<div dir="ltr"><p class="MsoNormal"><span lang="EN-GB">Hi camino experts,</span></p><p class="MsoNormal"><span lang="EN-GB"><br></span></p><p class="MsoNormal"><span lang="EN-GB">I need help becaues i</span> am not able to create synthetic data using datasynth command; so far I am basically following examples within the command itself. </p><p class="MsoNormal"><span lang="EN-GB"><br></span></p><p class="MsoNormal"><span lang="EN-GB">At this step I am simulating a number of voxels using a cyilinder geometry with square packing. This is what is written in the manual of datasynth</span></p><p class="MsoNormal"><br></p><p class="MsoNormal"><span lang="EN-GB"><i><span lang="EN-GB" style="font-size:10pt;line-height:115%;font-family:Arial,sans-serif;color:rgb(80,80,80)">datasynth -schemefile
tensorDirs_b=500.scheme -voxels 10000 -walkers 100000 -tmax 1000 -p 0.0
-initial uniform -snr 16.0 -G 0.022 -del 0.032 -DEL 0.04 -geometry cylinder
-packing SQUARE -cylinderrad 1.9E-6 -cylindersep 4E-6 > MCdata.Bfloat</span></i><br></span></p><p class="MsoNormal"><span lang="EN-GB"><br></span></p><p class="MsoNormal"><span lang="EN-GB">which I suppose having something strange, because schemefile was not written out; furthermore there is a tensorDirs_b option that I was not able to understand, it is not on the list. What does it stand for?</span></p><p class="MsoNormal"><span lang="EN-GB"><br></span></p><p class="MsoNormal"><span lang="EN-GB">However, l</span>ooking at the example scanner parameters details, I have created a scheme file with 10 b0 acquisitions and 61 diffusion weighted directions and the same bvalue as estimated from parameters inserted.</p><p class="MsoNormal"><br></p><p class="MsoNormal"><span lang="EN-GB">Thus, I type</span></p><p class="MsoNormal"><span lang="EN-GB"><br></span></p><p class="MsoNormal"><span lang="EN-GB"></span></p><p class="MsoNormal"><span lang="EN-GB"><i>datasynth -schemefile scheme.scheme -voxels 10000 -walkers 100000 -tmax 1000 -G 0.022 -del 0.032 -DEL 0.04 -geometry cylinder -packing SQUARE -cylinderrad 1.9E-6 -cylindersep 4E-6 -diffusivity 2E-09 -noisetype rician -snr 16.0 -p 0.0 -initial uniform > MCdata.Bfloat</i></span></p><div><br></div><div>But I get the following error</div><div><br></div><div><p class="MsoNormal"><span lang="EN-GB"><i>Oct 16, 2014 10:49:06 AM tools.CL_Initializer checkParsing</i></span></p><p class="MsoNormal"><span lang="EN-GB"><i>WARNING: WARNING: couldn't parse arg 10: '-G'</i></span></p><p class="MsoNormal"><span lang="EN-GB"><i>Oct 16, 2014 10:49:06 AM tools.CL_Initializer checkParsing</i></span></p><p class="MsoNormal"><span lang="EN-GB"><i>WARNING: WARNING: couldn't parse arg 11: '0.022'</i></span></p><p class="MsoNormal"><span lang="EN-GB"><i>Oct 16, 2014 10:49:06 AM tools.CL_Initializer checkParsing</i></span></p><p class="MsoNormal"><span lang="EN-GB"><i>WARNING: WARNING: couldn't parse arg 12: '-del'</i></span></p><p class="MsoNormal"><span lang="EN-GB"><i>Oct 16, 2014 10:49:06 AM tools.CL_Initializer checkParsing</i></span></p><p class="MsoNormal"><span lang="EN-GB"><i>WARNING: WARNING: couldn't parse arg 13: '0.032'</i></span></p><p