, you get the generic ROI names (i.e. 1, 2, 3,,,). In this case, you need to find a look-up table, which should be in the RoiEditor/Image directories.</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div style="color:#000;background-color:#fff;font-family:times new roman,new york,times,serif;font-size:12pt">
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<br>
3. When I load or create the tensor image file (.d file) in DIffeoMap I
am asked if I want to flip the eigenvectors. If I save the file as
eigenvectors being flipped when I created the file do I also have to
flip them again while opening the file afterwards or do I assume they
are now in the correct direction? <br>
<br></div></div></div></div></div></div></blockquote><div><br></div><div>The "flipping" business is important only when you happened to use a table with wrong +/- signs. I would suggest you to use a correct table and forget about this business. In old days, before the table information was stored in DICOM header, we had only one generic gradient table from each vendor. These generic tables had arbitrary +/- definition and we had to figure out the +/- sign empirically. In this case, we often calculated the tensor using the generic table first and correct the sign later by "flipping" the vector orientation. There are two occasions when the flipping becomes important. One is tractography. We load the eigenvector, flip the sign, and do tractography. The other is image transformation. We load the tensor file, flip the sign, and transform. Here, once the transformation is done, you don't have to do any further flipping.</div>
<div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div style="color:#000;background-color:#fff;font-family:times new roman,new york,times,serif;font-size:12pt">
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4. Finally, when I create an ROI in either DTIStudio or ROI editor I
save it as a binary map. When I then try to reload it in the fibre
tracking section I am informed that the<i> "Image parameters in this
file are not consistent with with current ones, continue?"</i> When I
select yes the ROI loads in the expected position. Is it a normal
occurance to get an error even though I created the ROI in the same image during the
same DTIStudio session? </div><div><br></div></div></div></div></div></div></blockquote><div><br></div><div>you get his message when the matrix size and file size don't match. Please check if your file size is correct. Also, please check FAQ#15 in here (<a href="https://www.mristudio.org/wiki/faq">https://www.mristudio.org/wiki/faq</a>).</div>
<div><br></div><div>Susumu</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div style="color:#000;background-color:#fff;font-family:times new roman,new york,times,serif;font-size:12pt">
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