Tutorials/Documentation

[ewalke31]

• [x] Decide if it is better to do a notebook for each broad step (preprocessing, registration, etc.) and link top of box to beginning of notebook & link each specific step to subsections of the notebook OR just do separate notebook for each specific step
• [x] Create HTML image map of fngs pipeline flowchart so that each step links to a notebook
• [x] Slice-timing correction writeup (adapt from the one I created earlier in the semester -- provide basic examples, link to FSL documentation on slicetimer)
• [x] Motion correction writeup (adapt from Tanay's writeup -- include examples, link to FSL documentation on MCFLIRT)
• [x] Self-registration writeup (register fMRI to T1w, here have a breakdown discussing FLIRT and epi_reg, adapt from Tanay's writeup on FLIRT, w/ links to FSL documentation, can include examples for each)
• [x] Template registration writeup (align T1w and MNI152, link to FLIRT discussion, breakdown of FNIRT)
• [x] Explanation of why we didn't use white matter nuisance correction (if I do notebook for each broad step this can just be viewed from the nuisance correction notebook -- otherwise put it in high pass filtering notebook)
• [x] Linear drift removal/quadratic detrending writeup
• [x] High pass filtering writeup
• [x] T1 effect removal writeup -- not specifically on the flowchart so maybe just include in overall nuisance correction notebook or in high pass filtering breakdown
• [x] Timeseries estimation writeup (include both voxel & ROI w/ explanation of why both are included)
• [x] Post-processing writeup (connectivity estimation, discriminability explanations)
• [x] Quality control writeup (include info on what quality control metrics we use/report and why) -- figure out where this should be linked from as it's not specifically on the flowchart (decide whether to have an overall notebook for this or just include it within any relevant notebooks)