[Rtk-users] .dat to .mha image

Tue May 28 14:30:13 EDT 2013

Hi Laura,
I think you are missing a point in the geometry definition. By
default, it assumes that the ray going through the source and the
isocenter (point of coordinate 0 0 0 in the volume) is intersecting
the projection at coordinate (0 0). In the projection that you have
sent, (0 0) is the corner of your image.
Two solutions :
- run the geometry specifying the translation
rtksimulatedgeometry -o geometry.xml -n 1 --sdd 300 --sid 150
--proj_iso_x -50 --proj_iso_y -50
rtkbackprojections -p . -r headerOneImage.mhd -o test.mha -g geometry.xml
- Change the origin of your image in your mhd file by adding the following line
Offset = -50 -50
Simon

On Mon, May 27, 2013 at 3:44 PM, Laura Trubuil
<laura.trubuil at mail.medecom.fr> wrote:
> Dear RTK-users,
>
> I am working on reconstruction with RTK backprojection algorithm.
> RTK Wiki examples worked fine but now, I am trying with my own images, and I
> obtain a result I cannot explain.
>
> I have 15 projections, simulated with GATE. My phantom is a water cylinder,
> containing 4 balls of different materials.
> I attached one of them with the mail, to give an example (the other are
> quite similar, only the place of the balls changes).
>
> I generate a geometry.xml file with the command : rtksimulatedgeometry -o
> geometry.xml -n 15 --sdd 300 --sid 150
> and then apply rtkbackprojection with : rtkbackprojections -o output.mha -g
> geometry.xml -r header.mhd -p.
> I display output.mha with VTK and obtain a white cube...
>
> Does anybody have an idea of what I am missing? Is the number of projections
> too small? Is it a display problem?
>
> Regards,
>
> Laura Trubuil
>
>
>
> Le 13/05/2013 16:14, Simon Rit a écrit :
>
> Dear Laura,
> If you use rtk::FDKConeBeamReconstructionFilter, there is a weighting
> by the angular gap (angular distance between the previous and the next
> projection) so that will be a problem. If you only use the
> backprojection, that should not be a problem.
> With FDK, there are a few solutions, the simplest being to trick the
> algorithm by adding 2 projections with zeros at the beginning and the
> end of your tomosynthesis acquisition.
> If you have some problems with the geometry, don't hesitate to provide
> your Gate macros and we can try to help.
> Simon
>
> On Tue, May 7, 2013 at 10:05 AM, Laura Trubuil
> <laura.trubuil at mail.medecom.fr> wrote:
>
> Dear Simon,
> Thank you for your help.
>
> It is a circular cone beam CT, yes.
> In fact, what I precisely do is working on tomosynthesis. I use the CT
> scanner simulator of GATE as a basis for a tomosynthesis simulation. The
> only differences are that the X-Ray dose is lower, and the angle is not 360°
> but 40° maximum. I do not think it is a problem for RTK, is it?
> First, I intend to use RTK backprojection, and then, I will try to enhance
> the quality of the reconstruction by filtering techniques.
>
> I have already done some simulations on GATE, for small animal in a first
> time (because the computation time is too long for real human chest
> detectors, which are much bigger). It allows me to work on algorithms and
> test reconstruction with something, for the moment! I will be glad to help
> you if I can.
>
> I will continue studying RTK examples, I will let you know if I make some
> progress. Thanks again.
>
> Regards,
>
> Laura
>
>
> Le 07/05/2013 01:50, Simon Rit a écrit :
>
> Hi,
> I don't know the CT simulation module of Gate so I can't help you. I
> will discuss this matter with my colleagues. We are currently working
> on a new CT simulation module but we definitely need to investigate
> how one can reconstruct from the existing module. What is the geometry
> of the scanner, is it circular cone-beam CT? It is the only geometry
> that RTK can handle.
> To understand how to use mhd files, you can look at other examples on
> RTK wiki. We will work on your problem and I'll let you know as soon
> as we have progressed but keep us informed if you make some progresses
> on your side.
