[Elastix] Elastix Digest, Vol 13, Issue 12

Maina Mambo mainamambo at gmail.com
Sat Apr 20 15:47:16 CEST 2013


Happy Birthday Stefan,

*Franklinmambo*
Doctorate Student,
Department of Electrical Engineering,
Faculty of Engineering and the Built Environment,
Tshwane University of Technology.
Private Bag X680 Pretoria 0001.
Cell Phone: +27 84 777 3864




On Sat, Apr 20, 2013 at 1:00 PM, <elastix-request at bigr.nl> wrote:

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> Today's Topics:
>
>    1. Re: RAS or LPS coordiante system? (S. Klein)
>    2. Re: RAS or LPS coordiante system? (Kannan U V)
>    3. Re: RAS or LPS coordiante system? (Bilal Tahir)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 19 Apr 2013 10:29:15 +0000
> From: "S. Klein" <s.klein at erasmusmc.nl>
> To: Bilal Tahir <b.tahir at sheffield.ac.uk>
> Cc: "elastix at bigr.nl" <elastix at bigr.nl>
> Subject: Re: [Elastix] RAS or LPS coordiante system?
> Message-ID:
>         <7C41B7569649A140AFBC0BDB59E932180EB36097 at EXCH-RX03.erasmusmc.nl>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Bilal, elastix takes into account the direction cosines of the images.
> Do you store the landmarks in world coordinates or in voxel coordinates?
> Do you use the .vtk format or the input point .txt format to supply the
> points to transformix?
> In your registration, did you set UseDirectionCosines to "true"?
> Kind regards,
> Stefan
>
> On 18/04/2013 02:52, Bilal Tahir wrote:
> Dear All,
>
> I recently moved from VV to Slicer for defining expert landmarks on fixed
> and moving images prior to registration. I then use transformix to deform
> the fixed points so I can compare them with original moving points via the
> target registration error.
>
> One thing I noticed is that Slicer defines the points (via fudicial
> markers in the annotations module) in the RAS coordinate system as default.
> Putting these values into transformix gives me completely wrong results. Is
> Elastix based on the LPS coordinate system as default or another one? Below
> is part of  my header data for the fixed image:
>
> ObjectType = Image
> NDims = 3
> BinaryData = True
> BinaryDataByteOrderMSB = False
> CompressedData = False
> TransformMatrix = 1 0 0 0 1 0 0 0 1
> Offset = -215.592 -417.592 -323.5
> CenterOfRotation = 0 0 0
> AnatomicalOrientation = RAI
> ElementSpacing = 0.816406 0.816406 1.78125
> DimSize = 512 512 160
> ElementType = MET_SHORT
> ElementDataFile = fixed.raw
>
> Here is the header data for the moving image:
>
> ObjectType = Image
> NDims = 3
> BinaryData = True
> BinaryDataByteOrderMSB = False
> CompressedData = False
> TransformMatrix = 1 0 0 0 1.52656e-015 -1 0 1 5.55112e-017
> Offset = -212.209 -155 200.502
> CenterOfRotation = 0 0 0
> AnatomicalOrientation = RSA
> ElementSpacing = 1.6797 1.6797 10
> DimSize = 256 256 24
> ElementType = MET_SHORT
> ElementDataFile = moving.raw
>
> I look forward to hearing your replies.
>
> Cheers,
>
> Bilal Tahir,
> James Morrison Researcher in Radiotherapy Imaging
>
>
>
> _______________________________________________
> Elastix mailing list
> Elastix at bigr.nl<mailto:Elastix at bigr.nl>
> http://lists.bigr.nl/cgi-bin/mailman/listinfo/elastix
>
>
>
> --
> Stefan Klein
> +31 10 7043049
> http://www.bigr.nl/people/StefanKlein
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> ------------------------------
>
> Message: 2
> Date: Fri, 19 Apr 2013 08:24:54 -0400
> From: Kannan U V <kannanuv at cshl.edu>
> To: Stefan Klein <s.klein at erasmusmc.nl>
