You can use <div>tracks2prob -template TDI.mif CST.tck CST_p.mif<div><br></div><div>However, it puzzles me that you want to extract statistics from (presumably) ultra-high resolution images. FA values should, in my opinion, be extracted from the original FA maps. On the other hand, it has been suggested that track densities are not something that is a quantifiable parameter for between-group analyses. I am hoping this opinion has changed and/or that some new way of analysis of TDI is available. Perhaps others can pitch in.</div>
<div><br></div><div>Luis</div><div><br></div><div><br></div><div><br><div class="gmail_quote">On Thu, Jul 5, 2012 at 4:39 PM, Kirles Bishay <span dir="ltr"><<a href="mailto:kirles@ualberta.ca" target="_blank">kirles@ualberta.ca</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>Hello,</div><div> </div><div>
I am currently trying to get statistics specifically on the corticospinal tract of my whole brain TDI images. So far, I have tried to create a mask of just the CST to apply to the whole brain image by using the tractography function in MRtrix, turning it into a TDI image, using ImageJ software to convert the TDI image into a mask and then applying the mask back in MRtrix to specify my ROI for the statistics function. While this works well with the TDI image of just the CST, it does not work with the whole brain image because the dimensions of the images are different. This is because the dimensions created with my ROI tractography differ from the dimensions of the whole brain tractography. I have tried to change the dimensions of my mask image using ImageJ, but I think this warps the mask inapropriately. Is there a way to control the output dimensions of the tractography images so that I can match the CST mask to my TDI image? Or do you have any other suggestions to get the data on the CST in my whole brain images that I have not thought of? </div>
<div> </div><div>Thank you,</div><div> </div><div>Kirles</div>
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