Yes, that's allowed, other people did it before. On Wed, Jun 3, 2020 at 6:28 PM Benjamin W. Maloney < benjamin.w.maloney...@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 <wucha...@gmail.com> > *Sent:* Wednesday, June 3, 2020 11:20 AM > *To:* Simon Rit <simon....@creatis.insa-lyon.fr> > *Cc:* Andreas Andersen <andreasg...@gmail.com>; > rtk-users@public.kitware.com <rtk-users@public.kitware.com>; Benjamin W. > Maloney <benjamin.w.maloney...@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....@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 <andreasg...@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: agravga...@protonmail.com > > Cell: +45 3165 8140 > > > On Wed, 3 Jun 2020 at 03:34, Benjamin W. Maloney < > benjamin.w.maloney...@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....@creatis.insa-lyon.fr> > *Sent:* Tuesday, June 2, 2020 5:28 PM > *To:* Benjamin W. Maloney <benjamin.w.maloney...@dartmouth.edu> > *Cc:* rtk-users@public.kitware.com <rtk-users@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...@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 > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users@public.kitware.com > https://public.kitware.com/mailman/listinfo/rtk-users > <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpublic.kitware.com%2Fmailman%2Flistinfo%2Frtk-users&data=02%7C01%7CBenjamin.W.Maloney.TH%40dartmouth.edu%7Ca9b964ae6a564833be9808d807d1be87%7C995b093648d640e5a31ebf689ec9446f%7C0%7C0%7C637267944718999001&sdata=5ekJcPKdQWlVJ6wBlE%2BWfU27jTthHxdY3l8pK3cT8QU%3D&reserved=0> > > _______________________________________________ > Rtk-users mailing list > Rtk-users@public.kitware.com > https://public.kitware.com/mailman/listinfo/rtk-users > <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpublic.kitware.com%2Fmailman%2Flistinfo%2Frtk-users&data=02%7C01%7CBenjamin.W.Maloney.TH%40dartmouth.edu%7Ca9b964ae6a564833be9808d807d1be87%7C995b093648d640e5a31ebf689ec9446f%7C0%7C0%7C637267944719008995&sdata=QMk%2FdR8JyuuWAhr1ygl097rPZQlO5bg3RtbGE%2B%2F4V9I%3D&reserved=0> > > _______________________________________________ > Rtk-users mailing list > Rtk-users@public.kitware.com > https://public.kitware.com/mailman/listinfo/rtk-users > <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpublic.kitware.com%2Fmailman%2Flistinfo%2Frtk-users&data=02%7C01%7CBenjamin.W.Maloney.TH%40dartmouth.edu%7Ca9b964ae6a564833be9808d807d1be87%7C995b093648d640e5a31ebf689ec9446f%7C0%7C0%7C637267944719008995&sdata=QMk%2FdR8JyuuWAhr1ygl097rPZQlO5bg3RtbGE%2B%2F4V9I%3D&reserved=0> > >
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