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<p><font size="3" face="Calibri"><span style="font-size:12pt;"><font color="black" face="Calibri,Arial,Helvetica,sans-serif"><span style="background-color:white;"><font color="#282828">Hi All,
<br>
I have a question about the option drawncrosssection of command datasynth.</font></span></font></span></font></p>
<p><font size="3" face="Calibri"><span style="font-size:12pt;"><font color="black" face="Calibri,Arial,Helvetica,sans-serif"><span style="background-color:white;"><font color="#282828"><br>
</font></span></font></span></font></p>
<p><font size="3" face="Calibri"><span style="font-size:12pt;"><font color="black" face="Calibri,Arial,Helvetica,sans-serif"><span style="background-color:white;"><font color="#282828">If I run the command:<br>
</font></span></font></span></font></p>
<p><font size="3" face="Calibri"><span style="font-size:12pt;"><font color="black" face="Calibri,Arial,Helvetica,sans-serif"><span style="background-color:white;"><font color="#282828"><br>
</font></span></font></span></font></p>
<p><font size="3" face="Calibri"><span style="font-size:12pt;"><font color="black" face="Calibri,Arial,Helvetica,sans-serif"><span style="background-color:white;"><font color="#282828"></p>
<p><font size="3" face="Calibri"><span style="font-size:12pt;"><font color="black" face="Calibri,Arial,Helvetica,sans-serif"><span style="background-color:white;"><font color="#282828"><span><span>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
</span><br>
</span></font></span></font></span></font></p>
<p><font size="3" face="Calibri"><span style="font-size:12pt;"><font color="black" face="Calibri,Arial,Helvetica,sans-serif"><span style="background-color:white;"><font color="#282828"><span><br>
</span></font></span></font></span></font></p>
<font size="3" face="Calibri"><span style="font-size:12pt;"><font color="black" face="Calibri,Arial,Helvetica,sans-serif"><span style="background-color:white;"><font color="#282828"><span>I do not obtain any file .gray</span></font></span></font></span></font><br>
</font></span></font></span></font>
<p></p>
<p><font size="3" face="Calibri"><span style="font-size:12pt;"><font color="black" face="Calibri,Arial,Helvetica,sans-serif"><span style="background-color:white;"><font color="#282828"><font size="3" face="Calibri"><span style="font-size:12pt;"><font color="black" face="Calibri,Arial,Helvetica,sans-serif"><span style="background-color:white;"><font color="#282828"><span>while,
if I change the substrate and run the command:</span></font></span></font></span></font><br>
</font></span></font></span></font></p>
<p><font size="3" face="Calibri"><span style="font-size:12pt;"><font color="black" face="Calibri,Arial,Helvetica,sans-serif"><span style="background-color:white;"><font color="#282828"><br>
</font></span></font></span></font></p>
<p><font size="3" face="Calibri"><span style="font-size:12pt;"><font color="black" face="Calibri,Arial,Helvetica,sans-serif"><span style="background-color:white;"></span></font></span></font><font size="3" face="Calibri"><span style="font-size:12pt;"><font color="black" face="Calibri,Arial,Helvetica,sans-serif"><span style="background-color:white;"><font color="#282828"><span>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
<br>
</span></font></span></font></span></font></p>
<p><font size="3" face="Calibri"><span style="font-size:12pt;"><font color="black" face="Calibri,Arial,Helvetica,sans-serif"><span style="background-color:white;"><font color="#282828"><span><br>
</span></font></span></font></span></font></p>
<p><font size="3" face="Calibri"><span style="font-size:12pt;"><font color="black" face="Calibri,Arial,Helvetica,sans-serif"><span style="background-color:white;"><font color="#282828"><span>I obtain a file .gray</span></font></span></font></span></font></p>
<p><font size="3" face="Calibri"><span style="font-size:12pt;"><font color="black" face="Calibri,Arial,Helvetica,sans-serif"><span style="background-color:white;"><font color="#282828"><span><br>
</span></font></span></font></span></font></p>
<p><font size="3" face="Calibri"><span style="font-size:12pt;"><font color="black" face="Calibri,Arial,Helvetica,sans-serif"><span style="background-color:white;"><font color="#282828"><span>What is the problem in the first command?
