[Rtk-users] Questions about xim / fdk

Tue Mar 17 21:01:51 CET 2026

Thanks for the feedback. Note that Adrian Thummerer (Bcc) has prepared some
preprocessing code for the COBRA reconstruction challenge (TBA, 1000 raw
pelvis datasets, Elekta and Varian, stay tuned). He has done some
outstanding work for Varian, including an implementation of Varian's
scatter correction. You might want to have a look at it if you start
playing with Varian data:
https://github.com/cobra-challenge-2026/preprocessing
Cheers,
Simon

On Tue, Mar 17, 2026 at 6:43 PM Sharp, Gregory C. <gcsharp at mgb.org> wrote:

> This is outstanding.  Thanks!
>
>
>
> By dark and flood field, I was referring to the files in the Calibration
> folder (e.g. GainImage.xim, OffsetImage.xim).  But it appears the xim files
> are indeed corrected.
>
>
>
> -Greg
>
>
>
> *From:* Simon Rit <simon.rit at creatis.insa-lyon.fr>
> *Sent:* Monday, March 16, 2026 6:25 PM
> *To:* Sharp, Gregory C. <gcsharp at mgb.org>
> *Cc:* rtk-users <rtk-users at openrtk.org>
> *Subject:* Re: [Rtk-users] Questions about xim / fdk
>
>
>
> *        External Email - Use Caution        *
>
> Hi Greg,
>
> - rtk can convert these files in any ITK file format. Run
>
> rtkprojections -p DIRECTORY -r FILENAME -o test.mha --nolineint
>
> - They are not already dark and flood corrected. See the converting class
>
>
> https://github.com/RTKConsortium/RTK/blob/main/include/rtkVarianObiRawImageFilter.h#L35-L38
> <https://secure-web.cisco.com/11Ab1IGr-lFK3XBotE4RuLXuERQtAXKQf3CkhfVQQ9iZT-KkC2_n6MGFVomQqfRUVPYVHoyjIMhJPWxr8hHKi-8YBVaeeGcbq2H63ARZVqGLOMtZiq_yWchaEt4rJcg_NIM3VMl-cjcyokmoyRKA974QvcFP8j1hvBP2j6gJbupfgIfkYlNecEpd4oU-sm86qjuaLipQElHPYBS2NWBQuKIegbBC72jAiPFu88hj9rKWwNxjX_1BB70jX1bIJTp_JS_PJCGeaEjHPFKH5p4Aef7LeMUMpl2pBl8k47bGhz7KWlcqpAWQFbPKwjSEX_P8x/https%3A%2F%2Fgithub.com%2FRTKConsortium%2FRTK%2Fblob%2Fmain%2Finclude%2FrtkVarianObiRawImageFilter.h%23L35-L38>
>
> - The FDK output are in 1/length unit. The length unit are a user choice,
> so if you set all ditances (spacings in image meta information and lengths
> in RTK geometry) in mm, then you reconstruct in 1/mm.
>
> - Conversion to HU requires a linear conversion after calibrating the
> value for air and water. We don't do that usually but I believe there is an
> ITK filter for this conversion.
>
> - If you want to use a subset of projections, you can use our tool
> rtksubselect :
>
> srit at srit-Precision-5480:~$ rtksubselect -h
> RTK 2.7.0, git hash 5e5929a510fc5940dccba9a96eec70aa6597f2fc
>
> Subselects a few projections from a list of projection files and a
> geometry
> file.
>
> Usage: RTK [OPTIONS]... [FILES]...
>
>   -h, --help                 Print help and exit
>   -V, --version              Print version and exit
>   -v, --verbose              Verbose execution  (default=off)
>   -g, --geometry=STRING      XML geometry file name
>       --out_geometry=STRING  Output geometry file name
>       --out_proj=STRING      Output projections stack file name
>   -f, --first=INT            First projection index  (default=`0')
>   -l, --last=INT             Last projection index
>   -s, --step=INT             Step between projections  (default=`1')
>       --list=INT             List of projection indices to keep (0-based)
>
>
>
> Good luck with all this,
>
> Simon
>
>
>
>
>
>
>
> On Mon, Mar 16, 2026 at 7:51 PM Sharp, Gregory C. <gcsharp at mgb.org> wrote:
>
> Hi all,  I have a few questions:
>
> Is there any viewer for these files and/or can I convert them into mha?
>
> Are the xim files already dark and flood corrected?
>
> What are the units for the fdk output?  Can they be scaled into something
> like HU?
>
> Is there a way to specify subsets of gantry angles to be used in the fdk
> recon?
>
> Thank you,
> Greg
>
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