Hi Simon,
Sorry to bother you again. Just want to check if I have used
itkChangeInformationImageFilter correctly in the snippet of code below:
using FilterType = itk::ChangeInformationImageFilter<ImageType>;
FilterType::Pointer filter = FilterType::New();
ImageType::ConstPointer inputImage = reader->GetOutput();
ImageType::PointType firstOrigin = inputImage->GetOrigin();
ImageType::SpacingType firstSpacing = inputImage->GetSpacing();
for (unsigned int i= 0; i < Dimension;i++) {
firstSpacing[i]*=0.2;
}
filter->SetOutputSpacing(firstSpacing);
filter->ChangeSpacingOn();
ImageType::PointType::VectorType translation;
translation[0] = -0.5*1951*0.2;
translation[1] = -0.5*1951*0.2;
translation[2] = -0.5*1951*0.2;
firstOrigin += translation;
filter->SetOutputOrigin(firstOrigin);
filter->ChangeOriginOn();
filter->SetInput(reader->GetOutput());
...
feldkamp->SetInput(0, constantImageSource->GetOutput());
feldkamp->SetInput(1, filter->GetOutput());
Also, I would like to ask if there are any difference to the PixelType being
unsigned short or unsigned char? This is because the source code fail to
compile when I used unsigned short on one computer but it works on the other
computer.
Looking forward to your reply and answers! Much thanks in advance!
Regards,
lyh
________________________________
From: Simon Rit <[email protected]>
Sent: Wednesday, January 13, 2021 5:07 PM
To: Lai Yao Hao <[email protected]>
Cc: [email protected] <[email protected]>
Subject: Re: [Rtk-users] FirstReconstruction questions
Hi,
For the first line (rtksimulatedgeometry), it's already there I believe. For
the second line, as I said, you need to use itkChangeInformationImageFilter and
set the origin and spacing of the projections equal to those given by
newspacing and neworigin.
Simon
On Wed, Jan 13, 2021 at 9:51 AM Lai Yao Hao
<[email protected]<mailto:[email protected]>> wrote:
Hi Simon
Thank you so much for your help; the reconstructed image is almost similar to
the image you sent (see attached file). In the previous email, for the command
lines
rtksimulatedgeometry -n 100 -o g --sid 278.044 --sdd $(echo 278.044+372.528 |
bc -l) -f 6.3
rtkfdk -p images -r p_[0-9]*.tif -o fdk.mha -g g --newspacing 0.2 --neworigin
$(echo -0.5*1951*0.2 | bc -l) --spacing 0.25 --dimension 512
how do I get this line into the test.cxx file? If there is no way to get these
lines into the test.cxx file, then do I run these lines in the terminal?
Look forward for your favourable reply.
With thanks
lyh
________________________________
From: Simon Rit
<[email protected]<mailto:[email protected]>>
Sent: Tuesday, January 12, 2021 4:22 AM
To: Lai Yao Hao <[email protected]<mailto:[email protected]>>
Cc: [email protected]<mailto:[email protected]>
<[email protected]<mailto:[email protected]>>
Subject: Re: [Rtk-users] FirstReconstruction questions
Hi lyh,
I had a look at what you've sent. I obtain a first result with the following
command lines:
rtksimulatedgeometry -n 100 -o g --sid 278.044 --sdd $(echo 278.044+372.528 |
bc -l) -f 6.3
rtkfdk -p images -r p_[0-9]*.tif -o fdk.mha -g g --newspacing 0.2 --neworigin
$(echo -0.5*1951*0.2 | bc -l) --spacing 0.25 --dimension 512
The newspacing and neworigin options set the projections spacing and origin
with the ChangeInformationImageFilter. The result is not perfect, I believe the
geometry is not right yet. Maybe there is a detector offset you're not aware
of? But your text file indicate no offset so I don't know what's wrong.
Attached is a snapshot. There are also some dead pixels which you could try to
prefilter.
I hope this helps. Cheers,
Simon
On Tue, Jan 5, 2021 at 5:35 PM Lai Yao Hao
<[email protected]<mailto:[email protected]>> wrote:
Hi,
I cannot send the projections via email as the projections are too big in size.
Instead, I am sharing the files on Drive, with the hyperlink as below. In the
folder, there is a subset of 100 projections out of the 800 projections, with
the angle between each projection being 3.6 degrees. There are other details on
the projects as listed in report.txt file in the folder.
