Short Survey - Help us create and curate a neuroimaging GitHub repo

Analyzing and Reusing Data
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1

Hey everyone,

Following up on the earlier post on May 19th about setting up a shared GitHub repo for imaging methods & scripts – we want to make sure we focus on what’s actually useful for you all.

1. What types of analyses would you love to see included first?

  • Data preprocessing (Accessing, download, conversion, management, QA, etc..).
  • Structural MRI (segmentation, volumetrics, cortical thickness, other)
  • Diffusion (DTI, free-water, tractography)
  • Functional (resting-state, connectivity, network analysis)
  • Quantitative mapping (QSM, T1/T2*, relaxometry)
  • Accessing, download, and data management
  • Structural Analyses
  • DTI
  • Functional MRI
  • QMRI( QSM, MPM, etc.)
  • DAT-SPECT
0 voters

2. Any “must-have” methods/pipelines you always wished someone had shared?
The repo will be community-driven, so your input will directly shape what we build first. Also—if you’re up for sharing your own scripts later, even better!

Looking forward to seeing what you all find most useful!

2

Thank you for championing this effort, @AmgadDroby ! While I don’t have much experience in neuroimaging myself, I’d be very excited to access and use the features generated by such a repo! So unfortunately I can’t contribute much in terms of suggesting types of analyses, but I hope to hear the guidance of this community about which analyses are most informative.

3

Hi @AmgadDroby, this is great – would you mind if I shared with the folks at the PPMI Imaging WG and an MJFF imaging mailing list?

5

@jgottesman : Yes definitely, that is a great idea!

6

Hi all! Bumping the survey in this thread to the top of the home page to see if any community members with interest in imaging have input as to which type of analyses they’d like to see in a neuroimaging repo on GitHub. @Shamabed @dmarinme @braah @Ollena5 @whiter @nisha @buddhi @tiago.azevedo @jf.daneault @kbarkut @ADalby @rickhelmich @bmarebwa @flokri @raybonj @sherinechan

The DCoP’s Imaging Interest Group (within the Data Modality and Methodology Task Force) will be developing methods and scripts to help accelerate your research, and your feedback is crucial to this effort!

7

Thanks for asking! In general I’d be interested in scripts to preprocess MRI, given it’s such a complex issue, and the FreeSurfer-processed MRI given by PPMI is only at baseline at the moment.

Another thing that I feel would be very useful is related to the datscans. As it was discussed in a previous thread it seems there’s information missing about how these scans have been preprocessed recently.

Thanks!