<div dir="ltr">Hi,<div><br></div><div>well, it doesn't work for me. I am just trying to load a Nifti (.nii) image:</div><div><br></div><div><pre style="overflow:auto;font-size:14px;padding:0px;margin-top:0px;margin-bottom:0px;line-height:17.0000591278076px;word-wrap:break-word;color:rgb(0,0,0);border:0px;border-radius:0px;white-space:pre-wrap;vertical-align:baseline"><span class="" style="color:rgb(70,130,180)"><span class="" style="color:rgb(0,100,0)">dwiImg <span class="" style="color:rgb(196,160,0)">=</span> sitk<span class="" style="color:rgb(196,160,0)">.</span>ReadImage<span class="" style="color:rgb(196,160,0)">(</span>glob<span class="" style="color:rgb(196,160,0)">.</span>glob<span class="" style="color:rgb(196,160,0)">(</span>dataPath<span class="" style="color:rgb(196,160,0)">+</span><span class="" style="color:rgb(0,0,139)">'/*DWI*/*.nii'</span><span class="" style="color:rgb(196,160,0)">)</span><span class="" style="color:rgb(196,160,0)">)</span></span></span></pre></div><div><br></div><div>when getting the error. Reinstallation didn't help either. There is nothing special about these files. It's MRIs.</div><div><br></div><div><pre style="overflow:auto;font-size:14px;padding:0px;margin-top:0px;margin-bottom:0px;line-height:17.0000591278076px;word-wrap:break-word;color:rgb(0,0,0);border:0px;border-radius:0px;white-space:pre-wrap;vertical-align:baseline"><span class="" style="color:rgb(70,130,180)"><span class="" style="color:rgb(0,100,0)"><span class="">home/tjklein/anaconda/envs/sitkpy/lib/python2.7/site-packages/SimpleITK/SimpleITK.py</span> in <span class="" style="color:rgb(70,130,180)">ReadImage<span class="" style="color:rgb(0,0,139)">(*args)</span>
<span class="" style="color:rgb(0,100,0)"> 7726</span> <span class="" style="color:rgb(196,160,0)"></span>
<span class="" style="color:rgb(0,100,0)"> 7727</span> """
<span class="" style="color:rgb(0,100,0)">-> 7728<span class="" style="color:rgb(196,160,0)"> <span class="" style="color:rgb(0,100,0)">return</span> _SimpleITK<span class="">.</span>ReadImage<span class="">(</span><span class="">*</span>args<span class="">)</span><span class=""></span>
<span class="" style="color:rgb(0,100,0)"> 7729</span> <span class="" style="color:rgb(0,100,0)">class</span> HashImageFilter<span class="">(</span>ProcessObject<span class="">)</span><span class="">:</span><span class=""></span>
<span class="" style="color:rgb(0,100,0)"> 7730</span> """
<span class="" style="color:rgb(139,0,0)">RuntimeError</span>: Exception thrown in SimpleITK ReadImage: /home/blowekamp/anaconda/conda-bld/work/Code/IO/src/sitkImageSeriesReader.cxx:143:
sitk::ERROR: The file in the series have unsupported 3 dimensions.</span></span></span></span></span></pre></div><div><br></div><div><br></div><div>Thanks,</div><div> Tassilo</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sat, Aug 29, 2015 at 11:12 AM, Bradley Lowekamp <span dir="ltr"><<a href="mailto:blowekamp@mail.nih.gov" target="_blank">blowekamp@mail.nih.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hello,<div><br></div><div>That is great you got SimpleITK up and running by following those updated instructions for Anaconda.</div><div><br></div><div>Could you describe what you are trying to do and have a snippet of code?</div><div><br></div><div>Brad</div><div><br></div><div><div><div><div class="h5"><div>On Aug 28, 2015, at 6:52 PM, Tassilo Klein <<a href="mailto:tjklein@gmail.com" target="_blank">tjklein@gmail.com</a>> wrote:</div><br></div></div><blockquote type="cite"><div><div class="h5"><div dir="ltr">Thanks Ziv,<div><br></div><div>I forgot to activate the environment before.</div><div><br></div><div>After following the steps, now I get a different error when trying to load an image, which worked some time before:</div><div><br></div><div><pre style="overflow:auto;font-size:14px;padding:0px;margin-top:0px;margin-bottom:0px;line-height:17.0000591278076px;word-wrap:break-word;border:0px;border-top-left-radius:0px;border-top-right-radius:0px;border-bottom-right-radius:0px;border-bottom-left-radius:0px;white-space:pre-wrap;vertical-align:baseline"><span style="color:rgb(70,130,180)"><span style="color:rgb(0,100,0)"><span>/home/tjklein/anaconda/envs/sitkpy3/lib/python2.7/site-packages/SimpleITK/SimpleITK.py</span> in <span style="color:rgb(70,130,180)">ReadImage<span style="color:rgb(0,0,139)">(*args)</span>
