Editing 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 
[http://stir.sourceforge.net/documentation  STIR documentation] and the [[STIR FAQ]].

= Using STIR executables =

# STIR only simulations: see the samples/PET_simulation directory in your downloaded files
# [[STIR-ASIM Howto | Combining XCAT, ASIM and STIR]]
# Running SimSET and STIR: see the SimSET directory in your downloaded files
# [http://ashgillman.github.io/2015/09/06/Developing-with-STIR-using-Docker.html 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 =
# [[STIR Howto Create Custom InputFileFormat | Create Custom InputFileFormat]]
Check also the [http://stir.sourceforge.net/documentation/STIR-developers-overview.pdf 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.

# [http://kth.diva-portal.org/smash/record.jsf?pid=diva2%3A866274&dswid=-4737 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).

# [[STIR_FAQ#How_do_I_add_my_own_scanner_to_STIR.3F | 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 <code>lm_to_projdata</code>, or the list mode reconstruction methods. You will need to create a
header file for the ROOT file first. There is an example <tt>root_header.hroot</tt> file in <tt>examples/samples</tt>.

You could also use <code>conv_GATE_raw_ECAT_projdata_to_interfile</code>.

== SPECT ==
Please check [https://www.researchgate.net/profile/Han_Kang5/post/How_can_I_reconstruct_SPECT_image_by_using_STIR/attachment/5cd425d9cfe4a7968d9df593/AS%3A756634762620929%401557407193778/download/%28STIR+User+Meeting%29%28Image+reconstruction+of+GATE+SPECT+simulation+data+using+STIR%29%282018_11_17_Han_Gyu_Kang_NIRS_QST_Final%29.pdf 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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