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6. Common problems
The master branch of Magia is not updated before it has been verified using the script magia_dev_test. This prevents releasing Magia versions that contain severe bugs. Despite this basic verification, it is possible that some bugs have not been caught. Please inform Tomi Karjalainen (tomi.karjalainen at utu.fi) of such cases.
In Turku PET Centre, by far the most common error source has been that the metadata have not been properly stored in AIVO. For example, frames are often missing. For instructions how to specify the metadata in AIVO, please see this page.
Another common problem is that the data have not been organised according to the instructions given in here.
Missing MRI It is quite common that when trying to MAGIA a study an error results because, even if the PET data are properly stored and AIVO correctly specifies the corresponding MRI code, the MR image files themselves are still missing. If you know where the MRI are, you should copy them under /scratch2/aivo/MRI and then try again.
Decay-correction The dc column of AIVO.PET informs magia whether the raw image files have already been corrected to injection time (1) or not (0). If it has not been specified, or it is -1, magia will terminate because it should apply decay-correction if the correction not been done already. For every study started at injection, you should aivo_set_info(image_id,'dc',1). If you have a late-scan, and the dicoms (or the ecats) have not been decay-corrected, then you need to set dc = 0 and the first number of the frames string must be time since injection. for example, frames = 60 65;65 70;70 75;75 80, or frames = 90 100. If you have a late scan, and the dicoms (or the ecats) have been decay-corrected, then you need to set dc = 1, but still the first number of the frames string must be time since injection. for example, frames = 60 65;65 70;70 75;75 80, or frames = 90 100. Thus, the frames will always carry the information about time since injection. The column injection_time in aivo.pet has nothing to do with how magia corrects for decay.