<div dir="ltr"><div>Hi Gael,<br><br></div>Beside the stuff in dipy that Elef mentioned, there is another brain image registration package that has slowly developed over the years, and could be useful to you (although it still crucially lacks documentation):<br><br><a href="https://github.com/nipy/nireg">https://github.com/nipy/nireg</a><br><div><br></div><div>This is rigid/affine registration only for the time being and has a BSD license too.<br></div><div><br></div><div>Best,<br><br></div><div>Alexis<br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Aug 21, 2015 at 9:57 AM, GORET Gael 246279 <span dir="ltr"><<a href="mailto:Gael.GORET@cea.fr" target="_blank">Gael.GORET@cea.fr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">





<div link="blue" vlink="purple" lang="FR">
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial","sans-serif"" lang="EN-US">Hi all,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial","sans-serif"" lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial","sans-serif"" lang="EN-US">Thanks for your quick replies,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial","sans-serif"" lang="EN-US">This project is just starting, and there is not too much materials …<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial","sans-serif"" lang="EN-US">However, to answer your questions, I just have created a public repo on my github account :<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial","sans-serif"" lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial","sans-serif"" lang="EN-US"><a href="https://github.com/ggoret/MUDRA" target="_blank"><span style="color:windowtext">https://github.com/ggoret/MUDRA</span></a><span style="color:#1f497d"><u></u><u></u></span></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial","sans-serif"" lang="EN-US"><u></u> <u></u></span></p>
<p><u></u><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"" lang="EN-US"><span>-<span style="font:7.0pt "Times New Roman"">         
</span></span></span><u></u><span style="font-size:11.0pt;font-family:"Arial","sans-serif"" lang="EN-US">In
<span style="color:#7030a0">/doc</span>, I have placed a summary (a pdf slideshow) of the project containing some pictures (and info on instruments)<u></u><u></u></span></p>
<p><span style="font-size:11.0pt;font-family:"Arial","sans-serif"" lang="EN-US"><u></u> <u></u></span></p>
<p><u></u><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"" lang="EN-US"><span>-<span style="font:7.0pt "Times New Roman"">         
</span></span></span><u></u><span style="font-size:11.0pt;font-family:"Arial","sans-serif"" lang="EN-US">In
<span style="color:#7030a0">/examples </span>I have put two data volumes (npy binary file format) the kind of data I need to register.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial","sans-serif"" lang="EN-US"><u></u> <u></u></span></p>
<p><u></u><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"" lang="EN-US"><span>-<span style="font:7.0pt "Times New Roman"">         
</span></span></span><u></u><span style="font-size:11.0pt;font-family:"Arial","sans-serif"" lang="EN-US">In
<span style="color:#7030a0">/mudra </span>a first (naive) try using the Fourier shell correlation as metric
<u></u><u></u></span></p>
<p><span style="font-size:11.0pt;font-family:"Arial","sans-serif"" lang="EN-US">And you can also find
<u></u><u></u></span></p>
<p><u></u><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"" lang="EN-US"><span>-<span style="font:7.0pt "Times New Roman"">         
</span></span></span><u></u><span style="font-size:11.0pt;font-family:"Arial","sans-serif"" lang="EN-US">a Cython wrapping of malik and perona’s algorithms implementation working (pretty quickly) on 3D Volumes :<u></u><u></u></span></p>
<p style="margin-left:72.0pt">
<u></u><span style="font-size:11.0pt;font-family:"Courier New""><span>o<span style="font:7.0pt "Times New Roman"">  
</span></span></span><u></u><span style="font-size:11.0pt;font-family:"Arial","sans-serif";color:#7030a0">/mudra/extensions/non_linear_filtering.pyx
</span><span style="font-size:11.0pt;font-family:"Arial","sans-serif""><u></u><u></u></span></p>
<p><span style="font-size:11.0pt;font-family:"Arial","sans-serif""><u></u> <u></u></span></p>
<p><u></u><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"" lang="EN-US"><span>-<span style="font:7.0pt "Times New Roman"">         
