[slicer-users] Wrong position for DICOM image
jiajialuo2000 at gmail.com
Wed Apr 28 17:01:35 EDT 2010
Hi Xiaodong and Steve,
Thanks for your explanations.
I will try 'rotate to volume plane' first. I think it can show the images in
its original orientation too. I will also try to rotate those cross-section
planes to get the [0 0 1] plane direction, since the original Image
Orientation (plane direction) is very close to [0 0 1]. There must be small
errors during the scan process. Then I can view it in axial view.
On Wed, Apr 28, 2010 at 4:17 PM, Steve Pieper <pieper at bwh.harvard.edu>wrote:
> Hi Jiajia, Xiaodong -
> As Xiaodong points out, slicer uses the /patient/ centered definition of
> the slice planes, so if the volume was acquired obliquely with respect to
> the patient you will see resampled slices in the slice viewers. (Some viewer
> software will show /pixel/ space by default, which is why it won't always
> look the same as the slicer default).
> For slicer we feel the patient centered display is more appropriate, since
> many studies will include several different orientations and slicer's
> display shows them overlaid in a common coordinate system.
> On the slice viewers there is a menu option called "Rotate to Volume Plane"
> that displays the pixel locations of the background volume. If you make the
> slices visible (with the eyeball icon) you can see the effect of this in the
> 3D viewer.
> On Apr/28/10 4:01 PM, Xiaodong Tao wrote:
>> 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.
>> On Apr 28, 2010, at 3:40 PM, Luo, Jiajia wrote:
>> Hi Xiaodong,
>>> Yes, the displayed axial orientation is different from the original
>>> 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...
>>> On Wed, Apr 28, 2010 at 9:37 AM, Tao, Xiaodong (GE, Research)
>>> <taox at research.ge.com <mailto: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)  - Image Orientation =
>>> 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.
>>> *From:* slicer-users-bounces at bwh.harvard.edu
>>> <mailto:slicer-users-bounces at bwh.harvard.edu>
>>> [mailto:slicer-users-bounces at bwh.harvard.edu
>>> <mailto:slicer-users-bounces at bwh.harvard.edu>] *On Behalf Of *Luo,
>>> *Sent:* Tuesday, April 27, 2010 3:47 PM
>>> *To:* slicer-users at bwh.harvard.edu
>>> <mailto:slicer-users at bwh.harvard.edu>
>>> *Subject:* [slicer-users] Wrong position for DICOM image
>>> 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?
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