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SyneRBI / SIRF-Exercises

SIRF Training and demonstration material
http://www.ccpsynerbi.ac.uk
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SPECT Y90 data #188

Closed KrisThielemans closed 1 year ago

KrisThielemans commented 1 year ago

The SPECT notebook(s) contain

!pwd
!cp -r /mnt/materials/SIRF/PSMRTBP2022/Y90-NEMA-NPL/SPECT/* .
!ls .

and commented-out lines to download the data.

ideally this data-set is on Zenodo, and we add it to the download_data.sh script. In addition, the above lines rely on Linux and should be replaced by Python lines (like in the PET notebooks).

KrisThielemans commented 1 year ago

@danieldeidda we probably have no time to fix that this week I guess. Let me know.

danieldeidda commented 1 year ago

That data is on OSF https://osf.io/pcfb4/ which is the one used at NPL. There is a way to download data from there (using osfclient) but at the time of the PSMR school it was not working

danieldeidda commented 1 year ago

Actually it seems to work now just need to pip install osfclient and osf -p pcfb4 clone .

this could go into download data

KrisThielemans commented 1 year ago

I've modified the notebook accordingly but keep the issue as it should be added to download_data.sh

danieldeidda commented 1 year ago

sure, I guess it would would need to go on the SPECT data download since there isn't one. However, when running the line above will also download PET data

KrisThielemans commented 1 year ago

@danieldeidda is there a chance this will ever be split in PET and SPECT data? Or even on Zenodo? If not, we should close this issue.

As the notebook works fine, I certainly don't want to modify anything now before 3.5.

danieldeidda commented 1 year ago

Hi, OSF was the NPL selected way of sharing this. I'd rather not creating zenodo copies of the same data as this data has already been cited. If we want a separate PET and SPECT repository we possibly can create another one, from a different experiment.

KrisThielemans commented 1 year ago

ok, if it already has a DOI, then I wouldn't duplicate it. That seems the wrong thing to do, even if it is for splitting.

So yes, if we ever got some other experimental data, then we can use that. Can still be NPL's preferred way of sharing of course.

So I'll close this issue.