> Cc: Elastix <elastix at bigr.nl>
> Subject: Re: [Elastix] RAS or LPS coordiante system?
> Message-ID:
>         <
> CAH1Audnv9dhYW-0WmLcHwXkRW5MUxNQ4CCfo5cwmEJNHczxfxw at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Bilal, did you take into account the fact that the transformation is
> inverse
> On Apr 19, 2013 6:29 AM, "S. Klein" <s.klein at erasmusmc.nl> wrote:
>
> >  Hi Bilal, elastix takes into account the direction cosines of the
> images.
> > Do you store the landmarks in world coordinates or in voxel coordinates?
> > Do you use the .vtk format or the input point .txt format to supply the
> > points to transformix?
> > In your registration, did you set UseDirectionCosines to "true"?
> > Kind regards,
> > Stefan
> >
> > On 18/04/2013 02:52, Bilal Tahir wrote:
> >
> > Dear All,
> >
> >  I recently moved from VV to Slicer for defining expert landmarks on
> > fixed and moving images prior to registration. I then use transformix to
> > deform the fixed points so I can compare them with original moving points
> > via the target registration error.
> >
> >  One thing I noticed is that Slicer defines the points (via fudicial
> > markers in the annotations module) in the RAS coordinate system as
> default.
> > Putting these values into transformix gives me completely wrong results.
> Is
> > Elastix based on the LPS coordinate system as default or another one?
> Below
> > is part of  my header data for the fixed image:
> >
> >  ObjectType = Image
> > NDims = 3
> > BinaryData = True
> > BinaryDataByteOrderMSB = False
> > CompressedData = False
> > TransformMatrix = 1 0 0 0 1 0 0 0 1
> > Offset = -215.592 -417.592 -323.5
> > CenterOfRotation = 0 0 0
> > AnatomicalOrientation = RAI
> > ElementSpacing = 0.816406 0.816406 1.78125
> > DimSize = 512 512 160
> > ElementType = MET_SHORT
> > ElementDataFile = fixed.raw
> >
> >  Here is the header data for the moving image:
> >
> >  ObjectType = Image
> > NDims = 3
> > BinaryData = True
> > BinaryDataByteOrderMSB = False
> > CompressedData = False
> > TransformMatrix = 1 0 0 0 1.52656e-015 -1 0 1 5.55112e-017
> > Offset = -212.209 -155 200.502
> > CenterOfRotation = 0 0 0
> > AnatomicalOrientation = RSA
> > ElementSpacing = 1.6797 1.6797 10
> > DimSize = 256 256 24
> > ElementType = MET_SHORT
> > ElementDataFile = moving.raw
> >
> >  I look forward to hearing your replies.
> >
> >  Cheers,
> >
> > Bilal Tahir,
> > James Morrison Researcher in Radiotherapy Imaging
> >
> >
> > _______________________________________________
> > Elastix mailing listElastix at bigr.nlhttp://
> lists.bigr.nl/cgi-bin/mailman/listinfo/elastix
> >
> >
> > --
> > Stefan Klein+31 10 7043049http://www.bigr.nl/people/StefanKlein
> >
> >
> > _______________________________________________
> > Elastix mailing list
> > Elastix at bigr.nl
> > http://lists.bigr.nl/cgi-bin/mailman/listinfo/elastix
> >
> >
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 3
> Date: Fri, 19 Apr 2013 16:40:21 +0100
> From: Bilal Tahir <b.tahir at sheffield.ac.uk>
> To: "S. Klein" <s.klein at erasmusmc.nl>, "elastix at bigr.nl"
>         <elastix at bigr.nl>
> Subject: Re: [Elastix] RAS or LPS coordiante system?
> Message-ID:
>         <CAFZ9P6Eq7cHsgEBOUZnDBROyiEEAK0=
> Hm+XSKDipmcDN65xw5w at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Stefan,
>
> I stored the landmarks in world coordinates.
> I used the input .txt format and did set the DirectionCosines to "true".
>
