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C.7.6.3.1.4 Pixel Data and C.7.6.2.1.1 Image Position And Image Orientation

Dear All,

How should I reconcile the definitions of image coordinates in the 
"Pixel Data" and "Image Position and Image Orientation" sections of the 
2009 DICOM standard?

"Pixel Data" says that the pixels are labelled:

(1,1)  (1,2)  (1,3)  (1,4)  etc.
(2,1)  (2,2)  (2,3)  (2,4)  etc.
etc.

i.e. (row starting at 1, column starting at 1)

But the formula on the "Image Position And Image Orientation" section it 
say is said to determine "The mapping of pixel location (i, j)" but 
WHERE i Column index to the image plane. The first column is index zero. 
and j Row index to the image plane. The first row index is zero.

Should the image data be considered to be indexed from 0 or from 1?

Should the pixel coordinates (i,j) be (row, col) or (col, row)?

Many thanks,

Dr Chris Rodgers
University of Oxford.


-- QUOTE from the standard --
ftp://medical.nema.org/medical/dicom/2009/09_03pu3.pdf

C.7.6.3.1.4 Pixel Data
Pixel Data (7FE0,0010) for this image. The order of pixels sent for each 
image plane is left to
right, top to bottom, i.e., the upper left pixel (labeled 1,1) is sent 
first followed by the remainder of
row 1, followed by the first pixel of row 2 (labeled 2,1) then the 
remainder of row 2 and so on.
For multi-plane images see Planar Configuration (0028,0006) in this Section.

C.7.6.2.1.1 Image Position And Image Orientation

....
The Image Plane Attributes, in conjunction with the Pixel Spacing 
Attribute, describe the position
and orientation of the image slices relative to the patient-based 
coordinate system. In each image
frame the Image Position (Patient) (0020,0032) specifies the origin of 
the image with respect to
the patient-based coordinate system. RCS and the Image Orientation 
(Patient) (0020,0037)
attribute values specify the orientation of the image frame rows and 
columns. The mapping of
pixel location (i, j) to the RCS is calculated as follows:

