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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Hi Stephania,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">The drawcrosssection switch as you’ve used it there only works with the distributed radius substrates. The fixed radius substrates
are so simple that we didn’t think anyone would need it! With a single radius, hexagonal packing, and a given cylinder separation the substrate is pretty easy to visualise with something like matlab – you just get a cylinder of radius r at each corner of repeating
equilateral triangles with sides length 2R.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Cheers,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Matt.
<o:p></o:p></span></p>
<p class="MsoNormal"><a name="_MailEndCompose"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></a></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",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> 03 April 2017 13:37<br>
<b>To:</b> camino-users@www.nitrc.org<br>
<b>Subject:</b> Re: [Camino-users] schemefile generation -problem is solved<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#282828;background:white">Hi All,
<br>
I have a question about the option drawncrosssection of command datasynth.</span><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#282828;background:white">If I run the command:</span><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#282828;background:white">datasynth -walkers ${WALKERS} -tmax ${TIMESTEPS} -substrate cylinder -packing hex -cylinderrad 1E-6 -cylindersep 2.1E-6 -voxels 1 -p 0.0 -schemefile ${SCHEMEFILE}
-initial uniform -diffusivity ${DIFF} -substrateinfo -drawcrosssection ${FNAME}.gray > ${OUTPUTDIR}/${FNAME}.Bfloat 2> ${FNAME}.txt
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#282828;background:white"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#282828;background:white">I do not obtain any file .gray</span><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#282828;background:white">while, if I change the substrate and run the command:</span><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#282828;background:white">datasynth -walkers ${WALKERS} -tmax ${TIMESTEPS} -geometry inflammation -numcylinders ${NUMCYL} -p 0 -initial uniform -seed ${INT_rnd} -voxels 1 -increments 1
-separateruns -latticesize ${LATSIZE} -schemefile ${SCHEMEFILE} -gamma ${GAMA} ${GAMB} -diffusivity ${DIFF} -substrateinfo -drawcrosssection ${FNAME}.gray > ${OUTPUTDIR}/${FNAME} 2> ${FNAME}.txt
</span><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#282828;background:white">I obtain a file .gray</span><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#282828;background:white">What is the problem in the first command?
</span><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#282828;background:white">Does option drawncrossssection work only with inflammation substrate?</span><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#282828;background:white"> </span><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#282828;background:white">Thanks a lot</span><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif;color:#282828;background:white">Cheers<br>
<br>
Stefania Oliviero<br>
ITAB, Università degli Studi G. d'Annunzio di Chieti</span><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">Da:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">
<a href="mailto:camino-users-bounces@www.nitrc.org">camino-users-bounces@www.nitrc.org</a> <<a href="mailto:camino-users-bounces@www.nitrc.org">camino-users-bounces@www.nitrc.org</a>> per conto di stefania oliviero <<a href="mailto:stefania.oliviero@hotmail.it">stefania.oliviero@hotmail.it</a>><br>
<b>Inviato:</b> lunedì 24 marzo 2014 10.35.24<br>
<b>A:</b> Ferizi, Uran; <a href="mailto:camino-users@www.nitrc.org">camino-users@www.nitrc.org</a><br>
<b>Oggetto:</b> Re: [Camino-users] schemefile generation -problem is solved</span><span style="font-family:"Calibri",sans-serif">
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Calibri",sans-serif">Hi Uran,<br>
Thank you so much! <br>
I did not know Stejskal-Tanner version of schemefile and now the problem is solved.<br>
<br>
Cheers <br>
Stefania Oliviero<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-family:"Calibri",sans-serif">From:
<a href="mailto:uran.ferizi.10@ucl.ac.uk">uran.ferizi.10@ucl.ac.uk</a><br>
To: <a href="mailto:stefania.oliviero@hotmail.it">stefania.oliviero@hotmail.it</a>;
<a href="mailto:camino-users@www.nitrc.org">camino-users@www.nitrc.org</a><br>
Subject: RE: [Camino-users] schemefile generation<br>
Date: Mon, 24 Mar 2014 08:39:47 +0000<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt;background:white"><span style="font-family:"Calibri",sans-serif;color:black">Hello Stefania,<br>
<br>
<br>
If you asked about how to write a Stejskal-Tanner scheme file, which is a text file, you could use Matlab.<br>
<br>
<br>
After constructing the matrix, e.g.: <br>
<em><span style="font-family:"Calibri",sans-serif">ST_scheme=[directions; |G|; DELTA; delta TE];</span></em><br>
you can write it out via:<br>
<br>
<br>
<em><span style="font-family:"Calibri",sans-serif">scheme_str=strcat('data.scheme');</span></em><br>
<em><span style="font-family:"Calibri",sans-serif">dlmwrite(scheme_str, ST_scheme, 'delimiter', ' ', 'precision', '%.6f');</span></em><br>
<em><span style="font-family:"Calibri",sans-serif">% write first line</span></em><br>
<em><span style="font-family:"Calibri",sans-serif">dlmwrite('output.txt', 'VERSION: STEJSKALTANNER', 'delimiter', '');</span></em><br>
<em><span style="font-family:"Calibri",sans-serif">% append rest of file</span></em><br>
<em><span style="font-family:"Calibri",sans-serif">dlmwrite('output.txt', fileread(scheme_str), '-append', 'delimiter', '');</span></em><br>
<em><span style="font-family:"Calibri",sans-serif">% overwrite on original file</span></em><br>
<em><span style="font-family:"Calibri",sans-serif">movefile('output.txt', scheme_str);</span></em><br>
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<br>
<br>
<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black">
<a href="mailto:camino-users-bounces@www.nitrc.org">camino-users-bounces@www.nitrc.org</a> <<a href="mailto:camino-users-bounces@www.nitrc.org">camino-users-bounces@www.nitrc.org</a>> on behalf of stefania oliviero <<a href="mailto:stefania.oliviero@hotmail.it">stefania.oliviero@hotmail.it</a>><br>
<b>Sent:</b> 24 March 2014 7:35 AM<br>
<b>To:</b> <a href="mailto:camino-users@www.nitrc.org">camino-users@www.nitrc.org</a><br>
<b>Subject:</b> [Camino-users] schemefile generation</span><span style="font-family:"Calibri",sans-serif;color:#282828">
<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Calibri",sans-serif;color:#282828"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Calibri",sans-serif;color:#282828">Hi All,
<br>
I have a question about the generation of a schemefile. I have an acquisition scheme like this:<br>
<br>
nx ny nz delta DELTA G TE<br>
<br>
0 0 0 0 0 0 30<br>
5 10 0 8 20 80 50<br>
... <br>
<br>
with nx, ny and nz as gradient directions. <br>
How can I report all these information in a scheme file? I would like to explicit in the file.scheme the values of delta, DELTA, G and TE. Which schemefile version can I use, please?<br>
The only scheme file version explained in the DTI tutorial is the BVECTOR one. <o:p>
</o:p></span></p>
<pre style="background:white"><span style="color:#282828">VERSION: BVECTOR<o:p></o:p></span></pre>
<pre style="background:white"><span style="color:#282828">nx_1 ny_1 nz_1 b1<o:p></o:p></span></pre>
<p class="MsoNormal" style="background:white"><span style="font-family:"Calibri",sans-serif;color:#282828">Thanks a lot<br>
Cheers<br>
<br>
Stefania Oliviero<br>
Università degli Studi di Napoli Federico II<br>
ITAB, Università degli Studi G. d'Annunzio di Chieti<o:p></o:p></span></p>
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