PPMI structural and diffusion MRI processing manual

Analyzing and Reusing Data
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Dear all,

We have recently processed the structural and diffusion MRI data of the PPMI dataset, and reported our processing pipeline at:
Imaging/PPMI_dMRI_Processing_Manual.pdf at main · MJFF-ResearchCommunity/Imaging · GitHub

We hope this manual will be useful for other PPMI users!

Sincerely,

Iman Aganj

https://iman.mgh.harvard.edu
Laboratory for Computational Neuroimaging
Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Harvard Medical School

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Thank you @Iman for the contribution.!!

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Hi Iman,

Thanks a lot for sharing this information!

I was thinking that for someone who doesn’t really know about neuroimaging, a great thing for your material to be more impactful would be to share more information about downloading everything. For example for me the LONI download dashboard is really confusing, and I never understand which files should be the ones to download or not (for example, which MRI files can I really download? Can I download the ones flagged as 2D or only sagittal/coronal? …). Assuming that we cannot share the idaSearch publicly, you could show how you selected the different parameters at the search space.

Also, for someone who doesn’t know much about coding might have difficulties in how to automatically transform your commands (like dcmunpack, recon-all, …) to all files downloaded. Maybe you could explain how one could “fill” in the command automatically rather than manually copying-pasting all files.

I hope you could work on these points, otherwise great resource, thanks a lot again! :slight_smile: