<div dir="ltr">Hello Hak.<div><br></div><div>You need to register your T1 and your DWI-derived maps. If you did not use some form of geometric distortion correction (<a href="https://github.com/jdtournier/mrtrix3/wiki/Tutorial-DWI-processing">revpe_distcorr</a> or <a href="http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TOPUP">topup</a>, for example), then getting a perfect registration between these two imaging modalities is virtually impossible. However, you can get usable results using a non-linear registration. You can spend months trying to improve your registration, if you want to go down the rabbit hole...</div><div><br></div><div>The trick I most like for this purpose was described by<a href="http://www.ncbi.nlm.nih.gov/pubmed/24814212"> Besson et al</a> and it involves obtaining the partial volume estimation of CSF from your T1 and to that you non-linearly register your ADC map or b=0 image. You can also do this between the white matter PVE estimation from T1 and your FA map. My implementation below, i hope it helps:</div><div><br></div><div><div><br></div><div>echo " STEP: Run FAST on the T1 volume"</div><div>fast -v -S 1 -n 3 -t 1 -I 1 -g -N \</div><div> -o Fast_t1 \</div><div> $t1</div></div><div><br></div><div><div>echo " STEP: Run FLIRT between the t1 CSF map and the ADC map"</div></div><div>flirt \<br></div><div><div> -in Fast_t1_pve_0 \</div><div> -ref $adc \</div><div> -omat ${outbase}_lin.mat \</div><div> -out lin_csf2adc_transformed</div><div><br></div><div>echo " STEP: Non-linear registration with FNIRT"</div><div>my_do_cmd fnirt -v \</div><div> --in=Fast_t1_pve_0 \</div><div> --ref=$adc \</div><div> --fout=${outbase}_field \</div><div> --aff=${outbase}_lin.mat</div><div><br></div><div>echo " STEP: Apply the resulting warp field"</div><div>my_do_cmd applywarp -v \</div><div> -i $t1 \</div><div> -o ${outbase}_t1_to_dwi \</div><div> -r $adc \</div><div> -w ${outbase}_field</div></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div dir="ltr">Dr. Luis Concha<br>Instituto de Neurobiología<br>Laboratorio C-13<br>UNAM, Campus Juriquilla<br>Boulervard Juriquilla 3001<br>Juriquilla, Querétaro.<br>C.P. 76230<br>México<br>Tel (442) 2 38 10 54<br>Fax (442) 2 38 10 46<br><a href="http://personal.inb.unam.mx/lconcha/" target="_blank">http://personal.inb.unam.mx/lconcha/</a><br></div></div></div>
<br><div class="gmail_quote">On Thu, Apr 23, 2015 at 8:09 AM, Hak Fujiyama <span dir="ltr"><<a href="mailto:Hak.Fujiyama@faber.kuleuven.be" target="_blank">Hak.Fujiyama@faber.kuleuven.be</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal">Dear all,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><span lang="EN-US">We got our DWI images through a Philips scanner. This spit out PAR/REC – files. Converting them to .nii could be done in FSL with the PARconv_v1.12 command.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">However, since this is no DICOM format, we were unable to co-register our dwi images to our structural scan in MRTRIX.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">Is there a way to do this? It would be a great help!<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><br>
For now, we’re getting nice tracts but we can’t visualize them because of this dwi/T1 mismatch.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">Many thanks!<span class="HOEnZb"><font color="#888888"><u></u><u></u></font></span></span></p><span class="HOEnZb"><font color="#888888">
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">H.</span><span lang="EN-US" style="font-size:10.0pt;color:black">
<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US"><u></u> <u></u></span></p>
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