<FORMULA>

Where:
Pxyz The coordinates of the voxel (i,j) in the frame’s image plane in 
units of mm.
Sxyz The three values of the Image Position (Patient) (0020,0032) 
attributes. It is the
location in mm from the origin of the RCS.
Xxyz The values from the row (X) direction cosine of the Image 
Orientation (Patient)
(0020,0037) attribute.
Yxyz The values from the column (Y) direction cosine of the Image 
Orientation (Patient)
(0020,0037) attribute.
i Column index to the image plane. The first column is index zero.
Δi Column pixel resolution of the Pixel Spacing (0028,0030) attribute in 
units of mm.
j Row index to the image plane. The first row index is zero.
Δj Row pixel resolution of the Pixel Spacing (0028,0030) attribute in 
units of mm."
0
Chris
6/8/2010 10:15:19 PM
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On 9 Cze, 00:15, Chris Rodgers <see-rodgers-org-uk-for-contact-
deta...@invalid.gg> wrote:
> Dear All,
>
> How should I reconcile the definitions of image coordinates in the
> "Pixel Data" and "Image Position and Image Orientation" sections of the
> 2009 DICOM standard?
>
> "Pixel Data" says that the pixels are labelled:
>
> (1,1) =C2=A0(1,2) =C2=A0(1,3) =C2=A0(1,4) =C2=A0etc.
> (2,1) =C2=A0(2,2) =C2=A0(2,3) =C2=A0(2,4) =C2=A0etc.
> etc.
>
> i.e. (row starting at 1, column starting at 1)
>
> But the formula on the "Image Position And Image Orientation" section it
> say is said to determine "The mapping of pixel location (i, j)" but
> WHERE i Column index to the image plane. The first column is index zero.
> and j Row index to the image plane. The first row index is zero.
>
> Should the image data be considered to be indexed from 0 or from 1?
>
> Should the pixel coordinates (i,j) be (row, col) or (col, row)?
>
> Many thanks,
>
> Dr Chris Rodgers
> University of Oxford.
>
> -- QUOTE from the standard --ftp://medical.nema.org/medical/dicom/2009/09=
_03pu3.pdf
>
> C.7.6.3.1.4 Pixel Data
> Pixel Data (7FE0,0010) for this image. The order of pixels sent for each
> image plane is left to
> right, top to bottom, i.e., the upper left pixel (labeled 1,1) is sent
> first followed by the remainder of
> row 1, followed by the first pixel of row 2 (labeled 2,1) then the
> remainder of row 2 and so on.
> For multi-plane images see Planar Configuration (0028,0006) in this Secti=
on.
>
> C.7.6.2.1.1 Image Position And Image Orientation
>
> ...
> The Image Plane Attributes, in conjunction with the Pixel Spacing
> Attribute, describe the position
> and orientation of the image slices relative to the patient-based
> coordinate system. In each image
> frame the Image Position (Patient) (0020,0032) specifies the origin of
> the image with respect to
> the patient-based coordinate system. RCS and the Image Orientation
> (Patient) (0020,0037)
> attribute values specify the orientation of the image frame rows and
> columns. The mapping of
> pixel location (i, j) to the RCS is calculated as follows:
>
> <FORMULA>
>
> Where:
> Pxyz The coordinates of the voxel (i,j) in the frame=E2=80=99s image plan=
e in
> units of mm.
> Sxyz The three values of the Image Position (Patient) (0020,0032)
> attributes. It is the
> location in mm from the origin of the RCS.
> Xxyz The values from the row (X) direction cosine of the Image
> Orientation (Patient)
> (0020,0037) attribute.
> Yxyz The values from the column (Y) direction cosine of the Image
> Orientation (Patient)
> (0020,0037) attribute.
> i Column index to the image plane. The first column is index zero.
> =CE=94i Column pixel resolution of the Pixel Spacing (0028,0030) attribut=
e in
> units of mm.
> j Row index to the image plane. The first row index is zero.
> =CE=94j Row pixel resolution of the Pixel Spacing (0028,0030) attribute i=
n
> units of mm."


Hi, I believe that column and row definition confuse people a little
bit.
When we move in column, we are taking pixels form each row (sic!).
Pixels in a single row are indexed by column index.

Voxel from column "i" and row "j" is V(i,j), we can think of it as
(x,y) on image.
Let as write a formula for the vector coordinates of voxel (i,j) in
the image plane ( units mm ).

First we have to move to the (0,0) 2D voxel position ( on image ) to
the patient 3D space - this is vector Sxyz  - the Image Position
(Patient).
The unit vector Xxyz is a direction of image row in 3D space, the
distance from point (0,0) to (i,j) in row direction is
i*PixelSpacing_x(column) and in column direction is
j*PicelSpacing_y(row) - this is i*delta_i, j*delta_j.
So if we want to move to the (i,j) position in 3D space we do as
follows:

Pxyz =3D Xxyz * ( i*delta_i,  j*delta_j, 0 ) + Yxyz * ( j*delta_j,
i*delta_i, 0 ) + Sxyz ,
where the vector multiplication is a dot product.

For example the 3D Px coordinate is:

Px =3D Xx*delta_i*i + Yx*delta_j*j + Sx .

This is the same equasion that can be derived from PS 3.3 just by
matrix vector multiplication.

So, to sum up:
In equation from C.7.6.2.1.1 Image Position And Image Orientation
(i,j) are (column,row)/(x,y) coordinates on image plane, the first
pixel (top left) has index (0,0) and it's position in patient 3D
coordinate space is vector Sxyz Image Position (Patient) (0020,0032) -
it is the location in mm from the origin of the RCS. The next pixel is
(1,0) - column 1, row 0.

image(i,j) =3D
                  0,0   1,0   3,0   4,0 ...       i=3D0,1,2... ; j=3D0
	          0,1   1,1   3,1   4,1 ...       i=3D0,1,2... ; j=3D1
	          ...



