Hi again I decided to go the easy way and read from the hard disk. So I get the path of the already loaded series, but I get the error<br><br> Could not open file /Users/osirix/Documents/Emmanouil/MyTestImages/MRkid/05050914/.1<br><br>the path is /Users/osirix/Documents/Emmanouil/MyTestImages/MRkid/05050914/<br>even when I hardcode the path i get the same result. Do you know what might be wrong? (btw is the <font size="-1">last forward slash </font>necessary ? ) <br><br><b><i>David Gobbi <dgobbi@atamai.com></i></b> wrote:<blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> Hi Emmanouil,<br><br>One thing you can do is create a vtkImageImport object for each DICOM <br>image, this will allow you to create a vtkImageData from each DICOM that <br>you have stored in memory. Then, you can use vtkImageAppend to create <br>an image volume out of the series of images. The output of <br>vtkImageAppend can
be used by vtkImageReslice.<br><br> - David<br><br><br>Emmanouil Moschidis wrote:<br>> Before being able to use some parts of the code I have to solve a <br>> different problem. (I posted a new question but either it was not <br>> quite clear or nobody has done that before (?) )<br>><br>> I work within a DICOM viewer so the DICOM series are already loaded (I <br>> do not read from a file like in case of the vtkImageReader2). Actually <br>> every DICOM image is stored in a custom class and all together in a <br>> NSArray (yes it is objective-C). So I want to load the images from the <br>> NSArray to the vtkImageReader2 object... I am not sure how should I do <br>> that.<br>><br>> Maybe first I need to load them into a vtkImageData object? (still I <br>> haven't found any example for that)<br>><br>> And then again I have the problem how to get the output properly. But <br>> I guess these questions do not belong to this
class.<br>><br>> */David Gobbi <dgobbi@atamai.com>/* wrote:<br>><br>> Hi Emmanouil,<br>><br>> The best example for what you are trying to do is probably this one:<br>><br>> VTK/Examples/ImageProcessing/Cxx/ImageSlicing.cxx<br>><br>> This example is only in the CVS version of VTK, it isn't in the VTK 5<br>> release.<br>><br>> What I do with tracking systems is use the coordinate/quaternion from<br>> the tracking system to create a vtkTransform, then I concatenate that<br>> transform with a vtkMatrix4x4 from the patient registration, and then<br>> feed the resulting transform to vtkImageReslice as the<br>> ResliceTransform.<br>><br>> If you have looked at the class page for vtkImageReslice, you will<br>> notice that there are two methods for setting orientations:<br>> SetResliceAxes() and SetResliceTransform().<br>><br>> For tracking, I always set
ResliceTransform to the<br>> position/orientation<br>> of the tool (in patient coordinates), and then set the ResliceAxes<br>> according to how I want to orient the slice relative to<br>> orientation of<br>> the tool. In that way, the ResliceAxes is used to choose the tool<br>> axes<br>> along which you will be extracting the slice.<br>><br>> The tricky thing with vtkImageReslice is getting the OutputOrigin,<br>> OutputSpacing, and OutputExtent set properly for your application.<br>> Together, these parameters can be used to describe an output slice<br>> plane<br>> with a particular pixel spacing. So for example:<br>><br>> OutputOrigin = (-127.5, -127.5, 0.0)<br>> OutputSpacing = (1.0, 1.0, 1.0)<br>> OutputExtent = (0, 255, 0, 255, 0, 0)<br>><br>> These describe a 256x256 output slice with 1mm pixel spacing. The<br>> first<br>> pixel is at
(-127.5,-127.5,0) in the "output coordinate system" of<br>> vtkImageReslice. The centre of the slice is at (0,0,0) in the "output<br>> coordinate system" of vtkImageReslice.<br>><br>> Now, the original input volume is in the "input coordinate system" of<br>> vtkImageReslice. We can call the input coordinate system "x" and the<br>> output coordinate system "x'". The relationship between these<br>> coordinates is as follows:<br>><br>> x = T*M*x' where "T" is ResliceTransform and "M" is ResliceMatrix<br>><br>> So this tells you that, if "M" is chosen to be a pure rotation<br>> matrix,<br>> and if "T" contains the position of the tool point in input image<br>> coordinates, then the point x' = (0,0,0), which is in the centre<br>> of our<br>> output plane, will correspond to the point x = tool_point. So, we<br>> will<br>> be extracting a slice through the tool point
position.<br>><br>> I know that is probably not the best description, let me know if<br>> things<br>> aren't quite clear.<br>><br>> - David<br>><br>><br>><br>><br>> Emmanouil Moschidis wrote:<br>> > Hello<br>> ><br>> > I want to use the vtkImageReslice class for reading a series of<br>> slices<br>> > and exctracting one slice based on coordinates and quaternions<br>> > received from a tracking system.<br>> ><br>> > Is there any specific documentation and/or any working examples for<br>> > this class? It is very powerful yet the only usable information<br>> I have<br>> > found is the class reference webpage.<br>> ><br>> > Any hint about how to proceed towards the insight of it would be<br>> > highly appreciated<br>> ><br>> > thanks<br>> ><br>>
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