[Rtk-users] .dat to .mha image

[Simon Rit]

I think you do not use an adequate window level when you display your
image. Try using vv (http://vv.creatis.insa-lyon.fr) which default WL
is adjusted to the min / max of your image.
Simon

On Wed, May 29, 2013 at 9:49 AM, Laura Trubuil
<laura.trubuil at mail.medecom.fr> wrote:
> Dear Simon,
> Thank you for your answer.
> I have tried this morning both of your techniques but, unfortunately, I
> obtain the same result as I had previously. There is still something I am
> missing I guess... If anybody has suggestions!
> Regards,
>
> Laura
>
>
>
> Le 28/05/2013 20:30, Simon Rit a écrit :
>
>> 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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>
>