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AthenaEPI / dmipy

The open source toolbox for reproducible diffusion MRI-based microstructure estimation
MIT License
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Refactor acquisition scheme to take empty deltas for clinical data #33

Closed sitek closed 5 years ago

sitek commented 5 years ago

I'm attempting to set up an acquisition scheme for CSD for some data from a collaborator, and I'm having trouble finding little delta and big Delta, despite having the DICOM header. Where should I start looking for these values?

In trying to set up my analysis, one reference has beentutorial_setting_up_acquisition_scheme.ipynb. That notebook sets up the acquisition scheme for HCP data and says that the delta and Delta times we know from the HCP documentation in seconds. However, I'm also unable to find those values in the HCP docs (for instance, under "Diffusion Session Scan Protocol" in https://humanconnectome.org/storage/app/media/documentation/s1200/HCP_S1200_Release_Appendix_I.pdf.

rutgerfick commented 5 years ago

Hi Kevin, W.r.t the delta/Delta information from the Dicom, unfortunately it is vendor specific and possibly not even there. You can try to find the specific field number for the specific brand and software version and hope you can find it this way. Perhaps you can ask your collaborator directly for this information?

However, if all you want to do is e.g. MT-CSD without using restricted models (cylinders/spheres), then this information is not even used - you can just use the HCP pulse times for example without any impact on your study.

In a future update this model-dependent usage will be better clarified - bear with us while Dmipy is still being developed :-)

rutgerfick commented 5 years ago

Concerning the WU-Minn HCP diffusion times, I don't know why they're not included in the scanning protocol, but you can find them their accompanying paper:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3720790/

sitek commented 5 years ago

Thank you @rutgerfick! I'll use the HCP times without restricted models for now.

rutgerfick commented 5 years ago

Reopening issue to remind making adjustments to the acquisition schemes take take empty deltas and only throw an error with models are used that require deltas.

rutgerfick commented 5 years ago

Hi @sitek , you should now be able to use the acquisition schemes directly without having to put in fake delta/Delta values. Just load the latest version and the tutorial notebook is updated.