<div dir="ltr">Hi David,<div>it worked out now. Thanks a lot!</div><div><br></div><div>Alessandro</div><div class="gmail_extra"><br><div class="gmail_quote">2014-10-16 13:45 GMT+02:00 Slater David <span dir="ltr"><<a href="mailto:David.Slater@chuv.ch" target="_blank">David.Slater@chuv.ch</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Hi Alessandro,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">I think your problem is coming from the scheme file you are using. Try creating a Stejskal-Tanner scheme as described here:
<a href="http://cmic.cs.ucl.ac.uk/camino/index.php?n=Docs.SchemeFiles" target="_blank">http://cmic.cs.ucl.ac.uk/camino//index.php?n=Docs.SchemeFiles</a>. It should take the following form:<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">VERSION: STEJSKALTANNER<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">x_1 y_1 z_1 |G_1| DELTA_1 delta_1 TE_1<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="FR" style="font-size:10.0pt;font-family:"Courier New"">x_2 y_2 z_2 |G_2| DELTA_2 delta_2 TE_2<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="FR" style="font-size:10.0pt;font-family:"Courier New"">:<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="FR" style="font-size:10.0pt;font-family:"Courier New"">:<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="FR" style="font-size:10.0pt;font-family:"Courier New"">x_N y_N z_N |G_N| DELTA_N delta_N TE_N<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="FR" style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Save it as something like
<i>‘myscheme.scheme’</i>. This type of scheme file contains the gradient pulse information so you can remove these options from the
<i>datasynth</i> command. Thus the following command will output synthetic data in .txt format:<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Courier New"">datasynth -schemefile myscheme.scheme -voxels 10000 -walkers 100000 -tmax 1000 -geometry cylinder -packing SQUARE -cylinderrad 1.9E-6 -cylindersep 4E-6 -diffusivity 2E-09 -noisetype
rician -snr 16.0 -p 0.0 -initial uniform | float2txt > SIMdata.txt<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Note that I have removed the
<i>–G</i>, <i>–del</i> and <i>–DEL</i> options which were causing you errors and used the
<i>float2txt</i> command to get the output in .txt format. <u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Try this with a corrected scheme file and you should get your synthetic voxel data.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Best,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">David<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span lang="FR" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">De :</span></b><span lang="FR" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> <a href="mailto:camino-users-bounces@www.nitrc.org" target="_blank">camino-users-bounces@www.nitrc.org</a> [mailto:<a href="mailto:camino-users-bounces@www.nitrc.org" target="_blank">camino-users-bounces@www.nitrc.org</a>]
<b>De la part de</b> Alessandro Calamuneri<br>
<b>Envoyé :</b> 16 October 2014 12:21<br>
<b>À :</b> <a href="mailto:camino-users@www.nitrc.org" target="_blank">camino-users@www.nitrc.org</a><br>
<b>Objet :</b> [Camino-users] datasynth ERROR on sequence parameters<u></u><u></u></span></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Hi camino experts,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I need help becaues i am not able to create synthetic data using datasynth command; so far I am basically following examples within the command itself. <u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">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<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><i><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#505050">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><u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">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?<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">However, looking 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.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Thus, I type<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><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><u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">But I get the following error<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal"><i>Oct 16, 2014 10:49:06 AM tools.CL_Initializer checkParsing</i><u></u><u></u></p>
<p class="MsoNormal"><i>WARNING: WARNING: couldn't parse arg 10: '-G'</i><u></u><u></u></p>
<p class="MsoNormal"><i>Oct 16, 2014 10:49:06 AM tools.CL_Initializer checkParsing</i><u></u><u></u></p>
<p class="MsoNormal"><i>WARNING: WARNING: couldn't parse arg 11: '0.022'</i><u></u><u></u></p>
<p class="MsoNormal"><i>Oct 16, 2014 10:49:06 AM tools.CL_Initializer checkParsing</i><u></u><u></u></p>
<p class="MsoNormal"><i>WARNING: WARNING: couldn't parse arg 12: '-del'</i><u></u><u></u></p>
<p class="MsoNormal"><i>Oct 16, 2014 10:49:06 AM tools.CL_Initializer checkParsing</i><u></u><u></u></p>
<p class="MsoNormal"><i>WARNING: WARNING: couldn't parse arg 13: '0.032'</i><u></u><u></u></p>
<p class="MsoNormal"><i>Oct 16, 2014 10:49:06 AM tools.CL_Initializer checkParsing</i><u></u><u></u></p>
<p class="MsoNormal"><i>WARNING: WARNING: couldn't parse arg 14: '-DEL'</i><u></u><u></u></p>
<p class="MsoNormal"><i>Oct 16, 2014 10:49:06 AM tools.CL_Initializer checkParsing</i><u></u><u></u></p>
<p class="MsoNormal"><i>WARNING: WARNING: couldn't parse arg 15: '0.04'</i><u></u><u></u></p>
<p class="MsoNormal"><i>Exception in thread "main" java.lang.ClassCastException: imaging.B_VectorScheme cannot be cast to imaging.SimulableScheme</i><u></u><u></u></p>
<p class="MsoNormal"><i> at tools.CL_Initializer.initDataSynthesizerFromSimulation(CL_Initializer.java:2031)</i><u></u><u></u></p>
<p class="MsoNormal"><i> at tools.CL_Initializer.initDataSynthesizer(CL_Initializer.java:2121)</i><u></u><u></u></p>
<p class="MsoNormal"><i> at apps.SyntheticData.initOptions(SyntheticData.java:55)</i><u></u><u></u></p>
<p class="MsoNormal"><i> at apps.Executable.<init>(Executable.java:24)</i><u></u><u></u></p>
<p class="MsoNormal"><i> at apps.SyntheticData.<init>(SyntheticData.java:34)</i><u></u><u></u></p>
<p class="MsoNormal"><i> at apps.EntryPoint.getExecutable(EntryPoint.java:222)</i><u></u><u></u></p>
<p class="MsoNormal"><i> at apps.EntryPoint.main(EntryPoint.java:282)</i><u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">There is something wrong with the scheme, as I do not see mistyping errors.<u></u><u></u></p>
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<p class="MsoNormal">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<u></u><u></u></p>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><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><u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></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><u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Same error occur. What is wrong?<u></u><u></u></p>
<p class="MsoNormal">As far as I know, bvalue is given by the formula<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">b=(gamma*delta*G)^2*(DELTA-delta/3)=q^2*(DELTA-delta/3) <u></u><u></u></p>
<p class="MsoNormal">where gamma should be 42e6*2*pi. All units follow SI<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Can you help me understanding why the command is not running? Is my formula wrong?<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Best,<u></u><u></u></p>
<p class="MsoNormal">Alessandro<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal"><u></u> </p></div></div></div></div></div></div></blockquote></div><div dir="ltr"><div><br></div></div>
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