[Rtk-users] .dat to .mha image

[Laura Trubuil]

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
>>>>
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at openrtk.org
>>>> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users
>>>>
>>>> ________________________________
>>>> The information contained in this message may be confidential and
>>>> legally
>>>> protected under applicable law. The message is intended solely for the
>>>> addressee(s). If you are not the intended recipient, you are hereby
>>>> notified
>>>> that any use, forwarding, dissemination, or reproduction of this
>>>> message is
>>>> strictly prohibited and may be unlawful. If you are not the intended
>>>> recipient, please contact the sender by return e-mail and destroy all
>>>> copies
>>>> of the original message.
>>>>
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at openrtk.org
>>>> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users
>>>>
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at openrtk.org
>>>> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at openrtk.org
>>>> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users
>>>>
>>