0
Bartosz
6/9/2010 7:13:57 AM
Dear Bartosz,

> So, to sum up:
> In equation from C.7.6.2.1.1 Image Position And Image Orientation
> (i,j) are (column,row)/(x,y) coordinates on image plane, the first
> pixel (top left) has index (0,0) and it's position in patient 3D
> coordinate space is vector Sxyz Image Position (Patient) (0020,0032) -
> it is the location in mm from the origin of the RCS. The next pixel is
> (1,0) - column 1, row 0.
>
> image(i,j) =
>                    0,0   1,0   3,0   4,0 ...       i=0,1,2... ; j=0
> 	          0,1   1,1   3,1   4,1 ...       i=0,1,2... ; j=1
> 	          ...

Thanks for the explanation. It is helpful. The geometry you describe is 
what I have actually programmed now and it seems to work.

However, it is NOT what the "Pixel Data" part of the DICOM standard says:

"C.7.6.3.1.4 Pixel Data
Pixel Data (7FE0,0010) for this image. The order of pixels sent for each 
image plane is left to
right, top to bottom, i.e., the upper left pixel (labeled 1,1) is sent 
first followed by the remainder of
row 1, followed by the first pixel of row 2 (labeled 2,1) then the 
remainder of row 2 and so on."

Do you think this part of the standard is erroneous?

If so, how should I propose a correction?

Chris.
0
Chris
6/9/2010 9:10:02 AM
On 9 Cze, 11:10, Chris Rodgers <see-rodgers-org-uk-for-contact-
deta...@invalid.gg> wrote:
> Dear Bartosz,
>
> > So, to sum up:
> > In equation from C.7.6.2.1.1 Image Position And Image Orientation
> > (i,j) are (column,row)/(x,y) coordinates on image plane, the first
> > pixel (top left) has index (0,0) and it's position in patient 3D
> > coordinate space is vector Sxyz Image Position (Patient) (0020,0032) -
> > it is the location in mm from the origin of the RCS. The next pixel is
> > (1,0) - column 1, row 0.
>
> > image(i,j) =3D
> > =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00,0 =A0 1,0 =A0 3,0 =A0 4,0 ... =
=A0 =A0 =A0 i=3D0,1,2... ; j=3D0
> > =A0 =A0 =A0 =A0 =A0 =A0 =A00,1 =A0 1,1 =A0 3,1 =A0 4,1 ... =A0 =A0 =A0 =
i=3D0,1,2... ; j=3D1
> > =A0 =A0 =A0 =A0 =A0 =A0 =A0...
>
> Thanks for the explanation. It is helpful. The geometry you describe is
> what I have actually programmed now and it seems to work.
>
> However, it is NOT what the "Pixel Data" part of the DICOM standard says:
>
> "C.7.6.3.1.4 Pixel Data
> Pixel Data (7FE0,0010) for this image. The order of pixels sent for each
> image plane is left to
> right, top to bottom, i.e., the upper left pixel (labeled 1,1) is sent
> first followed by the remainder of
> row 1, followed by the first pixel of row 2 (labeled 2,1) then the
> remainder of row 2 and so on."
>
> Do you think this part of the standard is erroneous?
>
> If so, how should I propose a correction?
>
> Chris.

