[Rtk-users] .dat to .mha image

Laura Trubuil laura.trubuil at mail.medecom.fr
Wed May 29 07:06:35 EDT 2013 

Ok I will do further reasearches and take a look at that book. Thanks again!

Laura

Le 29/05/2013 12:56, Simon Rit a écrit :
> I'm not sure what you expected but this is the definition of the
> backprojection operator : assign to the voxels along each ray the
> value at the intersection between the ray and the projection image. So
> with a cone-beam geometry and a squared projection, you obtain a
> pyramid provided that the volume is large enough. Maybe you should try
> to obtain some basic information on filtered backprojection from a
> person in your group or in a book? Kak and Slaney's book is famous and
> freely available online:
> http://www.slaney.org/pct/
> Simon
>
> On Wed, May 29, 2013 at 12:05 PM, Laura Trubuil
> <laura.trubuil at mail.medecom.fr> wrote:
>> I am sorry to annoy you again but I installed VV and read my backprojection
>> reconstruction (outputBP.mha) with it.
>> It seems that I obtain a cube with a pyramid inside. Not what I expected
>> from a backprojection, I really do not understand.
>>
>> Laura
>>
>>
>> Le 29/05/2013 09:52, Simon Rit a écrit :
>>
>>> 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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