<html><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:10pt"><div><span>Hi Ned,</span></div><div style="color: rgb(0, 0, 0); font-size: 13px; font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; background-color: transparent; font-style: normal;"><span><br></span></div><div style="color: rgb(0, 0, 0); font-size: 13px; font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; background-color: transparent; font-style: normal;"><span>Without going into the details of your specific simulations, </span><span style="font-size: 10pt;">o</span><span style="font-size: 10pt; background-color: transparent;">ne thing to check might be the number of spins. A</span><span style="background-color: transparent; font-size: 10pt;">t a quick glance you are using 10000 spins whereas it's not
uncommon to use considerably more than that, and the paper you cite used 10e^6.</span></div><div style="color: rgb(0, 0, 0); font-size: 10pt; font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; background-color: transparent; font-style: normal;"><span style="background-color: transparent;"><br></span></div><div style="color: rgb(0, 0, 0); font-size: 13px; font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; background-color: transparent; font-style: normal;"><span style="background-color: transparent;">It would be important to first check how similar (or dissimilar) your attenuation curves are under a single, identical condition but vary the number of spins and/or time steps for separate runs. Particularly at high q-values this can be quite important to get reliable signal estimates. </span></div><div><br></div><div style="color: rgb(0, 0, 0); font-size: 13px;
font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; background-color: transparent; font-style: normal;">-Matt</div><div style="color: rgb(0, 0, 0); font-size: 13px; font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; background-color: transparent; font-style: normal;"><br></div> <div style="font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; font-size: 10pt;"> <div style="font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; font-size: 12pt;"> <div dir="ltr"> <hr size="1"> <font size="2" face="Arial"> <b><span style="font-weight:bold;">From:</span></b> Ned Charles <ccha4217@uni.sydney.edu.au><br> <b><span style="font-weight: bold;">To:</span></b> "camino-users@www.nitrc.org" <camino-users@www.nitrc.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Friday, March 14,
2014 1:58 AM<br> <b><span style="font-weight: bold;">Subject:</span></b> [Camino-users] Question regarding Monte Carlo Data Synthesis<br> </font> </div> <div class="y_msg_container"><br><div id="yiv8659280389">
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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: rgb(255, 255, 255);">, at least the first "resonance",</span> that match up to the
literature for example: </span><a rel="nofollow" target="_blank" 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 rel="nofollow" target="_blank" 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 rel="nofollow" target="_blank" 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 rel="nofollow" target="_blank" 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: rgb(255, 255, 255);">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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