Yes, I think you are right, I's sorry, I misunderstood you, maybe my a
little bit elaborative answer will be helpful for someone.
This should be revised by someone, please comment on this.
If this topic will catch no attention maybe you should change a title,
I thing it is a good place to communicate possible standard errors.
0
Bartosz
6/9/2010 9:55:53 PM
On 9 Cze, 23:55, Bartosz Wiklak <bwik...@gmail.com> wrote:
> On 9 Cze, 11:10, Chris Rodgers <see-rodgers-org-uk-for-contact-
>
>
>
>
>
> deta...@invalid.gg> wrote:
> > Dear Bartosz,
>
> > > So, to sum up:
> > > In equation from C.7.6.2.1.1 Image Position And Image Orientation
> > > (i,j) are (column,row)/(x,y) coordinates on image plane, the first
> > > pixel (top left) has index (0,0) and it's position in patient 3D
> > > coordinate space is vector Sxyz Image Position (Patient) (0020,0032) =
-
> > > it is the location in mm from the origin of the RCS. The next pixel i=
s
> > > (1,0) - column 1, row 0.
>
> > > image(i,j) =3D
> > > =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A00,0 =A0 1,0 =A0 3,0 =A0 4,0 ..=
.. =A0 =A0 =A0 i=3D0,1,2... ; j=3D0
> > > =A0 =A0 =A0 =A0 =A0 =A0 =A00,1 =A0 1,1 =A0 3,1 =A0 4,1 ... =A0 =A0 =
=A0 i=3D0,1,2... ; j=3D1
> > > =A0 =A0 =A0 =A0 =A0 =A0 =A0...
>
> > Thanks for the explanation. It is helpful. The geometry you describe is
> > what I have actually programmed now and it seems to work.
>
> > However, it is NOT what the "Pixel Data" part of the DICOM standard say=
s:
>
> > "C.7.6.3.1.4 Pixel Data
> > Pixel Data (7FE0,0010) for this image. The order of pixels sent for eac=
h
> > image plane is left to
> > right, top to bottom, i.e., the upper left pixel (labeled 1,1) is sent
> > first followed by the remainder of
> > row 1, followed by the first pixel of row 2 (labeled 2,1) then the
> > remainder of row 2 and so on."
>
> > Do you think this part of the standard is erroneous?
>
> > If so, how should I propose a correction?
>
> > Chris.
>
> Yes, I think you are right, I's sorry, I misunderstood you, maybe my a
> little bit elaborative answer will be helpful for someone.
> This should be revised by someone, please comment on this.
> If this topic will catch no attention maybe you should change a title,
> I thing it is a good place to communicate possible standard errors.

Hi, I reissue Chris question, could someone take a look, please?
I believe we all know how to read pixel data but this description
could be erroneous.
0
Bartosz
7/14/2010 6:55:23 AM
Reply:

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Re: Puzzle: Converting 1-10 to 1,2,3,4,5,6,7,8,9,10 #3
Very nice! -Mary ----- Original Message -----=20 From: Toby Dunn=20 To: SAS-L@LISTSERV.UGA.EDU=20 Sent: Friday, October 03, 2008 3:55 PM Subject: Re: Puzzle: Converting 1-10 to 1,2,3,4,5,6,7,8,9,10 Data _Null_ ; Length NewString $ 200 ; String =3D '1-10,21,22,30-35,40,41' ; Do I =3D 1 To ( 1 + CountC( String , ',' ) ) ; TempA =3D Scan( String , I , ',' ) ; If Find( TempA , '-' ) Then Do ; Start =3D Input( Scan( TempA , 1 , '-' ) , Best12. ) ; Stop =3D Input( Scan( TempA , 2 , '-' ) , Best12. ) ; ...

Enhanced MR Image Storage/1.2.840.10008.5.1.4.1.1.4.1 : 2005,7e,Philips MR Imaging DD 001
Hi there, Could someone from Philips confirms that (2005,7e,Philips MR Imaging DD 001) is actually storing some kind of Z-spacing when the multiframe image in an Enhanced MR Image Storage is homogenous ? Thanks ...

how can i write this statement labels=[1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;2;3;3;3;3;3;3;3;3;3;3;3;3;3;3;3;3;3;3;3;3;3;3;3;3;]; in compress fo
How to write it in compact form to avoid repetition "shah " <shahkhn3@gmail.com> wrote in message <lodugh$8hr$1@newscl01ah.mathworks.com>... > How to write it in compact form to avoid repetition You'll find in this thread different solutions for similar question http://www.mathworks.fr/matlabcentral/newsreader/view_thread/335814 Bruno ...

