[Rtk-users] .dat to .mha image

Mon Jun 3 03:07:30 EDT 2013

Hi Laura,

Judging from the projection image you sent, you seem to be missing a crucial step.
The area around your water cylinder is white and the balls are black. This is probably what GATE generates, and it's the raw data you would obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations.
Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction.

I'm not a specialist of this step of the reconstruction, but some people on this list probably know the details and can help you further.

Regards,
Cyril

De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Laura Trubuil
Envoyé : lundi 27 mai 2013 15:45
À : rtk-users at openrtk.org
Objet : Re: [Rtk-users] .dat to .mha image

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><mailto: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><mailto: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><mailto: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>

[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<mailto: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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