<span style="color:rgb(0,100,0)"> 7726</span> <span style="color:rgb(196,160,0)"></span>
<span style="color:rgb(0,100,0)"> 7727</span> """
<span style="color:rgb(0,100,0)">-> 7728<span style="color:rgb(196,160,0)"> <span style="color:rgb(0,100,0)">return</span> _SimpleITK<span>.</span>ReadImage<span>(</span><span>*</span>args<span>)</span><span></span>
<span style="color:rgb(0,100,0)"> 7729</span> <span style="color:rgb(0,100,0)">class</span> HashImageFilter<span>(</span>ProcessObject<span>)</span><span>:</span><span></span>
<span style="color:rgb(0,100,0)"> 7730</span> """
<span style="color:rgb(139,0,0)">RuntimeError</span>: Exception thrown in SimpleITK ReadImage: /home/blowekamp/anaconda/conda-bld/work/Code/IO/src/sitkImageSeriesReader.cxx:143:
sitk::ERROR: The file in the series have unsupported 3 dimensions.
</span></span></span></span></span></pre></div><div><span style="color:rgb(70,130,180)"><span style="color:rgb(0,100,0)"><span style="color:rgb(70,130,180)"><span style="color:rgb(0,100,0)"><span style="color:rgb(196,160,0)"><br></span></span></span></span></span></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Aug 27, 2015 at 5:10 PM, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] <span dir="ltr"><<a href="mailto:zivrafael.yaniv@nih.gov" target="_blank">zivrafael.yaniv@nih.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-family:Tahoma;font-size:10pt">Hi Tassilo,<br>
<br>
Did you downgrade to libpng1.5 after creating the virtual environment? This is what I suggested in the thread you cited and was the solution at the time. It no longer works because anaconda upgraded additional packages.<br>
<br>
When you create the virtual environment with libpng set to 1.5 (conda create -n sitkpy anaconda libpng=1.5) all of the dependent packages are downgraded to work with this version of libpng and then you will not have this issue. The three steps are given in
the FAQ that I pointed you to - I am assuming here you did not follow that solution, it is pasted below for your convenience:<br>
<br>
conda create -n sitkpy anaconda libpng=1.5 <br>
conda install -c <a href="https://conda.binstar.org/simpleitk/channel/main" target="_blank">https://conda.binstar.org/simpleitk/channel/main</a> SimpleITK <br>
conda install libpng=1.5 <br>
<br>
If you followed this set of instructions and it doesn't work, let us know and we will try to recreate the problem and find a solution.<br>
<br>
regards<br>
Ziv<br>
<br>
<div style="font-family:'Times New Roman';font-size:16px">
<hr>
<div style="direction:ltr"><font face="Tahoma" size="2"><b>From:</b> Tassilo Klein [<a href="mailto:tjklein@gmail.com" target="_blank">tjklein@gmail.com</a>]<br>
<b>Sent:</b> Thursday, August 27, 2015 4:56 PM<br>
<b>To:</b> Yaniv, Ziv Rafael (NIH/NLM/LHC) [C]<br>
<b>Cc:</b> <a href="mailto:insight-users@itk.org" target="_blank">insight-users@itk.org</a><br>
<b>Subject:</b> Re: [ITK-users] SimpleITK Anaconda Issue<br>
</font><br>
</div><div><div>
<div></div>
<div>
<div dir="ltr">Hi Ziv,
<div><br>
</div>
<div>thanks. yes, that's what I did but then I get these errors:</div>
<div><br>
</div>
<div>
