Drop support for dcm and ecat files?

[tkkarjal]

Currently Magia can read the raw PET files in dcm, ecat or nifti format, and the MR images in dcm format. However, ecat is no longer used at least in Turku, so it would make sense to no longer support that option. While the raw image files are these days stored in dicom format, sometimes the study consists of several parts, and Magia cannot handle these cases. For example, in a recent FDG study there was a brain scan starting from an injection, and also a late scan 80-100 minutes after injection. For such cases, it would make a lot of sense to use all of these data in Patlak analyses, but Magia currently cannot handle that.

Another source of confusion is that sometimes the dicoms have not been decay-corrected to injection time, but the nifti has been corrected. It is possible that in such cases the user can misspecify the dc option in Magia, which may cause Magia to either double-correct for decay or not correct for it all. Having only one input image (the nifti) available would make this complication disappear.

Dropping support for dicoms would mean that the user would have to do the dcm2nii-conversion and the possible decay-corrections prior to magia analysis. However, that would not be too many lines of code in a script. Forcing the user to do the dcm2nii-conversion would also make visual quality control of the raw images more likely.

Many other pipelines only use niftis (e.g. fmriprep), and the change would not actually be that radical.

Of course relying only on niftis would also save disk space, as the dicoms could be deleted.

[tkkarjal]

Another reason for dropping support for dicoms: Sometimes the dicom-to-nifti conversion does not work. For example, recently in Turku we came across MRI data that SPM (and dcm2niix) refused to convert into nifti format.

[tkkarjal]

Maybe it would make sense to first enable using niftis also for MRIs, and once that works it might make sense to drop support for the dicoms completely.