</span></span></span><u></u><span style="font-size:11.0pt;font-family:"Arial","sans-serif"" lang="EN-US">In
<span style="color:#7030a0">/scripts </span>you will find mainly converters simplifying I/O<u></u><u></u></span></p>
<p><u></u><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"" lang="EN-US"><span>-<span style="font:7.0pt "Times New Roman"">         
</span></span></span><u></u><span style="font-size:11.0pt;font-family:"Arial","sans-serif"" lang="EN-US">In
<span style="color:#7030a0">/tools </span>3 very nice visualization tools based on VTK (not mayavi) working as standalone (npy input) :<u></u><u></u></span></p>
<p style="margin-left:72.0pt">
<u></u><span style="font-size:11.0pt;font-family:"Courier New"" lang="EN-US"><span>o<span style="font:7.0pt "Times New Roman"">  
</span></span></span><u></u><span style="font-size:11.0pt;font-family:"Arial","sans-serif";color:#7030a0" lang="EN-US">elevation.py
</span><span style="font-size:11.0pt;font-family:"Arial","sans-serif"" lang="EN-US">-> 2d image to 3d landscape<u></u><u></u></span></p>
<p style="margin-left:72.0pt">
<u></u><span style="font-size:11.0pt;font-family:"Courier New"" lang="EN-US"><span>o<span style="font:7.0pt "Times New Roman"">  
</span></span></span><u></u><span style="font-size:11.0pt;font-family:"Arial","sans-serif";color:#7030a0" lang="EN-US">plan_interpolator.py
</span><span style="font-size:11.0pt;font-family:"Arial","sans-serif"" lang="EN-US">-> 2d slicing of volume + isosurface rendering for given seeds<u></u><u></u></span></p>
<p style="margin-left:72.0pt">
<u></u><span style="font-size:11.0pt;font-family:"Courier New"" lang="EN-US"><span>o<span style="font:7.0pt "Times New Roman"">  
</span></span></span><u></u><span style="font-size:11.0pt;font-family:"Arial","sans-serif";color:#7030a0" lang="EN-US">scalar_field.py
</span><span style="font-size:11.0pt;font-family:"Arial","sans-serif"" lang="EN-US">-> volume rendering (color and opacity gradient)<u></u><u></u></span></p>
<p><span style="font-family:"Arial","sans-serif"" lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial","sans-serif"" lang="EN-US">Thanks in advance for your advices<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial","sans-serif"" lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial","sans-serif"" lang="EN-US">Cheers,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial","sans-serif"" lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial","sans-serif"" lang="EN-US">Gael<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial","sans-serif";color:#1f497d" lang="EN-US"><u></u> <u></u></span></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Arial","sans-serif"">De :</span></b><span style="font-size:10.0pt;font-family:"Arial","sans-serif""> Neuroimaging [mailto:<a href="mailto:neuroimaging-bounces%2Bgael.goret" target="_blank">neuroimaging-bounces+gael.goret</a>=<a href="mailto:cea.fr@python.org" target="_blank">cea.fr@python.org</a>]
<b>De la part de</b> Eleftherios Garyfallidis<br>
<b>Envoyé :</b> jeudi 20 août 2015 16:35<br>
<b>À :</b> Neuroimaging analysis in Python<br>
<b>Objet :</b> Re: [Neuroimaging] 3d registration for data fusion in material science<u></u><u></u></span></p><div><div class="h5">
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif""><u></u> <u></u></span></p>
<div>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif"">Hi Gael,<u></u><u></u></span></p>
<div>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif""><u></u> <u></u></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif"">Sounds exciting. There is no restriction to use our tools in other libraries or domains. <u></u><u></u></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif"">Look at these tutorials please (you need dipy development version)<u></u><u></u></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif""><u></u> <u></u></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif""><a href="https://github.com/nipy/dipy/blob/master/doc/examples/affine_registration_3d.py" target="_blank">https://github.com/nipy/dipy/blob/master/doc/examples/affine_registration_3d.py</a><u></u><u></u></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif""><a