> I think that as Slicer uses RAS coordinates as default, its just a matter
> of simply multiplying the X and Y coordinates by -1.
>
> For example, if we have the following RAS coordinates in slicer:
>
> 5, -4, 10
>
> The alternative to use would be:
>
> -5, 4, 10
>
> Notice how the Z in the sup-inf direction hasn't changed sign.
>
> This seems to have worked and is giving me appropriate TRE results.
>
> Here is the link for how slicer deals with coordinates:
>
> http://www.slicer.org/slicerWiki/index.php/Coordinate_systems
>
> I use slicer for landmarking over VV as it allows me to identify landmarks
> which can then be manually moved with the click of a mouse by a
> radiologist. However, I am interested to explore some other software for
> this. If anyone uses alternative software that they
> recommend specifically for landmarking then please let me know.
>
> Best wishes,
>
> Bilal
>
>
> On 19 April 2013 11:29, S. Klein <s.klein at erasmusmc.nl> wrote:
>
> >  Hi Bilal, elastix takes into account the direction cosines of the
> images.
> > Do you store the landmarks in world coordinates or in voxel coordinates?
> > Do you use the .vtk format or the input point .txt format to supply the
> > points to transformix?
> > In your registration, did you set UseDirectionCosines to "true"?
> > Kind regards,
> > Stefan
> >
> >
> > On 18/04/2013 02:52, Bilal Tahir wrote:
> >
> > Dear All,
> >
> >  I recently moved from VV to Slicer for defining expert landmarks on
> > fixed and moving images prior to registration. I then use transformix to
> > deform the fixed points so I can compare them with original moving points
> > via the target registration error.
> >
> >  One thing I noticed is that Slicer defines the points (via fudicial
> > markers in the annotations module) in the RAS coordinate system as
> default.
> > Putting these values into transformix gives me completely wrong results.
> Is
> > Elastix based on the LPS coordinate system as default or another one?
> Below
> > is part of  my header data for the fixed image:
> >
> >  ObjectType = Image
> > NDims = 3
> > BinaryData = True
> > BinaryDataByteOrderMSB = False
> > CompressedData = False
> > TransformMatrix = 1 0 0 0 1 0 0 0 1
> > Offset = -215.592 -417.592 -323.5
> > CenterOfRotation = 0 0 0
> > AnatomicalOrientation = RAI
> > ElementSpacing = 0.816406 0.816406 1.78125
> > DimSize = 512 512 160
> > ElementType = MET_SHORT
> > ElementDataFile = fixed.raw
> >
> >  Here is the header data for the moving image:
> >
> >  ObjectType = Image
> > NDims = 3
> > BinaryData = True
> > BinaryDataByteOrderMSB = False
> > CompressedData = False
> > TransformMatrix = 1 0 0 0 1.52656e-015 -1 0 1 5.55112e-017
> > Offset = -212.209 -155 200.502
> > CenterOfRotation = 0 0 0
> > AnatomicalOrientation = RSA
> > ElementSpacing = 1.6797 1.6797 10
> > DimSize = 256 256 24
> > ElementType = MET_SHORT
> > ElementDataFile = moving.raw
> >
> >  I look forward to hearing your replies.
> >
> >  Cheers,
> >
> > Bilal Tahir,
> > James Morrison Researcher in Radiotherapy Imaging
> >
> >
> > _______________________________________________
> > Elastix mailing listElastix at bigr.nlhttp://
> lists.bigr.nl/cgi-bin/mailman/listinfo/elastix
> >
> >
> > --
> > Stefan Klein+31 10 7043049http://www.bigr.nl/people/StefanKlein
> >
> >
>
>
> --
> Bilal Tahir,
> James Morrison Researcher in Radiotherapy Imaging
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> End of Elastix Digest, Vol 13, Issue 12
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