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jerdra / SDC-BIDS-fMRI_old

Scientific-Compute Working Group Workshop on performing analysis of neuroimaging data in python
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Ep 04 #20

Closed josephmje closed 5 years ago

josephmje commented 5 years ago

Currently, this notebook is in slide format. @jerdra can you post a link?

Decide where we want this. Before manipulating images or is its current spot ok?

jerdra commented 5 years ago

Yes! https://docs.google.com/presentation/d/1er6dQcERL-Yeb5-7A29tJnmqgHNaLpTLXM3e-SmpjDg/edit?usp=sharing

jerdra commented 5 years ago

Since we're dealing with processed data with filenames associated with processing. I think we should open with "The steps you need to know/do before beginning to analyze your data" section -which can be based on the pre-processing component of the slides/fmriprep bit.

josephmje commented 5 years ago

My argument for keeping it here is that it would be nice to start off with something practical right away instead of theory.

jerdra commented 5 years ago

sure we can compromise a bit and start with T1 images in the first nibabel notebook then talk a bit about pre-processing? I don't want to get into the nilearn section without first talking about pre-processing since we start using files with space-T1w/space-MNINonLinear*. Alternatively we could just use space-T1w and not mention anything until later..

josephmje commented 5 years ago

Yea that works! Are there any other concepts in the visualization section that you think we should cover with a practical example?

Not sure if registration is too much info

jerdra commented 5 years ago

nah I think we're good! Let me know if I can close this since it'll be completely based on the slides. We could have a very short notebook on just exploring the outputs?

But we're getting to a point of too much content (might be an issue...)

josephmje commented 5 years ago

This can be closed. I think the slides are enough. Can the slides be saved as a pdf or ppt somewhere in the repo?

jerdra commented 5 years ago

not sure but will try, I'll close it for now for the purposes of course preparation