<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
<div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Mathieu,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br class="webkit-block-placeholder"></div><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Courier; min-height: 16px; "><span class="Apple-style-span" style="font-size: 12px; -webkit-text-stroke-width: -1; "> That's correct MR also often -illegally- has a slope/intersept. So</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: normal normal normal 13px/normal Courier; ">does CT and I guess Secondary Capture. But we handle all of them</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: normal normal normal 13px/normal Courier; ">nicely when *reading* a DICOM file. The issue is that right now, we</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: normal normal normal 13px/normal Courier; ">are not able to store that image -just read- back to file.</font></div></blockquote><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br class="webkit-block-placeholder"></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Thanks for your response. I guess my question could be turned around : how should I format my output DICOM metadata to achieve, correctly, my goal. That is, what do I need to do to get ITK to output a DICOM file with rescale slope and rescale intercept specified - change modality? The post-processed data is clearly not PET data. Is there a special modality tag that indicates that the data is post-processed? </div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br class="webkit-block-placeholder"></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Courier; min-height: 16px; "><span class="Apple-style-span" style="font-size: 12px; -webkit-text-stroke-width: -1; "> To go into further details, PET for instance has a dynamic</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">slope/intersept. This make not only very efficient for this type of</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">data, but also completely necesseray since the scalar range is so wide</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">and would prevent people from storing such images on 16bits as per</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">DICOM definition. Which means that ITK should have a mechanism</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">(callback?) which would allow GDCM to pass the new slope/intercept for</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">each new 2D image when iterating over a 3D volume. So far I have not</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">look into it too much.</font></div></blockquote><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Courier; min-height: 16px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">But in summary: reading 'floating' point is handled, writing it back</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">is not unfortunately :(</font></div></blockquote><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br class="webkit-block-placeholder"></div>This seems like strange behavior. What I would expect is that either (in order of my preference)</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br class="webkit-block-placeholder"></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">1) rescaling would only happen if explicitly invoked</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">2) rescaling would happen invertibly when DICOM images are converted to float and vice versa...</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br class="webkit-block-placeholder"></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Since you can't correctly apply rescaling for integer conversions without loss of precision, it seems like a bad choice for the default behavior. As far as I understand it, since DICOM only supports 16 bit integer precision, anyone using DICOM files to encode/decode float data will need to know about rescaleSlope/rescaleIntercept... Those entries in the metadata seem to me to be providing the additional information necessary to do integer->float and float->integer conversions.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br class="webkit-block-placeholder"></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Matthias</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Courier; min-height: 16px; "><span class="Apple-style-span" style="font-size: 12px; -webkit-text-stroke-width: -1; ">-Mathieu</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 13px/normal Courier; min-height: 16px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">On Nov 26, 2007 11:15 PM, Bill Lorensen <<a href="http://www.itk.org/mailman/listinfo/insight-users"><font color="#4a2486" style="color: #4a2486"><u>bill.lorensen at gmail.com</u></font></a>> wrote:</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> Matthieu,</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> I'm not sure if this is relevant to the current discussion.</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> I think that PET data often rescales each pixel with a different rescale</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> value. The results should be a floating point value.</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> Bill</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> On Nov 26, 2007 4:44 PM, Mathieu Malaterre <</i><a href="http://www.itk.org/mailman/listinfo/insight-users"><font color="#4a2486" style="color: #4a2486"><u><i>mathieu.malaterre at gmail.com</i></u></font></a><i>></i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> wrote:</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> ></i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> ></i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> ></i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > Hi Matthias,</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> ></i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> ></i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > On Nov 26, 2007 8:37 PM, Matthias Schabel <</i><a href="http://www.itk.org/mailman/listinfo/insight-users"><font color="#4a2486" style="color: #4a2486"><u><i>mschabel at ucair.med.utah.edu</i></u></font></a><i>></i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> wrote:</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > > I may not fully understand this issue, so apologies in advance if I'm</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > > missing something, but if the support for rescaleSlope/</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > > rescaleIntercept was removed from the ITK GDCM in ITK 3.4, this change</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > > breaks my code in a way that makes it very difficult to fix...</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> ></i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > Here is what happen in between ITK 3.2 and 3.4, ITK-GDCM was simply</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > passing all DICOM element from the reader to the writer. This is a bad</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > idea since ITK is also at the same time decompressing (applying the</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > rescale+slope) to the Stored Pixel. Therefore whenever you would</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > read-write-read-write the linear transform would be applied multiple</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > time... yup this is a bug indeed !</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> ></i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > Now, to answer your question: I did not break any kind of backward</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > compatibility since -and it's been on my TODO list for a while- there</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > is no support for floating point image in ITK-GDCM.</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > So if you are using some kind of low-level script (at gdcm level), you</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > should still be able to use it. Simply completely by-pass any check</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > done at ITK-GDCM level (ie. do not pass the meta data dictionary from</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > reader to writer).</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> ></i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> ></i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > > In</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > > particular, I have code that performs pharmacokinetic modeling on</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > > dynamically acquired MRI data to generate quantitative maps of</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > > parameters (such as Ktrans, kep, Vp...) that take on floating point</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > > values in the approximate range of 0.0-2.0.</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> ></i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > 2.0 ? That's pretty high for Ktrans/kep/ve, isn't it :)</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> ></i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> ></i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > > These maps are then</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > > exported as DICOM, with appropriate rescale factors and offsets to</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > > minimize truncation error in conversion from float to short. Since the</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > > latest release of the ITK libraries appears to strip rescaleSlope and</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > > rescaleIntercept on DICOM write, I can no longer specify correct</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > > scaling to the visualization program I'm using (OsiriX). I don't</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > > understand the rationale behind this change - it makes it essentially</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > > impossible to deal with small floating point numbers in DICOM if you</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > > can't specify these scaling values...</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> ></i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > Please send your custom script, and I'll help you get it to work again.</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> Thanks.</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> ></i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> ></i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > ></i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > > PS The crashing problem in OSX 10.5 appears to only occur with</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > > dynamically linked versions of the ITK libraries - static linkage</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > > works fine.</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> ></i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > Great, thanks for the notice !</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> ></i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > --</i></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Courier" size="4" style="font: 13.0px Courier">><i> > Mathieu</i></font></div></blockquote></div></body></html>