Please explain PS3.3-6.1.1 and PS3.3-6.1.2
PS3.3-6.1.1 reads: ...When an instance of a Composite IOD is communicated, this entire context is exchanged between Application Entities.... PS3.3-6.1.2 reads: ...When an instance of a Normalized IOD is communicated, the context for that instance is not actually exchanged. Instead, the context is provided through the use of pointers to related Normalized IOD instances. If I understand it correctly, 6.1.1 says the composite object has all the info needed to fully understand the IOD. But I can't quite figure out what 6.1.2 is saying. By a "Pointer", Is it saying...

Re: Dependency problems migrating from 2.4.2 to [wx 2.6.1, WinXP, VC 7.1] #2
Hi Ben, > If it were unreasonable for a cross-platform app to use libjpeg (as you seem > to be implying) then a huge majority of cross-platform open-source apps out > there are "unreasonable." Is there, in fact, a shared jpeg library guaranteed to be available on all versions of Windows? > This is really bizarre to encounter this on the wx mailing list. Since when > does Microsoft have any say at all in how developers create cross-platform > apps? If they did, we wouldn't be using wxWidgets. If you develop wxWidgets applications for Microsoft...

Does Paramiko 1.7.2 and 1.6.4 work with CentOS 4
Hi Groups, Can you please help me on the following... 1. Does Paramiko 1.7.2 and 1.6.4 work with CentOS 4 2. If yes, what is the exact 'yum' command to install paramiko on CentOS 4? I have tried all possible ones without success. yum install paramiko yum install python-paramiko(with and without version numbers) python-paramiko.noarch Installing it without yum throws dependency problems which are never ending : starting with python-crypto and python(abi) - which I am unable to find. Is there any change that has to be made to the yum repository to point it t...

Upgrade of Xalan 1.2.2 and Xerces 1.4.4 to Xalan 2.6 and Xerces 2.6.2
I've been tasked with upgrading the JVM from 1.3 to 1.4, and the third party libraries used by my company on our existing Java framework. I'm most worried about any problems that may occur due to upgrading Xalan and Xerces as our framework performs much XML transformation and processing. Does anyone have a link to known issues with such an upgrade (besides the Xalan / Xerces sites) ? Or has anyone done such an upgrade and can share their pearls of wisdom? Thanks Chris ...

Web resources about - C.7.6.3.1.4 Pixel Data and C.7.6.2.1.1 Image Position And Image Orientation - comp.protocols.dicom

Orientation - Wikipedia, the free encyclopedia
In Animal navigation , turning the body to a desired heading, e.g. in the correct direction of migration Text is available under the Creative ...

Photo Academy: Orientation on the App Store on iTunes
Get Photo Academy: Orientation on the App Store. See screenshots and ratings, and read customer reviews.

DEMO Fall 2010 - Exhibitors Orientation - Flickr - Photo Sharing!
The Launchpad for Emerging Technology. DEMO Fall 2010 is taking place at the Hyatt in Silicon Valley, CA. Companies both large and small come ...

Rev. Phil Snider speech at Springfield City Council Meeting on sexual orientation - YouTube
PLEASE WATCH THE WHOLE VIDEO - A creative speech by the Rev. Phil Snider, at the the Springfield, Missouri City Council Meeting on August 13, ...

Immigration Minister Scott Morrison tells asylum seekers to go home in 'orientation video'
Immigration Minister Scott Morrison says he makes no apologies for an assertive video telling asylum seekers on Manus Island and Nauru that they ...

iFixit Apple Pencil teardown reveals twin emitters to measure angle & orientation, logic board folded ...
... that the plastic outer casing reveals a metal inner one. The tip contains two separate emitters, used to determine both the angle and orientation ...

Justice Department suggests that employment discrimination based on sexual orientation is already illegal ...
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Deadpool, His Sexual Orientation, And Twitter
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Science: Sexual Orientation Is Not Purely Biological
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Dede Gardner And Jeremy Kleiner: “‘The Big Short’ Isn’t A Film For Any One Particular Political Orientation” ...
Plan B co-presidents Dede Gardner and Jeremy Kleiner are producers operating at the highest level, finding themselves and their films in the ...

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