class="MsoNormal"><span lang="EN-GB"><i>Oct 16, 2014 10:49:06 AM tools.CL_Initializer checkParsing</i></span></p><p class="MsoNormal"><span lang="EN-GB"><i>WARNING: WARNING: couldn't parse arg 14: '-DEL'</i></span></p><p class="MsoNormal"><span lang="EN-GB"><i>Oct 16, 2014 10:49:06 AM tools.CL_Initializer checkParsing</i></span></p><p class="MsoNormal"><span lang="EN-GB"><i>WARNING: WARNING: couldn't parse arg 15: '0.04'</i></span></p><p class="MsoNormal"><span lang="EN-GB"><i>Exception in thread "main" java.lang.ClassCastException: imaging.B_VectorScheme cannot be cast to imaging.SimulableScheme</i></span></p><p class="MsoNormal"><span lang="EN-GB"><i> at tools.CL_Initializer.initDataSynthesizerFromSimulation(CL_Initializer.java:2031)</i></span></p><p class="MsoNormal"><span lang="EN-GB"><i> at tools.CL_Initializer.initDataSynthesizer(CL_Initializer.java:2121)</i></span></p><p class="MsoNormal"><span lang="EN-GB"><i> at apps.SyntheticData.initOptions(SyntheticData.java:55)</i></span></p><p class="MsoNormal"><span lang="EN-GB"><i> at apps.Executable.<init>(Executable.java:24)</i></span></p><p class="MsoNormal"><span lang="EN-GB"><i> at apps.SyntheticData.<init>(SyntheticData.java:34)</i></span></p><p class="MsoNormal"><span lang="EN-GB"><i> at apps.EntryPoint.getExecutable(EntryPoint.java:222)</i></span></p><p class="MsoNormal"><span lang="EN-GB"><i> at apps.EntryPoint.main(EntryPoint.java:282)</i></span></p><p class="MsoNormal"><span lang="EN-GB"> </span></p></div><div>There is something wrong with the scheme, as I do not see mistyping errors.</div><div>I then discarded my scheme file and created a scheme on the fly using options <b>fixedbvalue </b>and <b>fixedqmod</b>, hence the following</div><p class="MsoNormal"><span lang="EN-GB"><i><br></i></span></p><p class="MsoNormal"><span lang="EN-GB"><i>datasynth -fixedbvalue 10 61 1.0124E+09
-voxels 10000 -walkers 100000 -tmax 1000 -G 0.022 -del 0.032 -DEL 0.04
-geometry cylinder -packing SQUARE -cylinderrad 1.9E-6 -cylindersep 4E-6
-diffusivity 2E-09 -noisetype rician -snr 16.0 -p 0.0 -initial uniform> MCdata.Bfloat</i></span></p><p class="MsoNormal"><span lang="EN-GB"><br></span></p><p class="MsoNormal"><i>datasynth -fixedmodq 10 61 1.8578E+05 0.04
-voxels 10000 -walkers 100000 -tmax 1000 -G 0.022 -del 0.032 -DEL 0.04
-geometry cylinder -packing SQUARE -cylinderrad 1.9E-6 -cylindersep 4E-6
-diffusivity 2E-09 -noisetype rician -snr 16.0 -p 0.0 -initial uniform>
MCdata.Bfloat</i><br></p><p class="MsoNormal"><i><br></i></p><p class="MsoNormal">Same error occur. What is wrong?</p><p class="MsoNormal">As far as I know, bvalue is given by the formula</p><p class="MsoNormal"><br></p><p class="MsoNormal">b=(gamma*delta*G)^2*(DELTA-delta/3)=q^2*(DELTA-delta/3) </p><p class="MsoNormal">where gamma should be 42e6*2*pi. All units follow SI</p><p class="MsoNormal"><br></p><p class="MsoNormal">Can you help me understanding why the command is not running? Is my formula wrong?<br></p><p class="MsoNormal"><br></p><p class="MsoNormal">Best,</p><p class="MsoNormal">Alessandro</p><p class="MsoNormal"><br></p><div><br></div>
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