Now I understand.<br><br>Not all itk supported formats support orientation. Off the top of my head, the following do:<br>DICOM (the gdcm implementation GDCMImageIO)<br>nrrd<br>meta<br><br>For others, the application has to deal with it. There is a class in itk: OrientImageFilter that will reshuffle a volume into a selected orientation.<br>
<br>Handling medical image data properly is very tricky. We have tried in itk to the right thing in DICOM, which is the clinical medical imaging standard. meta and nrrd are great research formats and we think we handle orientation properly.<br>
<br>If you are working in a clinical environment, I would strongly recommend that you use DICOM. If you are in a research environment and will not be providing information to a clinical environment, then I guess you can use whatever works for your particular scanner protocols.<br>
<br>Bill<br><br><div class="gmail_quote">On Thu, Oct 1, 2009 at 10:37 AM, kevin cavin <span dir="ltr"><<a href="mailto:beibeiwen2003@yahoo.com">beibeiwen2003@yahoo.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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<div>Hello, Bill: </div>
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<div> At this moment I retrieve the dicom voume from the MR and CT machines and the images are in AVS field format due to internal reasons. Then I use ITK to register the MR and CT volume. I display both of voulme and find the orientation is different. I manually adjust the orientation and get good registration. </div>
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<div> If I understand what you said correctly, if both volume are read in dicom format, the registration should take care the difference of orientation automatically. If so, It will be necessary to retrieve the voume in dicom format. </div>
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<div> But I still do not understand how ITK can deal with issue automatically. Does it mean only the volume in DICOM will work in this way. If the volumes are saved in other format, such as VTK, AVS etc, the application should deal with the orientation transformation. </div>
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<div> More explanation will be appreciated. Thanks ! Since I am using python instead of C++ to programm, I do not know whether print command will work in the same way. </div>
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<div>Calvin </div><div class="im">
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<div><br><br>--- On <b>Thu, 10/1/09, Bill Lorensen <i><<a href="mailto:bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.com</a>></i></b> wrote:<br></div>
</div><blockquote style="border-left: 2px solid rgb(16, 16, 255); padding-left: 5px; margin-left: 5px;"><div class="im"><br>From: Bill Lorensen <<a href="mailto:bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.com</a>><br>
Subject: Re: [Insight-users] conversion of scan transofmration matrix between different modality<br>To: "kevin cavin" <<a href="mailto:beibeiwen2003@yahoo.com" target="_blank">beibeiwen2003@yahoo.com</a>><br>
Cc: <a href="mailto:insight-users@itk.org" target="_blank">insight-users@itk.org</a><br></div>Date: Thursday, October 1, 2009, 9:11 PM<div><div></div><div class="h5"><br><br>
<div>Calvin,<br><br>As I said, the orientation difference should be taken care of during the registration process. Is the data being read as DICOM? If not, how are you reading it?<br><br>Please ->Print(std::cout) the fixed and moving images after you read them and post the results of the Print.<br>
<br>Bill<br><br>
<div class="gmail_quote">On Thu, Oct 1, 2009 at 8:31 AM, kevin cavin <span dir="ltr"><<a href="http://us.mc1120.mail.yahoo.com/mc/compose?to=beibeiwen2003@yahoo.com" rel="nofollow" target="_blank">beibeiwen2003@yahoo.com</a>></span> wrote:<br>
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<div>Hello, Bill : </div>
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<div> Thanks for your reply. What I hve found with the orginal volume is the orientation for CT and MRI scan is different. If I directly register these two volume, I will get wrong registration result. I assume the transformtion of orientation for one scan is necessary. but how can I do that with available ITK ? </div>
<div> I am using ITK version 3.12. </div>
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<div>Kind regards </div>
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<div>Calvin </div>
<div><br><br>--- On <b>Wed, 9/30/09, Bill Lorensen <i><<a href="http://us.mc1120.mail.yahoo.com/mc/compose?to=bill.lorensen@gmail.com" rel="nofollow" target="_blank">bill.lorensen@gmail.com</a>></i></b> wrote:<br></div>
<blockquote style="border-left: 2px solid rgb(16, 16, 255); padding-left: 5px; margin-left: 5px;"><br>From: Bill Lorensen <<a href="http://us.mc1120.mail.yahoo.com/mc/compose?to=bill.lorensen@gmail.com" rel="nofollow" target="_blank">bill.lorensen@gmail.com</a>><br>
Subject: Re: [Insight-users] conversion of scan transofmration matrix between different modality<br>To: "kevin cavin" <<a href="http://us.mc1120.mail.yahoo.com/mc/compose?to=beibeiwen2003@yahoo.com" rel="nofollow" target="_blank">beibeiwen2003@yahoo.com</a>><br>
Cc: <a href="http://us.mc1120.mail.yahoo.com/mc/compose?to=insight-users@itk.org" rel="nofollow" target="_blank">insight-users@itk.org</a><br>Date: Wednesday, September 30, 2009, 11:36 PM
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<div>ITK should handle this. ITK uses the information stored in DICOM to compute an origin, spacing and direction. You should not have to convert the volume, assuming the patient scans are landmarked (in the scanner) at a similar location.<br>
<br>What version of ITK are you using? <br><br>
<div class="gmail_quote">On Wed, Sep 30, 2009 at 11:04 AM, kevin cavin <span dir="ltr"><<a href="http://us.mc1120.mail.yahoo.com/mc/compose?to=beibeiwen2003@yahoo.com" rel="nofollow" target="_blank">beibeiwen2003@yahoo.com</a>></span> wrote:<br>
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<div><br>Hi, Folks: </div>
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<div> When I use ITK to register two dicom volume from different modalities. I have found that MR and CT scan often have different scan transformation matrixes. For example for CT scan the z direction is the y direction of MR scan. This will pose problem to register the two volumes with ITK. I am wondering whether in ITK the probelm can be solved soneway by using some function embedded. Do I need to write individual program to manula convert one of the volume. Thanks in advance ! </div>
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<div>Kind regards </div>
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<div>Calvin </div>
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