> Regards,
> Simon
>
> On Mon, May 6, 2013 at 9:21 AM, Laura Trubuil
> <laura.trubuil at mail.medecom.fr> wrote:
>
> Dear Simon,
>
> Thank you for your answer.
> I  am using the CT Scanner simulation in GATE, so the output available
> are
> the ".root" and the ".dat" only.
>
> First, I simply tried to change the extension ".dat" to ".mhd" or to
> ".raw"
> but, as expected, it does not work because I need to specifiy which kind
> of
> data the file contains (the role of the header in fact...).
> Then, I tried to do something with the GateToImage Class, which contains
> a
> function called WriteMHD, but it was not a success... I did not find a
> way
> to directly obtain ".mhd" from a CT Scanner simulation from GATE. That is
> when I decided to ask the RTK users!
>
> With M. Mory's method, I am now able to open  my ".dat" files with
> ImageFileReader function from ITK, and visualize it with VTK.
>
>
> For the moment, I am trying to reconstruct slices from 15 projections
> acquired with the CT Scanner example in GATE.
> Have you got any example of reconstruction of slices from projections
> with
> RTK?
>
> I already studied the Sphere reconstruction tuto, but it does not help me
> to
> understand how I can make use of my ".mhd" files in the RTK algorithms. I
> will do further research work.
>
> Regards,
>
> Laura Trubuil
>
>
>
> Le 05/05/2013 11:20, Simon Rit a écrit :
>
> Dear Laura,
> I think that in the latest version of Gate, you should be able to
> write mhd files. hdr file format should also work in both platforms.
> What happens if you change the extension of your output files to .mhd?
> Regards,
> Simon
>
> On Thu, May 2, 2013 at 10:51 AM, MORY, CYRIL <Cyril.Mory at philips.com>
> wrote:
>
> Hi Laura,
>
> In the .mhd and .raw format, the .raw file is a binary file of floats
> (or
> whatever) representing the pixel intensities, and the .mhd a simple
> header
> that indicates the number of dimensions, the size in pixels along each
> dimension, ... Your .dat seems to be exactly the same as the .raw
> You can create the .mhd header yourself, using a text editor. Here is
> an
> example :
>
> ObjectType = Image
> NDims = 2
> BinaryData = True
> BinaryDataByteOrderMSB = False
> CompressedData = False
> TransformMatrix = 1 0 0 1
> Offset = -190.5 -190.5
> CenterOfRotation = 0 0
> ElementSpacing = 3 3
> DimSize = 128 128
> ElementType = MET_FLOAT
> ElementDataFile = SheppLogan.raw (try to replace this field with your
> .dat filename)
>
> If I were you, I'd start by trying to adjust these parameters until you
> manage to visualize a single projection (there are plenty of viewers
> that
> open mhd/raw files), and then create a header for the whole sequence
> (NDims
> = 3, etc ...) and concatenate the .dat binary files into a single one.
> You
> could use a script like the following :
>
> #!/bin/bash
> # Concatenate all projections into a single raw file
> NbProj=300
> i=0
> list="projection${i}.raw"
> for i in $(seq 1 1 $(($NbProj-1)))
> do
>           list="$list projection${i}.raw"
> done
> cat $list > SheppLogan.raw
>
> which would concatenate all files named "projection0.raw",
> "projection1.raw", ... into "SheppLogan.raw"
>
>
> -----Message d'origine-----
> De : rtk-users-bounces at openrtk.org
> [mailto:rtk-users-bounces at openrtk.org]
> De la part de Laura Trubuil
> Envoyé : jeudi 2 mai 2013 09:29
> À : rtk-users at openrtk.org
> Objet : [Rtk-users] .dat to .mha image
>
> Dear RTK users,
>
> I am working on GATE (from Geant4), to create projections images of
> tomosynthesis.
> I have projections but they are in ".dat" format (binary matrix of
> float
> numbers that stores the simulated tomosynthesis image and is produced
> for
> each time slice).
>
> I want to reconstruct a 3D volume, from projections, with RTK.
> To do that, I know I must change the format of my images (for example
> to
> .mhd/.raw or to .mha format) but my problem is that I do not know how.
>
> I anyone could help...
>
> Regards,
>
> Laura
>
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