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<div>One of the nice things about the mrtrix pipeline is that it's not a black box solution, but that it allows you to inspect the outcome of each individual processing step using mrview.</div>
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<div>Doing so, you will probably notice two things:</div>
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<div>1) your "brain mask" is probably very poor as the brain mask example in the manual is designed with _brain_ data in mind and not a synthetic phantom</div>
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<div>2) the fiber cup phantom has _no_ fibrous voxels with FA > 0.7, so your single fiber mask at best will be completely empty, which is exactly what estimate_response is telling you</div>
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<div id="divRpF827838" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> mrtrix-discussion-bounces@public.nitrc.org [mrtrix-discussion-bounces@public.nitrc.org] on behalf of Jesse Ross-Jones [jesse.rj@gmail.com]<br>
<b>Sent:</b> 07 May 2013 11:55<br>
<b>To:</b> mrtrix-discussion@public.nitrc.org<br>
<b>Subject:</b> [Mrtrix-discussion] FiberCup Phantom Spherical Deconvolution<br>
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<div>Dear MRtrix users/Devs,<br>
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<div>I am trying to use the spherical deconvolution method in MRtrix to calculate the tracts in the FiberCup phantom available here:
<a href="http://www.lnao.fr/spip.php?rubrique79" target="_blank">http://www.lnao.fr/spip.php?rubrique79</a>. I am running the commands listed below, but am unable to successfully run
<b>estimate_response</b>. Instead of showing the progress bar to 100% I simply get:
<span style="color:rgb(69,129,142)"><span style="color:rgb(204,0,0)">estimate_response: estimating response function... - ok<br>
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<div><span style="color:rgb(69,129,142)"><span style="color:rgb(204,0,0)"><font color="#000000">Do I need to modify some of the parameters or alter my approach in order to incorporate the separate gradients?<br>
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<div><span style="color:rgb(69,129,142)"><span style="color:rgb(204,0,0)"><font color="#000000">Many thanks for the help,<br>
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<div><span style="color:rgb(69,129,142)"><span style="color:rgb(204,0,0)"><font color="#000000">Jesse<br>
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the list of commands I am running are basically the default (except for using -grad to provide the modified gradient values):<br>
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<span style="color:rgb(69,129,142)"><b>mrconvert </b>\FiberCup\6x6x6\dwi-b2650.nii dwi.mif<br>
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<b>average </b>dwi.mif -axis 3 - | threshold - - | median3D - - | median3D - mask.mif<br>
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<b>dwi2tensor </b>dwi.mif -grad diffusion_directions_corrected_2650.txt dt.mif<br>
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<b>tensor2FA </b>dt.mif - | mrmult - mask.mif fa.mif<br>
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<b>tensor2vector </b>dt.mif - | mrmult - fa.mif ev.mif<br>
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<b>erode </b>mask.mif -npass 3 - | mrmult fa.mif - - | threshold - -abs 0.7 sf.mif<br>
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<b>estimate</b>_<b>response </b>dwi.mif sf.mif -grad diffusion_directions_corrected_2650.txt response.txt<br>
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<b>csdeconv </b>dwi.mif response.txt -lmax 8 -mask mask.mif CSD8.mif<br>
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<b>streamtrack </b>SD_PROB CSD8.mif -seed seed.mif -mask mask.mif cst_csd.tck</span><br>
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A sample from diffusion_directions_corrected_2650.txt:<br>
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<table border="0" cellspacing="0" cols="4">
<colgroup width="71"></colgroup><colgroup span="3" width="79"></colgroup>
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<td align="RIGHT" height="17">0</td>
<td align="RIGHT">0</td>
<td align="RIGHT">0</td>
<td align="RIGHT">0</td>
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<td align="RIGHT" height="17">1</td>
<td align="RIGHT">0</td>
<td align="RIGHT">0</td>
<td align="RIGHT">2650</td>
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<td align="RIGHT" height="17">0</td>
<td align="RIGHT">-0.987414</td>
<td align="RIGHT">-0.158158</td>
<td align="RIGHT">2650</td>
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<td align="RIGHT" height="17">-0.026007</td>
<td align="RIGHT">-0.761231</td>
<td align="RIGHT">0.64796</td>
<td align="RIGHT">2650</td>
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The problem I run into is running <b>estimate_response </b>(following is the output -debug):<br>
<span style="color:rgb(69,129,142)"><b>estimate_response </b>dwi.mif sf.mif -grad diffusion_directions_corrected_2650.txt response.txt -debug<br>
estimate_response [DEBUG]: reading key/value file "C:\mrtrix.conf"...<br>
estimate_response [INFO]: opening image "dwi.mif"...<br>
estimate_response [DEBUG]: reading key/value file ".\dwi.mif"...<br>
estimate_response [DEBUG]: sanitising transformation matrix...<br>
estimate_response [DEBUG]: preparing file ".\dwi.mif"<br>
estimate_response [DEBUG]: setting up image "dwi.mif"...<br>
estimate_response [DEBUG]: sanitising transformation matrix...<br>
estimate_response [DEBUG]: setting up data increments for "dwi.mif"...<br>
estimate_response [DEBUG]: data increments initialised with start = 0, stride =<br>
[ 1 64 -4096 4096 ]<br>
estimate_response [INFO]: opening image "sf.mif"...<br>
estimate_response [DEBUG]: reading key/value file ".\sf.mif"...<br>
estimate_response [DEBUG]: sanitising transformation matrix...<br>
estimate_response [DEBUG]: preparing file ".\sf.mif"<br>
estimate_response [DEBUG]: setting up image "sf.mif"...<br>
estimate_response [DEBUG]: sanitising transformation matrix...<br>
estimate_response [DEBUG]: setting up data increments for "sf.mif"...<br>
estimate_response [DEBUG]: data increments initialised with start = 0, stride =<br>
[ 1 64 -4096 ]<br>
estimate_response [INFO]: found 65x4 diffusion-weighted encoding<br>
estimate_response [INFO]: found b=0 images in studies [ 0 ]<br>
estimate_response [INFO]: found 64 diffusion-weighted directions<br>
estimate_response [INFO]: calculating even spherical harmonic components up to o<br>
rder 8<br>
estimate_response [DEBUG]: mapping image "dwi.mif"...<br>
estimate_response [DEBUG]: file ".\dwi.mif" mapped at 0x21e0000, size 532750 (re<br>
ad-only)<br>
estimate_response [DEBUG]: data mapper for image "dwi.mif" mapped with segment s<br>
ize = 266240<br>
estimate_response [DEBUG]: mapping image "sf.mif"...<br>
estimate_response [DEBUG]: file ".\sf.mif" mapped at 0x3d0000, size 768 (read-on<br>
ly)<br>
estimate_response [DEBUG]: data mapper for image "sf.mif" mapped with segment si<br>
ze = 4096<br>
<span style="color:rgb(204,0,0)">estimate_response [INFO]: found 0 single-fibre voxels<br>
estimate_response: estimating response function... - ok</span><br>
<span style="color:rgb(204,0,0)">estimate_response [INFO]: estimated response SH coefficients: [ nan nan nan nan<br>
nan ]</span><br>
estimate_response [INFO]: closing image "dwi.mif"...<br>
estimate_response [DEBUG]: unmapping file ".\dwi.mif"<br>
estimate_response [INFO]: closing image "sf.mif"...<br>
estimate_response [DEBUG]: unmapping file ".\sf.mif"</span><br>
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