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<div>Hi everyone,</div>
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<div>I have a question regarding Monte Carlo simulations using the datasynth module. I am using datasynth to verify q-space <span style="font-size: 12pt;">type diffusion diffraction patterns for various synthetic meshes that we create as .ply files. The simulation
works great </span><span style="font-size: 12pt;">and creates the diffraction patterns<span style="font-family: calibri, arial, helvetica, sans-serif; font-size: 16px; background-color: #ffffff;">, at least the first "resonance",</span>​ that match up to the
literature for example: </span><a href="http://130.235.71.204/Publication/62_jmrA_1995_116_77.pdf" title="http://130.235.71.204/Publication/62_jmrA_1995_116_77.pdf
Ctrl+click or tap to follow link" style="font-size: 12pt;">http://130.235.71.204/Publication/62_jmrA_1995_116_77.pdf</a></div>
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<div>When looking at the created signal created under certain conditions, however, the actual returned signal from camino <span style="font-size: 12pt;">becomes negative in a couple of areas as the gradient strength increases. To recreate the signal, the mesh
substrate I am </span><span style="font-size: 12pt;">using is a 15 micron diameter sphere, with the file here: </span><span style="font-size: 12pt;"><a href="https://onedrive.live.com/redir?resid=C4C5DBA3D21E3ED6!149&authkey=!AE5S46TChx1pxLM&ithint=file%2c.ply">https://onedrive.live.com/redir?resid=C4C5DBA3D21E3ED6!149&authkey=!AE5S46TChx1pxLM&ithint=file%2c.ply</a></span></div>
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<div>I am using a basic PGSE scheme with 101 different measurements at a small delta of 1 ms, a fixed big delta of 56 ms, TE of 66 ms, one gradient direction and an increasing gradient as in the scheme file here: <span style="font-size: 12pt;"><a href="https://onedrive.live.com/redir?resid=C4C5DBA3D21E3ED6!148&authkey=!APHn52CVBaXlHFo&ithint=file%2c.scheme">https://onedrive.live.com/redir?resid=C4C5DBA3D21E3ED6!148&authkey=!APHn52CVBaXlHFo&ithint=file%2c.scheme</a></span></div>
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<div>To replicate the experiment, I run datasynth on linux by:<br>
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<div>datasynth -voxels 1 -walkers 10000 -tmax 1000 -p 0.0 -initial intra -voxelsizefrac 1 -substrate ply -plyfile <PLY FILE <span style="font-size: 12pt;">ABOVE> -schemefile <SCHEME FILE ABOVE> -outputfile Sphere.Bfloat</span></div>
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<div>This should give a signal that has negative values in a couple of places. The question I have is whether the returned <span style="font-size: 12pt;">signal from Camino in this instance is supposed to be a magnitude signal? The actual signal appears to
be built in Camino by </span><span style="font-size: 12pt;">taking the summation of the cosine value of the accumulated phase for each walker's trajectory, which I'm assuming is the "real" part of the signal. I also browsed the code in AgnosticScan.java (version
2 DEC 13) and found that if an SNR is provided, a magnitude signal is created by taking the square root of the signal squared. Upon testing this, it inverts the lobes on the signal and gives a "double dip", especially in a log plot vs. (q-value*sphere radius)
as shown here: <a href="https://onedrive.live.com/redir?resid=C4C5DBA3D21E3ED6!150&authkey=!ANXxP6S9im65ACQ&v=3&ithint=photo%2c.png">
https://onedrive.live.com/redir?resid=C4C5DBA3D21E3ED6!150&authkey=!ANXxP6S9im65ACQ&v=3&ithint=photo%2c.png</a></span></div>
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<div>This plot is for four experiments with different big DELTA values. I also get the same results when saving the trajectories as a file and running different signals against that. <span style="font-family: calibri, arial, helvetica, sans-serif; font-size: 16px; background-color: #ffffff;">Please
let me know if you aren't able to replicate the issue. </span> Just wondering if anyone can provide any guidance on the nature of the negative output signals and whether I am using the correct parameters to perform the experiment. Any help would be appreciated.<br>
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<div>Cheers,</div>
<div>Ned Charles</div>
<div>University of Sydney</div>
<div>ccha4217@uni.sydney.edu.au<br>
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