[slicer-users] Wrong position for DICOM image

Luo, Jiajia 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.
> HTH,
> Steve
> 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.
>> 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 <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) [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>
>>>    [mailto: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
>>>    <mailto: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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