<div dir="ltr">Hi,<br><br>I've found that if i load a dicom image with MIPAV (last version) the coordinate system (origin etc.) is the same as ITK, and this is the true coordinate system.<br>If I decide to save with MIPAV the DICOM volume in a nifti format the coordinate system changes!! So the problem is clearly a MIPAV's problem...<br>
<br>Now, what I do is open with MIPAV the DICOM volume make preprocessing on DICOM volume and than save it in DICOM format too (in order to mantain the correct origin and orientation). <br><br>anyways what I want to do as preprocessing is pad or cut the image or put some markers on it.<br>
<br>Thanks<br><br>Elena Faggiano<br><br><div class="gmail_quote">2008/10/16 Luis Ibanez <span dir="ltr"><<a href="mailto:luis.ibanez@kitware.com">luis.ibanez@kitware.com</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Hi Elena,<br>
<br>
This looks like a problem in MIPAV, not really an ITK problem.<br>
<br>
If you are looking for applications for preprocessing images<br>
you may want to look at:<br>
<br>
<br>
Slicer: <a href="http://www.slicer.org/" target="_blank">http://www.slicer.org/</a><br>
SNAP: <a href="http://www.itksnap.org/" target="_blank">http://www.itksnap.org/</a><br>
<br>
<br>
That are both build based on ITK and VTK.<br>
<br>
<br>
What kind of pre-processing do you need to apply to these images ?<br>
<br>
<br>
Thanks<br>
<br>
<br>
Luis<br>
<br>
<br>
-----------------------<br>
Elena Faggiano wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="Wj3C7c">
Hi,<br>
<br>
I have a CT image (series of images) in DICOM format and I read it with DicomSeriesImageWrite, and I write a nifti file (.nii).<br>
Then I read the nifti image with an ImageFileReader and if I ask the information about the DICOM image and the nifti image they are equal:<br>
<br>
for the DICOM image:<br>
/OrientedImage (0x8f92fd0)<br>
RTTI typeinfo: itk::OrientedImage<short, 3u><br>
Reference Count: 1<br>
Modified Time: 2592<br>
Debug: Off<br>
Observers:<br>
none<br>
Source: (0x8f908e8)<br>
Source output index: 0<br>
Release Data: Off<br>
Data Released: False<br>
Global Release Data: Off<br>
PipelineMTime: 18<br>
UpdateMTime: 2593<br>
LargestPossibleRegion:<br>
Dimension: 3<br>
Index: [0, 0, 0]<br>
Size: [512, 512, 101]<br>
BufferedRegion:<br>
Dimension: 3<br>
Index: [0, 0, 0]<br>
Size: [512, 512, 101]<br>
RequestedRegion:<br>
Dimension: 3<br>
Index: [0, 0, 0]<br>
Size: [512, 512, 101]<br>
Spacing: [1.36719, 1.36719, 2.5]<br>
Origin: [-350, -350, -402]<br>
Direction:<br>
1 0 0<br>
0 1 0<br>
0 0 1<br>
<br>
PixelContainer:<br>
ImportImageContainer (0x8f93188)<br>
RTTI typeinfo: itk::ImportImageContainer<//unsigned long, short><br>
Reference Count: 1<br>
Modified Time: 66<br>
Debug: Off<br>
Observers:<br>
none<br>
Pointer: 0xb4d31008<br>
Container manages memory: true<br>
Size: 26476544<br>
Capacity: 26476544/<br>
<br>
for the NIFTI image:<br>
/RTTI typeinfo: itk::OrientedImage<short, 3u><br>
Reference Count: 1<br>
Modified Time: 119<br>
Debug: Off<br>
Observers:<br>
none<br>
Source: (0xa1788e8)<br>
Source output index: 0<br>
Release Data: Off<br>
Data Released: False<br>
Global Release Data: Off<br>
PipelineMTime: 12<br>
UpdateMTime: 120<br>
LargestPossibleRegion:<br>
Dimension: 3<br>
Index: [0, 0, 0]<br>
Size: [512, 512, 101]<br>
BufferedRegion:<br>
Dimension: 3<br>
Index: [0, 0, 0]<br>
Size: [512, 512, 101]<br>
RequestedRegion:<br>
Dimension: 3<br>
Index: [0, 0, 0]<br>
Size: [512, 512, 101]<br>
Spacing: [1.36719, 1.36719, 2.5]<br>
Origin: [-350, -350, -402]<br>
Direction:<br>
1 0 0<br>
0 1 0<br>
0 0 1<br>
<br>
PixelContainer:<br>
ImportImageContainer (0xa17b198)<br>
RTTI typeinfo: itk::ImportImageContainer<//unsigned long, short><br>
Reference Count: 1<br>
Modified Time: 117<br>
Debug: Off<br>
Observers:<br>
none<br>
Pointer: 0xb4d22008<br>
Container manages memory: true<br>
Size: 26476544<br>
Capacity: 26476544/<br>
<br>
<br>
Then I open the nifti image with MIPAV image viewer (<a href="http://mipav.cit.nih.gov/download.php" target="_blank">http://mipav.cit.nih.gov/download.php</a>) and if I re-save it using MIPAV I get incorrect origin:<br>
<br>
/OrientedImage (0x99ddfe0)<br>
RTTI typeinfo: itk::OrientedImage<short, 3u><br>
Reference Count: 1<br>
Modified Time: 119<br>
Debug: Off<br>
Observers:<br>
none<br>
Source: (0x99db8e8)<br>
Source output index: 0<br>
Release Data: Off<br>
Data Released: False<br>
Global Release Data: Off<br>
PipelineMTime: 12<br>
UpdateMTime: 120<br>
LargestPossibleRegion:<br>
Dimension: 3<br>
Index: [0, 0, 0]<br>
Size: [512, 512, 101]<br>
BufferedRegion:<br>
Dimension: 3<br>
Index: [0, 0, 0]<br>
Size: [512, 512, 101]<br>
RequestedRegion:<br>
Dimension: 3<br>
Index: [0, 0, 0]<br>
Size: [512, 512, 101]<br>
Spacing: [1.36719, 1.36719, 2.5]<br>
Origin: [-350, 350, -402]<br>
Direction:<br>
1 0 0<br>
0 1 0<br>
0 0 1<br>
<br>
PixelContainer:<br>
ImportImageContainer (0x99de198)<br>
RTTI typeinfo: itk::ImportImageContainer<//unsigned long, short><br>
Reference Count: 1<br>
Modified Time: 117<br>
Debug: Off<br>
Observers:<br>
none<br>
Pointer: 0xb4cbf008<br>
Container manages memory: true<br>
Size: 26476544<br>
Capacity: 26476544/<br>
<br>
<br>
I wonder that ti is a MIPAV problem but I'm not sure! I can't understand why MIPAV changes the origin...Anyone knows this problem?<br>
<br>
And if the problem is MIPAV I can use something else to do some pre-elaboration on the images and than work with itk?<br>
<br>
Thanks for any hints.<br>
Elena Faggiano<br>
<br>
<br></div></div>
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</blockquote>
</blockquote></div><br></div>