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<p class="MsoNormal">Dear SimNIBS,</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">First of all, thank you for the amazing program.</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="xxxmsonormal">I am struggling with creating a mesh (using headreco all) based on a NIFTI file that I converted from DICOM (with
<span style="font-size:11.5pt;font-family:"Arial",sans-serif;color:#404040;background:white">
dicm2nii)</span>. While the first steps few steps in Matlab run successful, I get the error value “axes don't match array” at the start of
<b>Binarizing tissue probability maps</b> and program terminates (see below for complete message). When I run headreco all with Ernie’s NIFTI file the headreco all it works fine, so I guess something went wrong with the conversion, but I cannot put my finger
on the problem. The scan is a standard 3T scan: voxel dimensions: 1x1x1mm and image (XYZ) dimensions: 192x256x256, and the NIFTI scan looks fine in MRICRO and MANGO.
</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I hope you can help me. Thank you very much for your valuable time and I look forward to hearing from you.</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best wishes,</p>
<p class="MsoNormal">Dennis</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="xxxmsonormal"><b>Binarizing tissue probability maps</b><o:p></o:p></p>
<p class="xxxmsonormal"> <o:p></o:p></p>
<p class="xxxmsonormal">Creating unity.xfm and ref_FS.nii.gz<o:p></o:p></p>
<p class="xxxmsonormal">Traceback (most recent call last):<o:p></o:p></p>
<p class="xxxmsonormal"> File "C:\Users\schut103\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\cli\headreco.py", line 13, in <module><o:p></o:p></p>
<p class="xxxmsonormal"> main()<o:p></o:p></p>
<p class="xxxmsonormal"> <o:p></o:p></p>
<p class="xxxmsonormal"> File "C:\Users\schut103\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\cli\headreco.py", line 10, in main<o:p></o:p></p>
<p class="xxxmsonormal"> headmodel(sys.argv)<o:p></o:p></p>
<p class="xxxmsonormal"> <o:p></o:p></p>
<p class="xxxmsonormal"> File "C:\Users\schut103\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\msh\headreco.py", line 286, in headmodel<o:p></o:p></p>
<p class="xxxmsonormal"> hmu.write_ref_fs(vols_conform[0])<o:p></o:p></p>
<p class="xxxmsonormal"> <o:p></o:p></p>
<p class="xxxmsonormal"> File "C:\Users\schut103\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\msh\hmutils.py", line 3454, in write_ref_fs<o:p></o:p></p>
<p class="xxxmsonormal"> data = np.transpose(np.zeros_like(vol.get_data()),(0,2,1))<o:p></o:p></p>
<p class="xxxmsonormal"> <o:p></o:p></p>
<p class="xxxmsonormal"> File "C:\Users\schut103\SimNIBS-3.2\simnibs_env\lib\site-packages\numpy\core\fromnumeric.py", line 639, in transpose<o:p></o:p></p>
<p class="xxxmsonormal"> return _wrapfunc(a, 'transpose', axes)<o:p></o:p></p>
<p class="xxxmsonormal"> <o:p></o:p></p>
<p class="xxxmsonormal"> File "C:\Users\schut103\SimNIBS-3.2\simnibs_env\lib\site-packages\numpy\core\fromnumeric.py", line 56, in _wrapfunc<o:p></o:p></p>
<p class="xxxmsonormal"> return getattr(obj, method)(*args, **kwds)<o:p></o:p></p>
<p class="xxxmsonormal"> <o:p></o:p></p>
<p class="xxxmsonormal">ValueError: axes don't match array<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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