Hi JS,<div><br></div><div><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I'm having some issues with my data, especially the encoding.b file<br>
generated after I performed the "mrinfo -grad" command-line. Here is the<br>
situation. First of all I'm working with the NIFTI format, so I have<br>
converted my data using the the "mrconvert" command.<br>
My paramaters used here is b=1000, direction=20, average=4. When I look at<br>
the encoding.b file resulting from the "mrinfo -grad", we noticed that the<br>
values are repeting themselves every 20 lines in the first three columns for<br>
4 times instead of being all different. Is that supposed to be that way ?<br></blockquote><div><br></div><div>Given that you have 4 repeats, this is exactly what I would expect. I assume there is no averaging done on the scanner, and you end up with 80 volumes? If so, this is correct, you have 4 sets of the same 20 directions. I'm not sure why you think this is odd, why would you expect to get different values in the different repeats of your gradient directions?</div>
<div><br></div><div>What is more problematic is that with 20 directions, you're not going to get good results with CSD - particularly with a b-value of only 1000. Why are you acquiring 4 repeats of 20, and not a full set of 80 unique directions? Is there any scope for changing the acquisition parameters? If so, I would strongly encourage you to increase the b-value to at least 2000s/mm², and acquire a minimum of 60 unique directions to get adequate sampling over the orientation domain.</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
I executed the "estimate_response" function but the values are way out of<br>
this world: 5.62455e+77 -9.96597e+75 3.52424e+76 -4.63953e+76 -3.93348e+75<br>
7.96634e+76. A colleague of mine noticed that the lmax was equal to 10 when<br>
I performed the "disp_profile" rendering suggesting that maybe mrtrix was<br>
considering that my data had 80 directions instead of 20. Is that good<br>
reasoning ?<br>
How can I go around this problem ?<br></blockquote><div><br></div><div>Yes, MRtrix only looks at the number of 'directions' in the directions file, and uses the lmax value assuming all these directions are unique. This will obviously not work where there are repeats in the DW scheme. In your case, you should specify "-lmax 4" to estimate_response, since this is the maximum you can characterise with 20 directions: lmax=4 requires 15 directions, lmax = 6 requires at least 28 directions. </div>
<div> </div><div>Hope this helps,</div><div><br></div><div>Cheers,</div><div><br></div><div>Donald.</div><div><br></div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Thank you very much for your help,<br>
<br>
JS<br>
<br>
<br>
<br>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><font color="#ff6600" size="1"><b>Dr Jacques-Donald Tournier<br></b></font><div><font color="#ff6600" size="1">Research Fellow</font></div><div><font size="1"><br>
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