STIR Howto

Summary

This page refers to a number for smaller projects on how you can achieve things with STIR. Please also refer to the STIR documentation and the STIR FAQ.

Using STIR executables

1. STIR only simulations: see the samples/PET_simulation directory in your downloaded files
2. Combining XCAT, ASIM and STIR
3. Running SimSET and STIR: see the SimSET directory in your downloaded files
4. Using STIR with Docker (a post by Ashley Gillman on how he uses Docker to run in STIR executables in a container)

Developing new code using STIR

1. Create Custom InputFileFormat

Check also the STIR developer's overview.

Using STIR on data of your scanner

Sadly, at present most commercial scanners do not disclose their data formats (although this is slowly changing). This means that STIR cannot just handle the data of your scanner and you will need to do extra work. Your first point of call is probably the STIR users mailing list (but please don't discuss confidential information on the list).

Some links that might help.

1. A report on using STIR for data of the Siemens Biograph 64, True Point, True V PET/CT by Sabine Lee. The report also contains some examples of image and sinogram templates. This reports provides nice information on how to investigate if you read the data correctly. (note that it doesn't talk about normalisation nor randoms).

1. a FAQ on the mechanics of adding an unsupported scanner

Using STIR with GATE

PET

It is recommended to use ROOT output and either use the STIR utility to convert to projection data lm_to_projdata, or the list mode reconstruction methods. You will need to create a header file for the ROOT file first. There is an example root_header.hroot file in examples/samples.

You could also use conv_GATE_raw_ECAT_projdata_to_interfile.

SPECT

Please check Han Gyu Kang's STIR User's Meeting 2018 presentation. It might be somewhat out-of-date as the STIR SPECT functionality is improving.

Content license

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