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UCL / STIR-GATE-Connection

Example files on how to run STIR on GATE data
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Segmentation Fault when Unlisting .root files from mMR scanner #96

Open averygong07 opened 1 month ago

averygong07 commented 1 month ago

Hi, I have been trying to run ExampleSTIR-GATE.sh with the provided mMR scanner. I have run PrepareScannerFiles.hs to ensure that UnlistingTemplates contained the correct template, but I keep running into this issue in the unlist step. Can anyone provide any insight into why this is happening? I tried the same with D690, and it worked just fine (despite not producing Delayed tree).

` LmToProjData NOT Using FRAME_BASED_DT_CORR lm to projdata parameters := input file := Output/Sim_mMR_test2.Coincidences.hroot template projdata := UnlistingTemplates/STIR_scanner.hs frame definition file := num events to store := -1 output filename prefix := Output/Unlisted/Coincidences/Sino_Sim_mMR_test2.Coincidences_S1R1 bin normalisation type for pre-normalisation := None

bin normalisation type for post-normalisation := None

maximum absolute segment number to process := 5 do pre normalisation := 0 num tof bins in memory := 1 num segments in memory := 11 store prompts := 1 store delayeds := 1 list event coordinates := 0 end :=

Processing time frame 1

Break segmentation violation

=========================================================== There was a crash. This is the entire stack trace of all threads:

0 0x00007f38fe612e0b in waitpid () from /lib64/libc.so.6

1 0x00007f38fe566747 in do_system () from /lib64/libc.so.6

2 0x00007f38ffb43e80 in TUnixSystem::StackTrace() () from /usr/lib64/root/libCore.so

3 0x00007f38ffb46465 in TUnixSystem::DispatchSignals(ESignals) () from /usr/lib64/root/libCore.so

4

5 0x00000000004ad9b9 in stir::InputStreamFromROOTFileForECATPET::get_next_record(stir::CListRecordROOT&) ()

6 0x00000000004f2b1f in stir::LmToProjData::process_data() ()

7 0x0000000000425a94 in main ()

===========================================================

The lines below might hint at the cause of the crash. If you see question marks as part of the stack trace, try to recompile with debugging information enabled and export CLING_DEBUG=1 environment variable before running. You may get help by asking at the ROOT forum https://root.cern/forum preferably using the command (.forum bug) in the ROOT prompt. Only if you are really convinced it is a bug in ROOT then please submit a report at https://root.cern/bugs or (preferably) using the command (.gh bug) in the ROOT prompt. Please post the ENTIRE stack trace from above as an attachment in addition to anything else that might help us fixing this issue.

5 0x00000000004ad9b9 in stir::InputStreamFromROOTFileForECATPET::get_next_record(stir::CListRecordROOT&) ()

6 0x00000000004f2b1f in stir::LmToProjData::process_data() ()

7 0x0000000000425a94 in main ()

===========================================================`

robbietuk commented 1 month ago

I believe there is an issue with the mMR example and the use of virtual crystals in STIR, see #88 and #87. I think the functionality to fix this is in STIR but I have not got much time to fix it.

KrisThielemans commented 1 month ago

It could be it, although that example was carefully written to avoid the use of virtual crystals. I'm not sure why it crashes. The best way to proceed would be recompile STIR in RelWithDebInfo (or ideally even Debug) mode, and run it again. we'll get more specific line number information.

Alternatively, you update the mMR example according to my updates in #88. a PR for that would be greatly welcomed.