Romain<br><br>The issue here is that estimate_response automatically determines the maximum harmonic order lmax based on the number of diffusion-weighted directions it finds in the DWI. In the case of your data, it finds 60 diffusion-weighted directions, so fits a spherical harmonic order of 8 (which requires 45 coefficients). However you only actually have 30 unique directions, with each acquired twice. So there is only enough angular resolution to fit a spherical harmonic order of 6 (which requires 28 coefficients). If you provide the option -lmax 6 to estimate_response, it calculates a response function similar to those you obtained from each half-dataset.<br>
<br>CSD is capable of calculating Fibre Orientation Distributions of a higher order than you have the data to support ('super-resolved' CSD), as it incorporates additional information from those directions where the FOD is negative. You _may_ be able to perform CSD with an lmax of 8, but it is possible that some voxels will fail to converge (this will give an error on the command-line, and the corresponding voxel in your image will be black and contain NAN values). If this occurs frequently in your images, you will be limited to using an lmax of 6 for CSD for these data (use "-lmax 6" at the command line for csdeconv).<br>
<br>Best regards<br>Rob<br><div class="gmail_extra"><br clear="all"><div><br>--<br><br>Robert Smith<br>PhD Candidate <br><br>The Florey Institute of Neuroscience and Mental Health<br>Melbourne Brain Centre - Austin Campus<br>
245 Burgundy Street<br>Heidelberg Vic 3084<br>Ph: +61 3 9035 7128<br>Fax: +61 3 9035 7301<br><a href="http://www.florey.edu.au" target="_blank">www.florey.edu.au</a><br><span style="font-size:9pt;font-family:"Times New Roman","serif";color:red"></span></div>
<br>
<br><br><div class="gmail_quote">On Wed, Dec 5, 2012 at 2:41 AM, romain valabregue <span dir="ltr"><<a href="mailto:romain.valabregue@upmc.fr" target="_blank">romain.valabregue@upmc.fr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear All<br>
<br>
I have an acquisition which has been done with the same direction twice. (this was an error intead of using a complementary set of direction it uses the same diffusion directions)<br>
<br>
when I do the estimate_response on the all data set I get wrong estimation<br>
<br>
cat response.txt<br>
-4.04413e+15 1.47696e+14 -1.52359e+15 -3.50894e+15 6.85026e+15<br>
<br>
<br>
but when I do the estimation on the half of the dataset (either the first one or the second one)<br>
I get a correct estimation<br>
<br>
cat response_sh.txt<br>
504.145 -226.698 65.6188 -14.786<br>
cat response_sh2.txt<br>
492.199 -215.285 64.4914 -10.5965<br>
<br>
<br>
Any idea how I can handle the 2 NEX correctly in mrtrix<br>
<br>
<br>
Thanks<br>
<br>
<br>
Romain<br>
<br>
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</blockquote></div><br></div>