href="https://github.com/nipy/dipy/blob/master/doc/examples/syn_registration_2d.py" target="_blank">https://github.com/nipy/dipy/blob/master/doc/examples/syn_registration_2d.py</a><u></u><u></u></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif""><a href="https://github.com/nipy/dipy/blob/master/doc/examples/syn_registration_3d.py" target="_blank">https://github.com/nipy/dipy/blob/master/doc/examples/syn_registration_3d.py</a><u></u><u></u></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif""><u></u> <u></u></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif"">Do you have a github repo of your project? Do you have any example pictures/volumes to show us that you would<u></u><u></u></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif"">like to register? <u></u><u></u></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif""><u></u> <u></u></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif"">Cheers,<u></u><u></u></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif"">Eleftherios<u></u><u></u></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif""><u></u> <u></u></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif""><u></u> <u></u></span></p>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif""><u></u> <u></u></span></p>
<div>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif"">On Thu, Aug 20, 2015 at 9:31 AM, GORET Gael 246279 <<a href="mailto:Gael.GORET@cea.fr" target="_blank">Gael.GORET@cea.fr</a>> wrote:<u></u><u></u></span></p>
<div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif"" lang="EN-US">Hi everybody,
</span><span style="font-family:"Arial","sans-serif""><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif"" lang="EN-US">I am a (French) newcomer, working on the development of the data fusion of Time-of-Flight Secondary Ion Mass Spectrometer
 (ToF-SIMS) and X ray Nano-Tomography (XuM) data at the CEA (the French state institute for energy, high-tech, etc.).
</span><span style="font-family:"Arial","sans-serif""><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif"" lang="EN-US">In terms of samples, we’re a bit far from the neuro-fields … Solid oxide fuel cell, 3D chips, Si/Li matrix, etc., but
 in terms of methodology I hope we have to share … my project is to combine a chemical information (from ToF-SIMS) with X-ray absorption (given by XuM) for a given volume (at nano-scale).  I am tackling a python module aiming to the registration of 3d datasets.
 it seems that nipy includes a such possibility (an a lot more …). </span><span style="font-family:"Arial","sans-serif""><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif"" lang="EN-US">I’m a computer guy, mostly Pythonist and I wander if you would let  me transpose your code (mainly the registration part)
 to my problematic, I would be very grateful for this.</span><span style="font-family:"Arial","sans-serif""><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif"" lang="EN-US">In this context would you have some advice for me ?</span><span style="font-family:"Arial","sans-serif""><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#141414;background:#fcfcff" lang="EN-US">I'm looking forward to hearing from you.</span><span style="font-family:"Arial","sans-serif""><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#141414;background:#fcfcff" lang="EN-US">Gael</span><span style="font-family:"Arial","sans-serif""><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif"" lang="EN-US"> </span><span style="font-family:"Arial","sans-serif""><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif"" lang="EN-US"> </span><span style="font-family:"Arial","sans-serif""><u></u><u></u></span></p>
<table style="border-collapse:collapse" border="0" cellpadding="0" cellspacing="0">
<tbody>
<tr>
<td style="width:77.6pt;padding:0cm 5.4pt 0cm 5.4pt" valign="top" width="103">
<p class="MsoNormal" style="line-height:120%;text-autospace:none">
<span style="font-size:10.0pt;line-height:120%;font-family:"Arial","sans-serif";color:#e60019"><img src="cid:image001.png@01D0DBF3.C1848DD0" height="151" border="0" width="113"></span><span style="font-family:"Arial","sans-serif""><u></u><u></u></span></p>
</td>
<td style="width:399.7pt;padding:0cm 5.4pt 0cm 5.4pt" valign="top" width="533">
<p class="MsoNormal" style="line-height:120%;text-autospace:none">
