<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi Shandra,<div><br></div><div>There are people on the list that could give a much more</div><div>complete and formal answer as to why you don’t do processing</div><div>using dicom images. I’ll simply defer to them and say that</div><div>you should use one of the more standard medical imaging</div><div>formats that ITK supports like nifti or nrrd or mhd.</div><div><br></div><div>Nick </div><div><br></div><div><br></div><div><br><div><div>On Jan 31, 2014, at 9:35 AM, Shandra Gutierrez Diaz <<a href="mailto:Shandra.GutierrezDiaz@UGent.be">Shandra.GutierrezDiaz@UGent.be</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Nick, <div><br></div><div>I have tried the ANTs version and it works properly with the examples. However when I am trying to do it with my images (dicoms) it doesn't seem to work. It generates a dicom image but it is empty. </div><div>Is it possible to use it with dicom images or should it be nifti?</div><div><br></div><div>Shandra</div><div><br><div><div>On 30/01/2014, at 15:30, Shandra Gutierrez Diaz wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Nick,<div><br></div><div>Thanks a lot for the feedback. I thought I was doing something wrong. I will try then with the ANTS version. </div><div><br></div><div>Best, </div><div>Shandra</div><div><div><div>On 30/01/2014, at 15:26, Nicholas Tustison wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html charset=windows-1252"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi Shandra,<div><br></div><div>I tried downloading the IJ code and it no longer works</div><div>with the current ITK because of the numerous changes</div><div>made to the core classes. The only N4 program that I </div><div>continue to maintain is the ANTs version </div><div><br></div><div><a href="http://stnava.github.io/ANTs/">http://stnava.github.io/ANTs/</a></div><div><br></div><div>The program, N4.cxx, evolved into N4BiasFieldCorrection.cxx</div><div><br></div><div><a href="https://github.com/stnava/ANTs/blob/master/Examples/N4BiasFieldCorrection.cxx">https://github.com/stnava/ANTs/blob/master/Examples/N4BiasFieldCorrection.cxx</a></div><div><br></div><div>and I can run it just fine using your command line.</div><div><br></div><div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(255, 255, 255); background-color: rgb(33, 33, 33);">[ntustison@d-172-25-171-144 Thu Jan 30 09:15:24] $ N4BiasFieldCorrection -d 2 -i t81slice.nii.gz -o t81sliceCorrect.nii.gz -s 4 -b [200] -c [50x50x50x50,0]</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(255, 255, 255); background-color: rgb(33, 33, 33); min-height: 15px;"><br></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(255, 255, 255); background-color: rgb(33, 33, 33);">Running N4 for 2-dimensional images.</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(255, 255, 255); background-color: rgb(33, 33, 33); min-height: 15px;"><br></div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(255, 255, 255); background-color: rgb(33, 33, 33);">Mask not read. Creating Otsu mask.</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(255, 255, 255); background-color: rgb(33, 33, 33);">Current level = 1</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(255, 255, 255); background-color: rgb(33, 33, 33);"> Iteration 1 (of 50). Current convergence value = 0.000515799 (threshold = 0)</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(255, 255, 255); background-color: rgb(33, 33, 33);"> Iteration 2 (of 50). Current convergence value = 0.000514015 (threshold = 0)</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(255, 255, 255); background-color: rgb(33, 33, 33);"> Iteration 3 (of 50). Current convergence value = 0.000512207 (threshold = 0)</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(255, 255, 255); background-color: rgb(33, 33, 33);"> Iteration 4 (of 50). Current convergence value = 0.000510627 (threshold = 0)</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(255, 255, 255); background-color: rgb(33, 33, 33);"> Iteration 5 (of 50). Current convergence value = 0.000508918 (threshold = 0)</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(255, 255, 255); background-color: rgb(33, 33, 33);"> Iteration 6 (of 50). Current convergence value = 0.000507124 (threshold = 0)</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(255, 255, 255); background-color: rgb(33, 33, 33);"> Iteration 7 (of 50). Current convergence value = 0.000505515 (threshold = 0)</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(255, 255, 255); background-color: rgb(33, 33, 33);"> Iteration 8 (of 50). Current convergence value = 0.000503797 (threshold = 0)</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(255, 255, 255); background-color: rgb(33, 33, 33);"> Iteration 9 (of 50). Current convergence value = 0.000502342 (threshold = 0)</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(255, 255, 255); background-color: rgb(33, 33, 33);"> Iteration 10 (of 50). Current convergence value = 0.000500771 (threshold = 0)</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(255, 255, 255); background-color: rgb(33, 33, 33);"> Iteration 11 (of 50). Current convergence value = 0.000499355 (threshold = 0)</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(255, 255, 255); background-color: rgb(33, 33, 33);"> Iteration 12 (of 50). Current convergence value = 0.000497954 (threshold = 0)</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(255, 255, 255); background-color: rgb(33, 33, 33);"> Iteration 13 (of 50). Current convergence value = 0.000496292 (threshold = 0)</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(255, 255, 255); background-color: rgb(33, 33, 33);"> Iteration 14 (of 50). Current convergence value = 0.000494926 (threshold = 0)</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(255, 255, 255); background-color: rgb(33, 33, 33);"> Iteration 15 (of 50). Current convergence value = 0.000493357 (threshold = 0)</div><div style="margin: 0px; font-size: 11px; font-family: Monaco; color: rgb(255, 255, 255); background-color: rgb(33, 33, 33);"> Iteration 16 (of 50). Current convergence value = 0.000491692 (threshold = 0)</div></div><div><br></div><div><br></div><div>Nick</div></div></blockquote></div><br>
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