<br>
</span></font></span></font></span></font></p>
<p><font size="3" face="Calibri"><span style="font-size:12pt;"><font color="black" face="Calibri,Arial,Helvetica,sans-serif"><span style="background-color:white;"><font color="#282828"><span>Does option drawncrossssection work only with inflammation substrate?<br>
</span></font></span></font></span></font></p>
<p><font size="3" face="Calibri"><span style="font-size:12pt;"><font color="black" face="Calibri,Arial,Helvetica,sans-serif"><span style="background-color:white;"><font color="#282828"><span><br>
</span></font></span></font></span></font></p>
<p><font size="3" face="Calibri"><span style="font-size:12pt;"><font color="black" face="Calibri,Arial,Helvetica,sans-serif"><span style="background-color:white;"><font color="#282828"><span> </span></font></span></font></span></font><br>
</p>
<font size="3" face="Calibri"><span style="font-size:12pt;"><font color="black" face="Calibri,Arial,Helvetica,sans-serif"><span style="background-color:white;"><font color="#282828">Thanks a lot</font></span></font></span></font><br>
<font size="3" face="Calibri"><span style="font-size:12pt;"><font color="black" face="Calibri,Arial,Helvetica,sans-serif"><span style="background-color:white;"></span></font></span></font>
<p><font size="3" face="Calibri"><span style="font-size:12pt;"><font color="black" face="Calibri,Arial,Helvetica,sans-serif"><span style="background-color:white;"><font color="#282828">Cheers<br>
<br>
Stefania Oliviero<br>
ITAB, Università degli Studi G. d'Annunzio di Chieti</font></span></font></span></font><br>
</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>Da:</b> camino-users-bounces@www.nitrc.org <camino-users-bounces@www.nitrc.org> per conto di stefania oliviero <stefania.oliviero@hotmail.it><br>
<b>Inviato:</b> lunedì 24 marzo 2014 10.35.24<br>
<b>A:</b> Ferizi, Uran; camino-users@www.nitrc.org<br>
<b>Oggetto:</b> Re: [Camino-users] schemefile generation -problem is solved</font>
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<div dir="ltr">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<br>
<div>
<hr id="stopSpelling">
From: uran.ferizi.10@ucl.ac.uk<br>
To: stefania.oliviero@hotmail.it; camino-users@www.nitrc.org<br>
Subject: RE: [Camino-users] schemefile generation<br>
Date: Mon, 24 Mar 2014 08:39:47 +0000<br>
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<div style="font-size:12pt;color:#000000;background-color:#FFFFFF;font-family:Calibri,Arial,Helvetica,sans-serif;">
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>ST_scheme=[directions; |G|; DELTA; delta TE];</em><br>
you can write it out via:<br>
<br>
<br>
<em>scheme_str=strcat('data.scheme');</em><br>
<em>dlmwrite(scheme_str, ST_scheme, 'delimiter', ' ', 'precision', '%.6f');</em><br>
<em>% write first line</em><br>
<em>dlmwrite('output.txt', 'VERSION: STEJSKALTANNER', 'delimiter', '');</em><br>
<em>% append rest of file</em><br>
<em>dlmwrite('output.txt', fileread(scheme_str), '-append', 'delimiter', '');</em><br>
<em>% overwrite on original file</em><br>
<em>movefile('output.txt', scheme_str);</em><br>
<br>
<br>
<br>
<br>
<div style="color:rgb(40, 40, 40);">
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<div id="ecxdivRplyFwdMsg" dir="ltr"><font style="font-size:11pt;" color="#000000" face="Calibri, sans-serif"><b>From:</b> camino-users-bounces@www.nitrc.org <camino-users-bounces@www.nitrc.org> on behalf of stefania oliviero <stefania.oliviero@hotmail.it><br>
<b>Sent:</b> 24 March 2014 7:35 AM<br>
<b>To:</b> camino-users@www.nitrc.org<br>
<b>Subject:</b> [Camino-users] schemefile generation</font>
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<div dir="ltr">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. <br>
<pre class="ecxescaped">VERSION: BVECTOR
nx_1 ny_1 nz_1 b1</pre>
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<br>
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