Google drive share link:
https://drive.google.com/drive/folders/1wMRo3Rmr6HszUVil0vEsLPtLSLftFyfQ?usp=sharing
Regards
lyh
________________________________
From: Simon Rit
<[email protected]<mailto:[email protected]>>
Sent: Tuesday, January 5, 2021 5:21 PM
To: Lai Yao Hao <[email protected]<mailto:[email protected]>>
Cc: [email protected]<mailto:[email protected]>
<[email protected]<mailto:[email protected]>>
Subject: Re: [Rtk-users] FirstReconstruction questions
Hi,
I think the issue is that your projection images are given in the TIFF file
format which does not contain important meta information such as the origin and
the spacing of the projections. You should use
ChangeInformationFilter<https://itk.org/Doxygen/html/classitk_1_1ChangeInformationImageFilter.html>
to set these. I'm guessing that the origin is currently (0,0) and since you do
not set any offsets when using AddProjection, it comes down to having the
corner of your projection aligned with the central ray (line defined by the
source and the center of rotation).
You can share projections or a subset of them if you'd like us to give it a try
with your code.
Good luck!
Simon
On Mon, Jan 4, 2021 at 4:35 PM Lai Yao Hao
<[email protected]<mailto:[email protected]>> wrote:
Hi,
The code is as attached. Just for further reference, I am given images as
attached, and there are 800 of them, with 0.45 degrees separating each frame.
The naming of the screenshots depicts the frame that it is in.
Thanks in advance for the advice and help!! I really appreciate this community 🙂
Regards
lyh
________________________________
From: Simon Rit
<[email protected]<mailto:[email protected]>>
Sent: Wednesday, December 30, 2020 9:35 PM
To: Lai Yao Hao <[email protected]<mailto:[email protected]>>
Cc: [email protected]<mailto:[email protected]>
<[email protected]<mailto:[email protected]>>
Subject: Re: [Rtk-users] FirstReconstruction questions
Hi,
RTK cone beam reconstruction filters expect line integrals but the projection
that you are showing seems to have the highest value in air. RTK automatically
processes such projections with log and normalization if the pixels are
unsigned short. Otherwise, you need to do it yourself.
It is not clear if the geometry is correct from the reconstruction screen shot.
The best would be to share your code if you want us to have a look.
Simon
On Mon, Dec 28, 2020 at 8:34 AM Lai Yao Hao
<[email protected]<mailto:[email protected]>> wrote:
Dear Simon and the RTK community
Really thank you for the answer, and really sorry for the late reply. I am
trying to reconstruct a 3d model using 800 images, rotating an object 360
degrees using rtk::ThreeDCircularProjectionGeometry, rtk::ConstantImageSource
and rtk:: FDKConeBeamReconstructionFilter from the FirstReconstruction example
as well as itk::ImageSeriesReader.
However, the reconstruction created is shown above in the screenshot and after
checking all the parameters, I have no idea on how to move forward from here.
From reading the forums, I think that I should do one more image filter before
applying the cone beam reconstruction? However, I am not too sure. Please
advise on the next steps that can enable me to get the 3d reconstruction.
Thanks so much in advance and look forward to everyone's reply!!
PS: the tif file is just 1 of the 800 images I am given to reconstruct the
object
Regards
lyh
________________________________
From: Simon Rit
<[email protected]<mailto:[email protected]>>
Sent: Wednesday, December 9, 2020 4:23 PM
To: Lai Yao Hao <[email protected]<mailto:[email protected]>>
Cc: [email protected]<mailto:[email protected]>
<[email protected]<mailto:[email protected]>>
Subject: Re: [Rtk-users] FirstReconstruction questions
Hi,
constantImageSource creates a constant volume. In the example, one is used as
input of the simulation of projections of an ellipsoid (rei) and one as input
of the reconstruction algorithm (feldkamp). fieldofview masks out (i.e., set to
0) voxels which are not in the field of view.
I don't understand your screenshot either but if you use the tiff format, make
sure you use a viewer capable of dealing with 3D tiff images (e.g.,
vv<http://vv.creatis.insa-lyon.fr> or ImageJ).
Simon
On Wed, Dec 9, 2020 at 8:59 AM Lai Yao Hao
<[email protected]<mailto:[email protected]>> wrote:
Hi to all the rtk-users
I am a new user of rtk, and I have some questions regarding the
FirstReconstruction example given in github. I have generated an image as
attached, with 4 tiny ball-like drawing hanging from the top. Can anyone
explain to me why do I get such image and what are the implications of
constantImageSource, rei, constantImageSource2, feldkamp and fieldofview?
Your explanation will be much appreciated. Thanks in advance!
Regards
lyh
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