<pre style="overflow:auto;font-size:14px;padding:0px;margin-top:0px;margin-bottom:0px;line-height:17.0000591278076px;word-wrap:break-word;border:0px;white-space:pre-wrap;vertical-align:baseline"><span style="color:rgb(70,130,180)"><span style="color:rgb(0,100,0)"><span style="color:rgb(70,130,180)"><span style="color:rgb(0,100,0)"><span style="color:rgb(196,160,0)"><span style="color:rgb(70,130,180)"><span style="color:rgb(0,100,0)"><span style="color:rgb(70,130,180)"><span><span style="color:rgb(0,100,0)"><span style="color:rgb(70,130,180)"><span style="color:rgb(0,100,0)"><span style="color:rgb(70,130,180)"><span style="color:rgb(0,100,0)"><span style="color:rgb(70,130,180)"><span style="color:rgb(0,100,0)"><span style="color:rgb(70,130,180)"><span style="color:rgb(0,100,0)"><span style="color:rgb(196,160,0)"><span style="color:rgb(70,130,180)"><span style="color:rgb(0,100,0)"><span style="color:rgb(196,160,0)"><span style="color:rgb(70,130,180)"><span style="color:rgb(0,100,0)"><span style="color:rgb(196,160,0)"><span style="color:rgb(70,130,180)"><span style="color:rgb(0,100,0)"><span style="color:rgb(196,160,0)"><span style="color:rgb(70,130,180)"><span style="color:rgb(0,100,0)"><span style="color:rgb(196,160,0)"><span style="color:rgb(70,130,180)"><span style="color:rgb(0,100,0)"><span style="color:rgb(196,160,0)"><span style="color:rgb(0,100,0)">/home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/font_manager.py</span> in <span style="color:rgb(70,130,180)"><module><span style="color:rgb(0,0,139)">()</span>
<span style="color:rgb(0,100,0)"> 56</span> <span style="color:rgb(0,100,0)">import</span> matplotlib<span style="color:rgb(196,160,0)"></span>
<span style="color:rgb(0,100,0)"> 57</span> <span style="color:rgb(0,100,0)">from</span> matplotlib <span style="color:rgb(0,100,0)">import</span> afm<span style="color:rgb(196,160,0)"></span>
<span style="color:rgb(0,100,0)">---> 58<span style="color:rgb(196,160,0)"> <span style="color:rgb(0,100,0)">from</span> matplotlib <span style="color:rgb(0,100,0)">import</span> ft2font<span></span>
<span style="color:rgb(0,100,0)"> 59</span> <span style="color:rgb(0,100,0)">from</span> matplotlib <span style="color:rgb(0,100,0)">import</span> rcParams<span>,</span> get_cachedir<span></span>
<span style="color:rgb(0,100,0)"> 60</span> <span style="color:rgb(0,100,0)">from</span> matplotlib<span>.</span>cbook <span style="color:rgb(0,100,0)">import</span> is_string_like<span></span>
<span style="color:rgb(139,0,0)">ImportError</span>: libpng16.so.16: cannot open shared object file: No such file or directory</span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></pre>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Thu, Aug 27, 2015 at 3:55 PM, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C]
<span dir="ltr"><<a href="mailto:zivrafael.yaniv@nih.gov" target="_blank">zivrafael.yaniv@nih.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-family:Tahoma;font-size:10pt">Hello Tassilo,<br>
<br>
Please follow the instructions found in our FAQ 'I am using the binary distribution of SimpleITK for Anaconda, why do I get an error about libpng?' found here:
<a href="http://www.itk.org/Wiki/SimpleITK/FAQ" target="_blank">http://www.itk.org/Wiki/SimpleITK/FAQ</a><br>
<br>
We are working on a more permanent solution for our next release.<br>
<br>
regards<br>
Ziv<br>
<br>
<div style="font-family:'Times New Roman';font-size:16px">
<hr>
<div style="direction:ltr"><font face="Tahoma" size="2"><b>From:</b> Tassilo Klein [<a href="mailto:tjklein@gmail.com" target="_blank">tjklein@gmail.com</a>]<br>
<b>Sent:</b> Thursday, August 27, 2015 3:42 PM<br>
<b>To:</b> <a href="mailto:insight-users@itk.org" target="_blank">insight-users@itk.org</a><br>
<b>Subject:</b> [ITK-users] SimpleITK Anaconda Issue<br>
</font><br>
</div>
<div>
<div>
<div></div>
<div>
<div dir="ltr">Hi,
<div><br>
</div>
<div>I have issues getting my SimpleITK running on a Linux machine.</div>
<div><br>
</div>
<div>I used to get errors:</div>
<div><br>
</div>
<div><a href="http://public.kitware.com/pipermail/community/2015-May/009117.html" target="_blank">http://public.kitware.com/pipermail/community/2015-May/009117.html</a><br>
</div>
<div><br>
</div>
<div>
<pre style="white-space:pre-wrap">ImportError: libpng15.so.15: cannot open shared object file: No such</pre>
</div>
<div><br>
</div>
<div><br>
</div>
