[Rtk-users] Reconstruction Artifact

Wed Jun 3 13:04:45 EDT 2020

Yes, that's allowed, other people did it before.

On Wed, Jun 3, 2020 at 6:28 PM Benjamin W. Maloney <
Benjamin.W.Maloney.TH at dartmouth.edu> wrote:

> Hi all,
>
> Thanks for the help!
> I'll be sure to make sure my preprocessed data is handled correctly.
>
> The reconstruction is meant to be a square, it is of a CIRS ACR digital
> mammography phantom
>
> I'm trying to send an example of my data but I can't get it under 147 MB
> data limit, is there a preferred method for sending this? I could send a
> google drive link if that is allowed
>
> Thanks again!
> Ben
>
> ------------------------------
> *From:* Chao Wu <wuchao04 at gmail.com>
> *Sent:* Wednesday, June 3, 2020 11:20 AM
> *To:* Simon Rit <simon.rit at creatis.insa-lyon.fr>
> *Cc:* Andreas Andersen <andreasga22 at gmail.com>;
> rtk-users at public.kitware.com <rtk-users at public.kitware.com>; Benjamin W.
> Maloney <Benjamin.W.Maloney.TH at dartmouth.edu>
> *Subject:* Re: [Rtk-users] Reconstruction Artifact
>
> If your projections record the number of X-ray photon counts instead of
> attenuation, an I0 must be set correctly and a logarithmic operation is
> needed before the projection data can be fed to the reconstruction loop.
> Both the I0 and the logarithmic operation can be handled by the RTK
> projection reader or manually, depending on your implementation. Zero and
> negative numbers must be coerced for the logarithmic operation by you if
> this is not the case in the RTK code you use.
>
> Regards,
> Chao
>
> Simon Rit <simon.rit at creatis.insa-lyon.fr> 于2020年6月3日周三 下午2:35写道：
>
> Yes, there is no such limitation as far as I know, you can use negative
> numbers and value above 1.
> Your result is really strange, it it supposed to be a square? I don't know
> what is the problem but that's clearly a geometry issue. We can always have
> a look if you're able to share some data.
> Simon
>
> On Wed, Jun 3, 2020 at 1:56 PM Andreas Andersen <andreasga22 at gmail.com>
> wrote:
>
> I don't think there are any restrictions technically.
> You should be able to use negative values, as the main arithmetic is just
> a sum
> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FSimonRit%2FRTK%2Fblob%2Fmaster%2Finclude%2FrtkBackProjectionImageFilter.hxx%23L106&data=02%7C01%7CBenjamin.W.Maloney.TH%40dartmouth.edu%7Ca9b964ae6a564833be9808d807d1be87%7C995b093648d640e5a31ebf689ec9446f%7C0%7C0%7C637267944718989010&sdata=vjk%2FNtQ43Dnf%2Bboaz1dCEIacZSG1gDh5LSqA76wDS%2Fg%3D&reserved=0>
> and a multiplication
> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FSimonRit%2FRTK%2Fblob%2Fmaster%2Finclude%2FrtkBackProjectionImageFilter.hxx%23L115&data=02%7C01%7CBenjamin.W.Maloney.TH%40dartmouth.edu%7Ca9b964ae6a564833be9808d807d1be87%7C995b093648d640e5a31ebf689ec9446f%7C0%7C0%7C637267944718989010&sdata=ehz4gp3sMhs%2Bi0onEIdlbC%2Fnc%2FG4YFT27qN6FAwlGgo%3D&reserved=0>
> .
>
> The only restriction I can see is that this sum and multiplication should
> not overflow (or underflow for negative values) the underlying type of the
> output image, as that would be undefined behaviour. Over- and underflow is
> unlikely for float, unless you have extremely high values (see wikipedia
> for floating point range
> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fen.wikipedia.org%2Fwiki%2FFloating-point_arithmetic%23Range_of_floating-point_numbers&data=02%7C01%7CBenjamin.W.Maloney.TH%40dartmouth.edu%7Ca9b964ae6a564833be9808d807d1be87%7C995b093648d640e5a31ebf689ec9446f%7C0%7C0%7C637267944718999001&sdata=0NX7PRKcro7Knu2wq8VuePPleTRH1MdAvJlL10xmQHk%3D&reserved=0>
> ).
>
> /Andreas
>
> __________________________________
>
> Andreas Gravgaard Andersen
>
> Danish Center for Particle Therapy,
>
> Aarhus University Hospital
>
> Palle Juul-Jensens Blvd. 99,
>
> 8200, Aarhus
>
> Mail:     agravgaard at protonmail.com
>
> Cell:      +45 3165 8140
>
>
> On Wed, 3 Jun 2020 at 03:34, Benjamin W. Maloney <
> Benjamin.W.Maloney.TH at dartmouth.edu> wrote:
>
> Hi,
>
> I thought the same in regards to trying to rotating in the other
> direction. Unfortunately, that has a similar artifact but with the
> reconstruction flipped.
> Interestingly the overlap happens in a similar place but the internal
> structures are flipped
>
> 1. Thanks!
> 2. I should have worded that better. My projection images will be
> preprocessed in a float format. I wanted to check if there were
> restrictions on these float values. Can input image data have negative
> values or high values? Or are they expected to have values between 0 and 1?
> I ask because some of the tools I have used to do this preprocessing
> (outside of RTK) have given negative values or 'stretched' the data from 0
> to 255 before saving.
>
> Ben
>
> ------------------------------
> *From:* Simon Rit <simon.rit at creatis.insa-lyon.fr>
> *Sent:* Tuesday, June 2, 2020 5:28 PM
> *To:* Benjamin W. Maloney <Benjamin.W.Maloney.TH at dartmouth.edu>
> *Cc:* rtk-users at public.kitware.com <rtk-users at public.kitware.com>
> *Subject:* Re: [Rtk-users] Reconstruction Artifact
>
> Hi,
> Sometimes rotating in the wrong direction gives this kind of artefacts.
> It's quite possible that we don't use the same convention as other toolkits
> regarding this.
> For other questions:
> 1. Yes, you can use pixel as the unit. Then the image spacing should be 1
> obviously and indeed, sdd and sid should be in pixels.
> 2. I don't fully understand. If your data is the output of a count
> detector, then you either rely on RTK to guess the counts without object to
> compute the line integral, or your preprocess your projections to pass line
> integrals in a float format.
> Simon
>
> On Tue, Jun 2, 2020 at 4:51 PM Benjamin W. Maloney <
> Benjamin.W.Maloney.TH at dartmouth.edu> wrote:
>
> Hi all,
>
> Not sure if this is the right group to post to but here's my question:
>
> I have a code that pulls in my own projection images and uses
> the FDKConeBeamReconstructionFilter for reconstruction
>
> The reconstruction I am getting has an artifact where it looks like there
> are two overlapping objects rotated.
> I have used other reconstruction toolboxes (mainly TIGRE in MATLAB) with
> the similar geometry inputs and not had this issue. I suspect the
> difference is in the parts of the geometry that are set by default. My
> question is if anyone has seen this before and what input I should look
> into?
>
> I have a few more questions I may or may not be related:
> 1. I assume that since I set the origin etc of my images in pixel, sid and
> sdd should be in pixels as well?
> 2. Are there restrictions related the scalar values of the projection
> data? My data will be in detector counts rather than linear attenuation
> coefficients, is that okay?
> I have attached an image to show this issue. It is supposed to be a
> rectangular mammography phantom. It is a slice in XZ plane
>
> Thanks for the help!
> Ben
>
>
>
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