Hello everyone,
I’m currently working on a study involving various pet images with different units of measurement. Some images are in BQML (Becquerels/milliliter), which is manageable as I can easily convert them to SUV (Standardized Uptake Value) in SLICER. However, I’m encountering difficulty with images measured in CNTS (Counts) and PROPCNTS (proportional to counts). My goal is to standardize all images to Becquerels/milliliter for registration and SUV factor computation.
I understand that I’ll need certain information from the DICOM, such as frame duration, to convert counts to counts per second. However, I’m unsure about the exact process. I’m sure someone has dealt with a similar issue before, and I’m hoping you can provide some guidance.
MR DICOM images from Siemens and GE typically embed all the details you need for processing the images. This is not the case for PET DICOM data: the manufacturer does not control the radiotracer and therefore they can not confidently include this into the DICOM tags. For this reason, the PET DICOM images are not sufficient for subsequent processing.
I would suggest using PET2BIDS which includes documentation. This will derive many parameters from the DICOM data, but also allows you to provide a spreadsheet with details not included in the DICOMs.
Hello @neurolabusc,
Thank you for your answer, but I am having trouble using this package. Is something to do with the Python version. Additionally, I already extracted some data from the Dicom files and asked for the acquisition parameters of the studies, but I have not seen any information that isn’t in the Dicoms files already, so I am not sure about what should i provide in the spreadsheet. Also, I managed to organize and correct the dicoms images to compute the SUV factor on SLICER ( PET Standard Uptake Value Computation — 3D Slicer documentation. As you said that DICOM images are not sufficient for processing this type of measure, i would like to be sure about this results.
2024-02-13T23:00:00Z To proceed with PET2BIDS, I require additional data in a spreadsheet to complement what I have already extracted from the DICOM files. In order to convert the images from counts units to BQML units, I need a specific conversion factor from the PET scanner and/or the radionuclide used (e.g., F-FDG). Among the attributes available in the DICOM files, I have access to “Actual Duration of Frame,” “Specific Activity,” and “Radionuclide Total Dose.” However, it remains uncertain whether this information alone is sufficient to determine the conversion factor, as it also depends on the actual sensitivity of the scanner. Aditionally, the python instalation of pypet2bids package is giving me trouble to properly use it.
Hi @Enrique_Franky could you elaborate on the issues you’re having installing pet2bids? Namely the output/errors from running:
pip install pypet2bids
Additionally, if you could provide what operating system you’re using and the version of python as well that would be helpful in diagnosing your issue.
Concerning radioactivity data neurolabusc is correct when stating that:
“the manufacturer does not control the radiotracer and therefore they can not confidently include this into the DICOM tags.”
Sometimes the necessary data will be included in the dicom header, but typically we rely on these measurement as recorded outside of the scanner room. Hence why PET2BIDS allows for the injection of these values via command line args or in the form of a PET spreadsheet.
That said, it seems like someone handed you a pile of PET data and asked you to put it into BIDS. I think it may be difficult to convert from Counts per second and Proportional to Counts without a calibration factor between the counter and a known radioactive source; unless Proportional to Counts is that factor.
Are you able to reach out to the person who made that measurement? Or do you have access to any papers/methods associated with this data?
Hello @bendhouseart,
I contacted the responsible for the images and they clarified that I still could calculate the SUV with those units, so the problem was solved. Regarding the PET2bids problem that I have is not on the installation from pip, is regarding the usage of the command dcm2niix4pet as a file could not be found within the package: template_json.json from the metadata.
Ah, that’s a bug that I believe was fixed in past few months. I really need to yank the affected verisions of pypet2bids from PyPi…
I’d encourage you to try running the latest version of pypet2bids to see if the error occurs again.
Thanks,
Anthony