<div>Then I took an earlier version of libpng as mentioned here:</div>
<div><br>
</div>
<div><a href="http://public.kitware.com/pipermail/community/2015-May/009120.html" target="_blank">http://public.kitware.com/pipermail/community/2015-May/009120.html</a><br>
</div>
<div>
<pre style="white-space:pre-wrap">conda install libpng=1.5.13</pre>
</div>
<div><br>
</div>
<div><br>
</div>
<div>But then I get the following error:</div>
<div><br>
</div>
<div>
<pre style="overflow:auto;font-size:14px;padding:0px;margin-top:0px;margin-bottom:0px;line-height:17.0000591278076px;word-wrap:break-word;border:0px;white-space:pre-wrap;vertical-align:baseline"><span style="color:rgb(70,130,180)"><span style="color:rgb(0,100,0)"><span style="color:rgb(70,130,180)"><span style="color:rgb(0,100,0)"><span style="color:rgb(196,160,0)"><span style="color:rgb(70,130,180)"><span style="color:rgb(0,100,0)"><span style="color:rgb(70,130,180)"><span><span style="color:rgb(0,100,0)"><span style="color:rgb(70,130,180)"><span style="color:rgb(0,100,0)"><span style="color:rgb(70,130,180)"><span style="color:rgb(0,100,0)"><span style="color:rgb(70,130,180)"><span style="color:rgb(0,100,0)"><span style="color:rgb(70,130,180)"><span style="color:rgb(0,100,0)"><span style="color:rgb(196,160,0)"><span style="color:rgb(70,130,180)"><span style="color:rgb(0,100,0)"><span style="color:rgb(196,160,0)"><span style="color:rgb(0,100,0)">/home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py</span> in <span style="color:rgb(70,130,180)"><module><span style="color:rgb(0,0,139)">()</span>
<span style="color:rgb(0,100,0)"> 32</span> <span style="color:rgb(0,100,0)">import</span> matplotlib<span style="color:rgb(196,160,0)">.</span>artist <span style="color:rgb(0,100,0)">as</span> martist<span style="color:rgb(196,160,0)"></span>
<span style="color:rgb(0,100,0)"> 33</span> <span style="color:rgb(0,100,0)">import</span> matplotlib<span style="color:rgb(196,160,0)">.</span>cbook <span style="color:rgb(0,100,0)">as</span> cbook<span style="color:rgb(196,160,0)"></span>
<span style="color:rgb(0,100,0)">---> 34<span style="color:rgb(196,160,0)"> <span style="color:rgb(0,100,0)">import</span> matplotlib<span>.</span>collections <span style="color:rgb(0,100,0)">as</span> collections<span></span>
<span style="color:rgb(0,100,0)"> 35</span> <span style="color:rgb(0,100,0)">import</span> matplotlib<span>.</span>colors <span style="color:rgb(0,100,0)">as</span> colors<span></span>
<span style="color:rgb(0,100,0)"> 36</span> <span style="color:rgb(0,100,0)">import</span> matplotlib<span>.</span>contour <span style="color:rgb(0,100,0)">as</span> contour<span></span>
<span style="color:rgb(0,100,0)">/home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/collections.py</span> in <span style="color:rgb(70,130,180)"><module><span style="color:rgb(0,0,139)">()</span>
<span style="color:rgb(0,100,0)"> 25</span> <span style="color:rgb(0,100,0)">import</span> matplotlib<span style="color:rgb(196,160,0)">.</span>artist <span style="color:rgb(0,100,0)">as</span> artist<span style="color:rgb(196,160,0)"></span>
<span style="color:rgb(0,100,0)"> 26</span> <span style="color:rgb(0,100,0)">from</span> matplotlib<span style="color:rgb(196,160,0)">.</span>artist <span style="color:rgb(0,100,0)">import</span> allow_rasterization<span style="color:rgb(196,160,0)"></span>
<span style="color:rgb(0,100,0)">---> 27<span style="color:rgb(196,160,0)"> <span style="color:rgb(0,100,0)">import</span> matplotlib<span>.</span>backend_bases <span style="color:rgb(0,100,0)">as</span> backend_bases<span></span>
<span style="color:rgb(0,100,0)"> 28</span> <span style="color:rgb(0,100,0)">import</span> matplotlib<span>.</span>path <span style="color:rgb(0,100,0)">as</span> mpath<span></span>
<span style="color:rgb(0,100,0)"> 29</span> <span style="color:rgb(0,100,0)">from</span> matplotlib <span style="color:rgb(0,100,0)">import</span> _path<span></span>
