[Rtk-users] Questions about xim / fdk

[Sharp, Gregory C.]

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<mailto: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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