Bryce<br><br>Normally I'd leave this one to Donald, b<span style="font-family:arial,helvetica,sans-serif">ut he's off sippi</span>ng wine somewhere.<br><br>This appears to be a small glitch that managed to sneak its way into version 0.2.10. It will not cause any problems other than the unnecessary error message.<br>
<br>If you want to get rid of the message, you can make the following change to the source code.<br>In the file cmd/disp_profile.cpp, line 130 reads:<br><pre class=""><span class=""></span><span class="">if</span><span class=""> </span><span class="">(</span><span class="">values</span><span class="">.</span><span class="">columns</span><span class="">()</span><span class=""> </span><span class="">!=</span><span class=""> guint </span><span class="">(</span><span class="">DWI</span><span class="">::</span><span class="">SH</span><span class="">::</span><span class="">NforL</span><span class=""> </span><span class="">(</span><span class="">lmax</span><span class="">)))</span><span class=""> </span><span class="">{<br>
<br>change it to:<br></span><br><span class="">if</span><span class=""> </span><span class="">(!</span><span class="">is_response </span><span class="">&&</span><span class=""> values</span><span class="">.</span><span class="">columns</span><span class="">()</span><span class=""> </span><span class="">!=</span><span class=""> guint </span><span class="">(</span><span class="">DWI</span><span class="">::</span><span class="">SH</span><span class="">::</span><span class="">NforL</span><span class=""> </span><span class="">(</span><span class="">lmax</span><span class="">)))</span><span class=""> </span><span class="">{</span><span class=""><span style="font-family:arial,helvetica,sans-serif"><br>
<br><br>In case you're curious as to what's going on:<br>The disp_profile command can display the profiles of both spherical harmonic (e.g. diffusion signal profiles, Fibre Orientation Distributions) and rotational harmonics (e.g. single-fibre response function). The -response option you provided is supposed to tell the program that the text file you are feeding it contains the latter rather than the former. In the 0.2.10 code, the program erroneously ignores this information, but subsequently figures it out itself (based on the number of coefficients in the text file); hence the erroneous error message telling you what you already know.<br>
<br>Best regards<br>Rob<br></span></span></pre><div class="gmail_extra"><br clear="all"><div><br>--<br><br>Robert Smith<br>PhD Candidate <br><br>The Florey Institute of Neuroscience and Mental Health<br>Melbourne Brain Centre - Austin Campus<br>
245 Burgundy Street<br>Heidelberg Vic 3084<br>Ph: +61 3 9035 7128<br>Fax: +61 3 9035 7301<br><a href="http://www.florey.edu.au" target="_blank">www.florey.edu.au</a><br><span style="font-size:9pt;font-family:"Times New Roman","serif";color:red"></span></div>
<br>
<br><br><div class="gmail_quote">On Sat, Dec 1, 2012 at 9:43 AM, Bryce Wilkins <span dir="ltr"><<a href="mailto:brycewil@usc.edu" target="_blank">brycewil@usc.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
Dear mrTrix community,<br>
<br>
I am currently running mrTrix 0.2.10 (mrtrix-0.2.10_2012-02-10) on
Linux and repeatedly encounter the error message:<br>
<br>
<tt><b>disp_profile: unexpected number of SH coefficients - assuming
response function</b></tt><br>
<br>
when I run the following command to plot the estimated single fiber
response function:<br>
<br>
<tt><b>disp_profile -response sf_response.txt</b></tt><br>
<br>
I have followed the documentation, specifically "Data
pre-processing" section, where it describes how to generate a
single-fiber mask, and call <b><tt>estimate_response</tt></b> to
determine the SH coefficients for the single fiber. I edited a
custom single-fiber mask, based on FA levels, and ensured that all
voxels in the mask were in white matter regions, and not be voxels
of erroneous FA values (e.g. FA > 1). <br>
<br>
Examples from two of my <tt><b>sf_response.txt</b></tt> files are:<br>
<br>
<tt>1862.36 -570.495 84.5122 -8.29821 0.629007</tt><br>
<br>
<tt>1296.21 -909.403 383.255 -116.241 28.1946</tt><br>
<br>
These values seem consistent with what is described in the
documentation. So, I find it very odd that I am receiving the above
error message. Furthermore, even though the error appears, the
actual SH profile displayed changes (i.e. it doesn't seem to assume
and then load a default response function as the error states).<br>
<br>
Can anyone explain what is causing the <tt><b>disp_profile</b></tt>
error above? May be the outputting of the error message is the
error itself? Can anyone check <tt><b>disp_profile -response</b></tt>
using the values I have listed above. What are your outcomes?<br>
<br>
Thank-you researchers!<span class="HOEnZb"><font color="#888888"><br>
Bryce<br>
<br>
</font></span></div>
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<br></blockquote></div><br></div>