<span style="color:rgb(0,100,0)">/home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/backend_bases.py</span> in <span style="color:rgb(70,130,180)"><module><span style="color:rgb(0,0,139)">()</span>
<span style="color:rgb(0,100,0)"> 54</span> <span style="color:rgb(196,160,0)"></span>
<span style="color:rgb(0,100,0)"> 55</span> <span style="color:rgb(0,100,0)">import</span> matplotlib<span style="color:rgb(196,160,0)">.</span>tight_bbox <span style="color:rgb(0,100,0)">as</span> tight_bbox<span style="color:rgb(196,160,0)"></span>
<span style="color:rgb(0,100,0)">---> 56<span style="color:rgb(196,160,0)"> <span style="color:rgb(0,100,0)">import</span> matplotlib<span>.</span>textpath <span style="color:rgb(0,100,0)">as</span> textpath<span></span>
<span style="color:rgb(0,100,0)"> 57</span> <span style="color:rgb(0,100,0)">from</span> matplotlib<span>.</span>path <span style="color:rgb(0,100,0)">import</span> Path<span></span>
<span style="color:rgb(0,100,0)"> 58</span> <span style="color:rgb(0,100,0)">from</span> matplotlib<span>.</span>cbook <span style="color:rgb(0,100,0)">import</span> mplDeprecation<span></span>
<span style="color:rgb(0,100,0)">/home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/textpath.py</span> in <span style="color:rgb(70,130,180)"><module><span style="color:rgb(0,0,139)">()</span>
<span style="color:rgb(0,100,0)"> 17</span> <span style="color:rgb(0,100,0)">from</span> matplotlib<span style="color:rgb(196,160,0)">.</span>path <span style="color:rgb(0,100,0)">import</span> Path<span style="color:rgb(196,160,0)"></span>
<span style="color:rgb(0,100,0)"> 18</span> <span style="color:rgb(0,100,0)">from</span> matplotlib <span style="color:rgb(0,100,0)">import</span> rcParams<span style="color:rgb(196,160,0)"></span>
<span style="color:rgb(0,100,0)">---> 19<span style="color:rgb(196,160,0)"> <span style="color:rgb(0,100,0)">import</span> matplotlib<span>.</span>font_manager <span style="color:rgb(0,100,0)">as</span> font_manager<span></span>
<span style="color:rgb(0,100,0)"> 20</span> <span style="color:rgb(0,100,0)">from</span> matplotlib<span>.</span>ft2font <span style="color:rgb(0,100,0)">import</span> FT2Font<span>,</span> KERNING_DEFAULT<span>,</span> LOAD_NO_HINTING<span></span>
<span style="color:rgb(0,100,0)"> 21</span> <span style="color:rgb(0,100,0)">from</span> matplotlib<span>.</span>ft2font <span style="color:rgb(0,100,0)">import</span> LOAD_TARGET_LIGHT<span></span>
<span style="color:rgb(0,100,0)">/home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/font_manager.py</span> in <span style="color:rgb(70,130,180)"><module><span style="color:rgb(0,0,139)">()</span>
<span style="color:rgb(0,100,0)"> 56</span> <span style="color:rgb(0,100,0)">import</span> matplotlib<span style="color:rgb(196,160,0)"></span>
<span style="color:rgb(0,100,0)"> 57</span> <span style="color:rgb(0,100,0)">from</span> matplotlib <span style="color:rgb(0,100,0)">import</span> afm<span style="color:rgb(196,160,0)"></span>
<span style="color:rgb(0,100,0)">---> 58<span style="color:rgb(196,160,0)"> <span style="color:rgb(0,100,0)">from</span> matplotlib <span style="color:rgb(0,100,0)">import</span> ft2font<span></span>
<span style="color:rgb(0,100,0)"> 59</span> <span style="color:rgb(0,100,0)">from</span> matplotlib <span style="color:rgb(0,100,0)">import</span> rcParams<span>,</span> get_cachedir<span></span>
<span style="color:rgb(0,100,0)"> 60</span> <span style="color:rgb(0,100,0)">from</span> matplotlib<span>.</span>cbook <span style="color:rgb(0,100,0)">import</span> is_string_like<span></span>
<span style="color:rgb(139,0,0)">ImportError</span>: libpng16.so.16: cannot open shared object file: No such file or directory</span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></pre>
</div>
<div><br>
</div>
<div><br>
</div>
<div>Any idea?</div>
<div><br>
</div>
<div>Best,</div>
<div> Tassilo</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</div></div></div>
</div>
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