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Hi,
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<div class="">One of the key feature of ITK is that images are not just voxel, but oriented object that have a physical location. This is why the Image class has associated with the an Origin, Spacing, and Direction. You can use the Image::TransformIndexToPhysicalPoint
to see this mapping. Also print the SimpleITK image and look at these attributes.</div>
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<div class="">The ResampleImageFilter applies a geometric transform from the input image's physical space to the output image's physical space defined by the Output parameters of the ResampleImageFiler. In your first attempt, your input image and output image
are in the same physical space so it is expected that they would be the same. The input and output image maintain the same meta-data, because of the call the SetReferenceIamge(img).</div>
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<div class="">From your initial post, it sounds like you want to resample a set of images to a common reference frame. So you need to define that common reference image’s origin, spacing, direction, and size. And use that information in the ResampleImageFilter.
This assumes that you don’t want to change the physical location of the image.</div>
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<div class="">HTH,</div>
<div class="">Brad</div>
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<div class="">On May 4, 2016, at 4:17 PM, fausto milletarì <<a href="mailto:fausto.milletari@gmail.com" class="">fausto.milletari@gmail.com</a>> wrote:</div>
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Hello,
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<div class="">just as a brief attempt i tried:</div>
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<pre style="background-color: rgb(255, 255, 255); font-family: Menlo; font-size: 9pt;" class="">resample=sitk.ResampleImageFilter()<br class="">resample.SetReferenceImage(img)<br class="">resample.SetOutputDirection(img.GetDirection())</pre>
<div class="">Seems that, after I obtain the numpy array as: </div>
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<pre style="background-color: rgb(255, 255, 255); font-family: Menlo; font-size: 9pt;" class="">test=resample.Execute(img)<br class="">volume=sitk.<span style="background-color:#e4e4ff;" class="">GetArrayFromImage</span>(test)</pre>
<pre style="background-color: rgb(255, 255, 255); font-size: 9pt;" class=""><font face="Helvetica" class=""><span style="white-space: normal;" class="">Nothing changes in terms of data array.</span></font></pre>
<pre style="background-color: rgb(255, 255, 255);" class=""><font face="Helvetica" style="font-size: 9pt;" class=""><span style="white-space: normal;" class="">If I also add </span></font><span style="font-size: 9pt;" class=""><font face="Menlo" class="">resample.SetOutputSpacing(img.GetSpacing()/2.) </font><font face="Helvetica" class="">then the numpy array changes and depicts a </font></span><font face="Helvetica" class="">down-sampled<span style="font-size: 9pt;" class=""> version of the image.</span></font></pre>
<pre style="background-color: rgb(255, 255, 255);" class=""><span style="font-size: 9pt;" class=""><font face="Helvetica" class="">I suspect i have to use </font></span><span style="font-family: Menlo; font-size: 9pt;" class="">resample.SetTransform() </span><font face="Helvetica" class="">but I will need to create this transform using one of the transform types available in sitk. How can I create a transform that is equivalent to the one contained in the header of my MHD file? Should I create a transform starting from the volume direction and maybe offset? I could not find any example of this so far…</font></pre>
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<pre style="background-color: rgb(255, 255, 255);" class=""><font face="Helvetica" class="">Best regards and thanks much for your help and your answers,</font></pre>
<pre style="background-color: rgb(255, 255, 255);" class=""><font face="Helvetica" class="">Fausto </font></pre>
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<div class="">On 04 May 2016, at 20:40, fausto milletarì <<a href="mailto:fausto.milletari@gmail.com" class="">fausto.milletari@gmail.com</a>> wrote:</div>
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Hello,
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<div class="">I thank you for you fast and accurate answer. This was exactly what I was looking for. Actually I don’t need to visualise the data but further process it in a common reference frame. I think that your answer solves the problem. I will look into
the ResampleImageFilter (that so far I was using only to adjust the resolution of different volumes acquired with different scanners to a common one).</div>
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<div class="">Thanks a lot!</div>
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<div class="">Fausto Milletari<br class="">
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<div class="">On 04 May 2016, at 20:36, Lowekamp, Bradley (NIH/NLM/LHC) [C] <<a href="mailto:blowekamp@mail.nih.gov" class="">blowekamp@mail.nih.gov</a>> wrote:</div>
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Hello,
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<div class="">If I understand you correctly you want to rotate the image and pad it for visualization before exporting to numpy.</div>
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<div class="">Have you looked into the ResampleImageFilter? It accepts a transform, along with output image geometry so that you can readily manipulate the image for display. You also may want to scale the image’s intensity with a WindowLevelImageFilter for
better visualization of the range of interest.</div>
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<div class="">HTH,</div>
<div class="">Brad</div>
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<div class="">On May 4, 2016, at 1:14 PM, fausto milletarì <<a href="mailto:fausto.milletari@gmail.com" class="">fausto.milletari@gmail.com</a>> wrote:</div>
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Hello everyone,
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<div class="">I have a probably naive question about simpleITK. I find simpleITK extremely useful to process medical data such as MRI scans but I would like also to enjoy being able to convert my images in numpy format while respecting the transformation of
the volume.</div>
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<div class="">In other words I would like to get the MRI image in numpy rotated by the correct amount around each axis with zero padding for example.</div>
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<div class="">when i do simply <span style="color: rgb(128, 128, 128); font-style: italic; font-family: Menlo; font-size: 9pt; background-color: rgb(255, 255, 255);" class="">sitk.GetArrayFromImage(imgResampledCropped)</span>I get back the raw data itself,
but what I would like to do is to have a numpy array that contains the data “ready to visualise” by simple slicing of the array itself.</div>
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<div class="">Do you think this is doable? Is there a standard way of doing it?</div>
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<div class="">Kind regards,</div>
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<div class="">Fausto</div>
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