<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">Hi Luis,<br><br> Thank you again for your reply. With regard to " Yes, the Patient position is the source of the data for the<br>image origin values" in your reply, how does -255, -255, -30 make sense ? I'm not sure I understand the logic behind the "Image Patient Position" tag in a dicom file (0020 - 0032 bytes) . <br>The IPP in my dicom file is listed as -255, -255, -33. Unless the images are centered, should these values be (0, 0, 0) for the first slice ?<br><br>Emma<br><br><br>Could you point me to some references if there is a lengthy explanation for this ?<br><br><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div><br>Question 1:<br><br>When the Similarity3DTransform gets a negative
value in the Scale<br>parameter, that performs a reflection of the space on the origin<br>of coordinates.... not a good thing at all, particularly in medical<br>images.<br><br>The scale shouldn't approach a zero value either...<br><br>This however, is possible when you use an optimizer that assumes<br>that the parameters of the transform are in a Vector space, as<br>most of the GradientDescent optimizers do.<br><br><br>In practice you could have prevented the scale from deforming that<br>far by setting proper values in the parameter scaling array that<br>you pass to the optimizer. The purpose of this array is to let<br>the optimizer know that we don't expect big changes to occur in<br>the Scale parameter of Transform.<br><br><br><br>Question 2:<br><br>You should only need a Similarity transform is you are registering<br>images from different patients, that will naturally have slightly<br>different organ sizes. Note however that the size variability of<br>human specimens is
not as large as to need scales smaller than 0.5<br>or larger than 2.0.<br><br>If you are registering two different patients, then, in addition<br>to having the origin & spacing taken into account, you may also<br>need this type of scaling in space.<br><br><br>Question 3:<br><br>Resampling will take the image spacing into account. You just<br>need to make sure that the spacing is set correctly in the images.<br>Note that the resampling also use the transform anyways.<br><br><br>Question 4:<br><br>No, you don't need to manually compensate for the resolution.<br>ITK already takes the pixel spacing into account. All the<br>process of image registration is done in physical coordinates.<br><br><br>Question 5:<br><br>Yes, the Patient position is the source of the data for the<br>image origin values.<br><br><br><br><br> Regards,<br><br><br> Luis<br><br><br><br>-----------------<br>Emma Ryan wrote:<br>> Hi,<br>>
<br>> I am using the itk Similarity3DTranform to obtain a registration <br>> between two volumes.<br>> Dataset1 : 512 x 512 x 30 (Resolution = 0.684 x 0.684 x 1.0) : Image <br>> Patient Position : -175, -175, 125 (from dicom header)<br>> Dataset2: 512 x 512 x 30 (Resolution = 1.0 x 1.0 x 1.0 ) : Image Patient <br>> Position: -255, -255, 101 (from dicom header)<br>> <br>> Both are of the same modality (CT).<br>> <br>> I have a few questions.<br>> <br>> 1. How does one interpret the scale value of (-0.00008). What does <br>> negative mean ? Division ?<br>> <br>> 2. Prior to registration I mention the size, origin and spacing for both <br>> the fixed and moving volumes. At resampling, the moving volume are <br>> resampled to match the spacing and origin of the fixed volume. So should <br>> I care to include the scale transform in my registration/optimization <br>> parameters
?<br>> <br>> 3. Does resampling take care of the resolution difference ?<br>> <br>> 4. Is it necessary that I set the initial scaling to 1.428 to compensate <br>> for the resolution ?<br>> <br>> 5. Dicom images have Image Patient Postion tag. Is this the information <br>> that goes into the "Origin" variable ? If not, where do I get the <br>> image origin information ?<br>> <br>> I have read a lot of literature on resampling and all the pdfs and ppts <br>> on ITK, but I fail to understand these.<br>> <br>> Please help !<br>> <br>> Emma<br>> <br>> ------------------------------------------------------------------------<br>> Get the Yahoo! toolbar and be alerted to new email <br>> <<a target="_blank"
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