Hi Kerstin,<div><br></div><div>Not sure what you mean by 'higher resolution'. Do you mean spatial resolution? If so all you'd need to do is to interpolate the CSD image to a higher resolution prior to feeding it into find_SH_peaks. I think mrtransform might do the trick if you give it a higher resolution anatomical image (for example) as the template image.</div>
<div><br></div><div>If you meant angular resolution, then I should point out that the find_SH_peaks command does a full Newton-Raphson type gradient ascent, and finds the exact peak direction. The direction set that you need to provide to the command simply specifies a set of initial directions from which to start the search. So basically find_SH_peaks already provides 'full' angular resolution.</div>
<div><br></div><div>Cheers,</div><div><br></div><div>Donald.</div><div><br><br><div class="gmail_quote">On 16 February 2011 12:58, Kerstin Pannek <span dir="ltr"><<a href="mailto:uqkpann1@uq.edu.au">uqkpann1@uq.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div style="word-wrap:break-word"><div>Hi</div><div><br></div><div>is it possible to get the peaks at a higher resolution than the input csd?</div>
<div><br></div><div>Cheers</div><div>Kerstin</div><div><div></div><div class="h5"><div><br></div><div><br></div><br><div><div>On 15/02/2011, at 9:42 AM, Donald Tournier wrote:</div><br><blockquote type="cite">Hi Jeong,<br>
<br><div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div lang="EN-US" link="blue" vlink="purple"><div><p class="MsoNormal">I wonder the order of fiber directions saved in the output file of "find_SH_peaks".</p>
<p class="MsoNormal">This is what I did:</p><p class="MsoNormal">gendir 100 dir100.txt</p><p class="MsoNormal">find_SH_peak CSD8.mif dir100.txt SH_peaks_CSD8.mif</p><div> <br></div><p class="MsoNormal">The output file consists of 9 different 3-D volumes. </p>
<p class="MsoNormal">Which ones are for X, Y, Z to indicate the direction of the 1st fiber ?</p><p class="MsoNormal">I am guessing the first three volumes indicates the X, Y, Z of the first vector, next three indicates those of the second vector, and so on.</p>
<p class="MsoNormal">Is it correct? </p></div></div></blockquote><div><br></div><div>Yes, this is correct. Also, the norm of each of these X,Y,Z vectors provides the amplitude of the FOD along the corresponding peak direction.</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div lang="EN-US" link="blue" vlink="purple"><div><p class="MsoNormal">Also, I would like to know whether 100 directions are good enough to estimate the directions of three fibers.</p>
</div></div></blockquote><div><br></div><div>Yes, that's more than enough. In my experience, 60 is already enough for lmax 8.</div><div> </div><div>Cheers,</div><div><br></div><div>Donald.</div><div><br></div><div><br>
</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">_______________________________________________<br>
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<br></blockquote></div><br><br clear="all"><br>-- <br>Jacques-Donald Tournier (PhD)<br>Brain Research Institute, Melbourne, Australia<br>Tel: +61 (0)3 9496 4078<br>
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</blockquote></div><br></div></div></div></blockquote></div><br><br clear="all"><br>-- <br>Jacques-Donald Tournier (PhD)<br>Brain Research Institute, Melbourne, Australia<br>Tel: +61 (0)3 9496 4078<br>
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