<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi,<div class=""><br class=""></div><div class="">a few updates...<br class=""><div class=""><br class=""></div><div class="">Instead of using .nii, I tried to save the output overlay image in:</div><div class=""> .png - the resulting image is in grey levels, but I cannot see any red (or other colors)</div><div class="">.dcm - the resulting image looks corrupted both opened with imagej and Osirix</div><div class=""><br class=""></div><div class="">Any ideas?</div><div class=""><br class=""></div><div class="">Thanks</div><div class="">Alberto</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 28 Jan 2016, at 11:30, Alberto Bert <<a href="mailto:bert.alberto@gmail.com" class="">bert.alberto@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html charset=us-ascii" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi all,<div class=""><br class=""></div><div class="">I am trying to produce a coloured overlay between a UInt16 grey-level image and a segmentation mask extracted from such image. The segmentation mask is a UInt8 image valued 1 in the segmented area and 0 elsewhere.</div><div class=""><br class=""></div><div class="">If I try to:</div><div class=""><br class=""></div><div class=""> mask_overlay = sitk.LabelOverlay(image, mask, opacity = 0, backgroundValue = 0) # I am using SimpleITK 0.9.1 with Python 2.7</div><div class=""><br class=""></div><div class="">and then I write the mask_overlay (as .nii), I get an image almost completely <i class="">reddish</i>, while I expected to get the original grey-level image, with some red (or other color) corresponding only to the pixels valued 1 in the mask. (I did check the mask itself, and very few pixels are valued 1)</div><div class=""><br class=""></div><div class="">What am I doing (or expecting) wrong?</div><div class=""><br class=""></div><div class="">Thank you in advance,</div><div class="">Best</div><div class="">Alberto</div></div></div></blockquote></div><br class=""></div></div></body></html>