<b><span style="font-size:10.0pt;line-height:120%;font-family:"Arial","sans-serif";color:#888888">Dr. Gaël Goret</span></b><span style="font-family:"Arial","sans-serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="line-height:120%;text-autospace:none">
<span style="font-size:10.0pt;line-height:120%;font-family:"Arial","sans-serif";color:#888888">Chercheur Postdoctoral</span><span style="font-family:"Arial","sans-serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="line-height:120%;text-autospace:none">
<span style="font-size:8.0pt;line-height:120%;font-family:"Arial","sans-serif";color:#888888">Département des Technologies Silicium</span><span style="font-family:"Arial","sans-serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="line-height:120%;text-autospace:none">
<b><span style="font-size:8.0pt;line-height:120%;font-family:"Arial","sans-serif";color:#888888">S</span></b><span style="font-size:8.0pt;line-height:120%;font-family:"Arial","sans-serif";color:#888888">ervice de
<b>C</b>aractérisation des <b>M</b>atériaux & <b>C</b>omposants</span><span style="font-family:"Arial","sans-serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="line-height:120%;text-autospace:none">
<span style="font-size:8.0pt;line-height:120%;font-family:"Arial","sans-serif";color:#888888"><img src="cid:image002.jpg@01D0DBF3.C1848DD0" height="5" border="0" width="322"></span><span style="font-family:"Arial","sans-serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="line-height:120%;text-autospace:none">
<span style="font-size:8.0pt;line-height:120%;font-family:"Arial","sans-serif";color:#888888">Commissariat à l’énergie atomique et aux énergies alternatives</span><span style="font-family:"Arial","sans-serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="line-height:120%;text-autospace:none">
<span style="font-size:8.0pt;line-height:120%;font-family:"Arial","sans-serif";color:#888888">MINATEC Campus
</span><b><span style="font-size:8.0pt;line-height:120%;font-family:"Arial","sans-serif";color:#91c30a">|</span></b><span style="font-size:8.0pt;line-height:120%;font-family:"Arial","sans-serif";color:#888888"> 17 rue des martyrs
</span><b><span style="font-size:8.0pt;line-height:120%;font-family:"Arial","sans-serif";color:#91c30a">|</span></b><span style="font-size:8.0pt;line-height:120%;font-family:"Arial","sans-serif";color:#888888"> F-38054 Grenoble Cedex</span><span style="font-family:"Arial","sans-serif""><u></u><u></u></span></p>
<p class="MsoNormal" style="line-height:120%;text-autospace:none">
<span style="font-size:8.0pt;line-height:120%;font-family:"Arial","sans-serif";color:#888888">T. +33 (0)4 38 7<b>8 49 29
</b></span><b><span style="font-size:8.0pt;line-height:120%;font-family:"Arial","sans-serif";color:#91c30a">|
</span></b><span style="font-size:8.0pt;line-height:120%;font-family:"Arial","sans-serif";color:black"><a href="mailto:gael.goret@cea.fr" target="_blank"><span style="color:#91c30a">gael.goret@cea.fr</span></a></span><span style="font-family:"Arial","sans-serif""><u></u><u></u></span></p>
</td>
</tr>
</tbody>
</table>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif""> <u></u><u></u></span></p>
</div>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-family:"Arial","sans-serif""><br>
_______________________________________________<br>
Neuroimaging mailing list<br>
<a href="mailto:Neuroimaging@python.org" target="_blank">Neuroimaging@python.org</a><br>
<a href="https://mail.python.org/mailman/listinfo/neuroimaging" target="_blank">https://mail.python.org/mailman/listinfo/neuroimaging</a><u></u><u></u></span></p>
</div>
<p class="MsoNormal"><span style="font-family:"Arial","sans-serif""><u></u> <u></u></span></p>
</div>
</div></div></div>
</div>

<br>_______________________________________________<br>
Neuroimaging mailing list<br>
<a href="mailto:Neuroimaging@python.org">Neuroimaging@python.org</a><br>
<a href="https://mail.python.org/mailman/listinfo/neuroimaging" rel="noreferrer" target="_blank">https://mail.python.org/mailman/listinfo/neuroimaging</a><br>
<br></blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature">Lead Clinical Research<br>Advanced Clinical Imaging Technology<br>Siemens/CHUV/EPFL<br>1015 Lausanne, Switzerland<br>Phone: +41 21 545 9972<br><a href="https://sites.google.com/site/alexisroche" target="_blank">https://sites.google.com/site/alexisroche</a></div>
</div>