[slicer-users] Wrong position for DICOM image

Xiaodong Tao taox at ge.com
Wed Apr 28 16:01:56 EDT 2010


Hello Jiajia,

When "Ignore File Orientation" is checked, slicer loads in a dicom series ignoring information on ImageOrientationPatient, and therefore the display may not confirm to radiological convention of space (RAS or LPS) -- this is what you meant by "totally wrong". This is not a recommended way of loading images for any coordinate critical process -- such as registration of volume overlay. It just show you how the original slices are acquired. 

As a matter of fact, the image shown in your original post of THE "CORRECT" way of displaying a volume in that every voxel has the same and correct coordinates as piece of tissue that was imaged. Since the original images were acquired in oblique planes -- not axial, not coronal, not sagittal -- when you display an axial cross-section, it does not confirm with the original acquisition matrix.

Hope this clarifies things.

Xiaodong


On Apr 28, 2010, at 3:40 PM, Luo, Jiajia wrote:

> Hi Xiaodong,
>  
> Yes, the displayed axial orientation is different from the original image.
>  
> If I choose 'Ignore File orientation', the displayed image is totally wrong (see attached image 1). I also attached the original image viewed through RadPix (image 2).
>  
> I also tried other DICOM images which can be loaded corretly without choosing 'Ignore File orientation' and got same wrong displayed view when choosing 'Ignore file orientation'.  So I do not think we can check 'Ignore File orientation' to display correct orientation.
>  
> The interesting thing is when I load the DICOM images into slicer2, I can view the same images like through RadPix. So I exported those series DICOM images as .nrrd and then imported into slicer3. The result was perfect.
>  
> Now, the slicer 3 makes me confused...
>  
> Jiajia
> 
> On Wed, Apr 28, 2010 at 9:37 AM, Tao, Xiaodong (GE, Research) <taox at research.ge.com> wrote:
> Hello Jiajia,
>  
> When you say "wrong position", do you mean the images are not displayed in the axial orientation?
>  
> From my looking at the header and the image you sent, the display is correct. The images were acquired in oblique orientation:
>  
> (0020,0037) [102]   - Image Orientation   = 0.99810707569122\0.03886961564421\0.04765984416007\-0.0383889339864\0.99920278787612\-0.0109602091833
>  
> which indicates that the slices in the DICOM series are on plane normal to (-0.048 0.0091, 0.9988). Since Slicer3 takes into account image orientation, it will display a cross section that is perpendicular to (0,0,1).
>  
> If you want to see the images as acquired, you can check "Ignore File Orientation" before you click on "Apply".
>  
> Hope this helps.
> Xiaodong
> 
> From: slicer-users-bounces at bwh.harvard.edu [mailto:slicer-users-bounces at bwh.harvard.edu] On Behalf Of Luo, Jiajia
> Sent: Tuesday, April 27, 2010 3:47 PM
> To: slicer-users at bwh.harvard.edu
> Subject: [slicer-users] Wrong position for DICOM image
> 
> Hi,
>  
> I am using slicer 3.4 to add DICOM through file->add volume. The position of the DICOM image was wrong and I don't why (see attached picture). This is the first time I meet this kind of problem in Slicer 3 (slicer 2 can load this DICOM image). There may be something wrong with the header (attached header file). Can anyone help to figure out what is the problem?
>  
> Thanks,
>  
> Jiajia
> 
> <image1.png><image2.png>

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