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<body class='hmmessage'><div dir='ltr'>Thanks a lot Matt, I didn't understand this. <br><br><div><hr id="stopSpelling">From: matt.hall@ucl.ac.uk<br>To: stefania.oliviero@hotmail.it<br>CC: camino@cs.ucl.ac.uk<br>Subject: RE: [Camino-users] datasynth ERROR with bvector scheme<br>Date: Fri, 17 Oct 2014 14:15:32 +0000<br><br>
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<p class="ecxMsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;">Hi Stefania,</span></p>
<p class="ecxMsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;">Because simulations calculate an explicit phase shift for each spin based on its trajectory through the substrate, they need to know more details of the pulse
sequence than is available from the scheme you are using. You need to specify G, delta and DELTA (not just b-value and gradient direction). The BVECTOR format doesn’t have enough information (its not a “simulable scheme” and so the simulation complains.</span></p>
<p class="ecxMsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;"> </span></p>
<p class="ecxMsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;">Matt.</span></p>
<p class="ecxMsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D;"> </span></p>
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<p class="ecxMsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";"> camino-users-bounces@www.nitrc.org [mailto:camino-users-bounces@www.nitrc.org]
<b>On Behalf Of </b>stefania oliviero<br>
<b>Sent:</b> 17 October 2014 15:05<br>
<b>To:</b> camino-users@www.nitrc.org<br>
<b>Subject:</b> [Camino-users] datasynth ERROR with bvector scheme</span></p>
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<p class="ecxMsoNormal"> </p>
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<p class="ecxMsoNormal"><span style="font-family:"Calibri","sans-serif";">Hi all users<br>
I also have a problem with datasynth.<br>
I'm using this command to generate a substrate.<br>
<br>
</span><i><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";">datasynth -walkers ${WALKERS} -tmax ${TIMESTEPS} -geometry inflammation -numcylinders ${NUMCYL} -p 0.02 -initial uniform -seed ${INT_rnd} -voxels 1 -increments 1 -separateruns -latticesize
${LATSIZE} -schemefile ${SCHEMEFILE} -gamma ${GAMA} ${GAMB} -diffusivity ${DIFF} -substrateinfo -drawcrosssection ${FNAMEINFO}.gray > ${OUTPUTDIR}/${FNAME} 2> ${FNAMEINFO}.txt
</span></i><span style="font-family:"Calibri","sans-serif";"><br>
<br>
When I use a scheme file with a stejskaltanner format It works.<br>
If I try to use a scheme file with a bvector format It doesn't work and the follow error appears:<br>
<br>
</span><i><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";">Exception in thread "main" java.lang.ClassCastException: imaging.B_VectorScheme cannot be cast to imaging.SimulableScheme<br>
at tools.CL_Initializer.initDataSynthesizerFromSimulation(CL_Initializer.java:2031)<br>
at tools.CL_Initializer.initDataSynthesizer(CL_Initializer.java:2121)<br>
at apps.SyntheticData.initOptions(SyntheticData.java:55)<br>
at apps.Executable.<init>(Executable.java:24)<br>
at apps.SyntheticData.<init>(SyntheticData.java:34)<br>
at apps.EntryPoint.getExecutable(EntryPoint.java:222)<br>
at apps.EntryPoint.main(EntryPoint.java:282)<br>
<br>
</span></i><span style="font-family:"Calibri","sans-serif";">The scheme file in bvector format is that downloaded from the tutorial DTI 4Ddwi_bvector.scheme</span><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";">:</span><span style="font-family:"Calibri","sans-serif";"></span></p>
<pre><i>#B-vector scheme. Contains gradient directions and b-values</i></pre>
<pre><i>#g_x g_y g_z b</i></pre>
<pre><i>VERSION: BVECTOR</i></pre>
<pre><i> 0.000000 0.000000 0.000000 0.000E00</i></pre>
<pre><i> 0.557286 0.673159 -0.486096 1.000E09</i></pre>
<pre><i> 0.411008 -0.525405 -0.744998 1.000E09</i></pre>
<pre><i> -0.576000 0.585141 -0.570819 1.000E09</i></pre>
<pre><i> -0.058952 -0.998228 0.008080 1.000E09</i></pre>
<pre><i> 0.671827 -0.643902 -0.366113 1.000E09</i></pre>
<pre><i> -0.147877 0.617325 -0.772685 1.000E09</i></pre>
<pre><i> -0.527370 0.221392 -0.820285 1.000E09</i></pre>
<pre><i> 0.091543 -0.251136 -0.963613 1.000E09</i></pre>
<pre><i> -0.850415 -0.498192 0.169112 1.000E09</i></pre>
<pre><i> -0.764016 -0.584574 -0.273045 1.000E09</i></pre>
<pre><i> 0.000000 0.000000 0.000000 0.000E00</i></pre>
<pre><i> 0.300301 0.470652 -0.829642 1.000E09</i></pre>
<pre><i> -0.527168 -0.551126 -0.646804 1.000E09</i></pre>
<pre><i> 0.723852 0.265109 -0.636989 1.000E09</i></pre>
<pre><i> -0.878656 0.262998 -0.398492 1.000E09</i></pre>
<pre><i> -0.286924 0.886166 -0.363848 1.000E09</i></pre>
<pre><i> 0.938309 -0.334647 -0.087105 1.000E09</i></pre>
<pre><i> -0.397842 0.913244 0.087796 1.000E09</i></pre>
<pre><i> -0.085190 -0.635081 -0.767733 1.000E09</i></pre>
<pre><i> 0.307272 0.873671 0.377204 1.000E09</i></pre>
<pre><i> 0.448367 0.003264 -0.893843 1.000E09</i></pre>
<pre><i> 0.000000 0.000000 0.000000 0.000E00</i></pre>
<pre><i> 0.955559 0.060361 -0.288553 1.000E09</i></pre>
<pre><i> -0.157881 -0.866147 0.474197 1.000E09</i></pre>
<pre><i> 0.178264 -0.864319 -0.470292 1.000E09</i></pre>
<pre><i> -0.510729 -0.858184 0.051732 1.000E09</i></pre>
<pre><i> 0.726454 -0.673055 0.138787 1.000E09</i></pre>
<pre><i> -0.059404 0.198388 -0.978322 1.000E09</i></pre>
<pre><i> -0.368122 -0.199753 -0.908067 1.000E09</i></pre>
<pre><i> -0.777683 -0.149878 -0.610528 1.000E09</i></pre>
<pre><i> 0.762668 -0.240762 -0.600309 1.000E09</i></pre>
<pre><i> 0.973096 0.146769 0.177601 1.000E09</i></pre>
<p class="ecxMsoNormal"><i><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";"> </span></i><span style="font-family:"Calibri","sans-serif";">What is the problem? Where am I doing wrong?<br>
Thanks for interest.<br>
<br>
Best regards<br>
Stefania Oliviero</span></p>
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