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# System prepended metadata

title: Lunch and Learn Q&A

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# Lunch and Learn Q&A

## Helpful Links

### Today's Lesson Links

Set-Up instructions:  https://carpentries-incubator.github.io/SDC-BIDS-sMRI/setup.html

Binder Link: https://mybinder.org/v2/gh/carpentries-incubator/SDC-BIDS-sMRI/gh-pages

Gather.town (for questions after class): https://gather.town/app/crw4gUbf3vie7Wxm/brainhack-ON-lounge 

Gather.town password: BrainHackON

Post Workshop Survey: https://docs.google.com/forms/d/e/1FAIpQLSeIwpGs_GSTFA29jj7w8mHGs4YopbpIFNMH_WIjhLKE6zd9xg/viewform

### Full Series Links

Full Lunch and Learn Series Resources: https://conp-pcno-training.github.io/2021-05-28-conp-online/

Another index for neurocarpentry lessons: https://conp-pcno-training.github.io/neuroimaging-carpentry/

Intro MRI carpentry gitrepo (last week): https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/

Intro MRI carpentry notes (last week): https://hackmd.io/t3Cl-gWjS-m6lnwpAYkLag?both

### Related resources

INCF-NeuroStars (stackoverflow for neuroscience/neuroimaging): https://neurostars.org 

BIDS-startkit (for more info on using BIDS): https://github.com/bids-standard/bids-starter-kit

The BIDS specification website: https://bids-specification.readthedocs.io/en/stable/

For hundreds of examples of data in BIDS format: https://openneuro.org/



## Questions & Answers

**Question**: After clicking the binder link. How do I find the notebooks?

The notebooks are inside the `code/` folder in the binder instance

**Question**: (RE: bias field correction) Is this to replace B0 shimming or is it a complement to reduce inhomogeneities artefact?

JB: This is to complement shimming : shimming is generally not perfect. But there would be an awful lot of bias if there was no shimming :)

**Question**: What are the images normalized by?
[nikhil] MR image intensites themselves don't have much meaning. It's the contrast that matters. So many algorithms with normalize the intensity ranges to specific mean or min-max ranges. This helps with subsequent analysis e.g. segmentation of tissues.  

**Question**: Are there specific templates for brains undergoing aging, neurodegeneration (like Alzheimer’s disease) or cerebral small vessel disease/stroke?

[Sridar]: Yes, many groups have created population-specific templates for different diseases such as AD, MS, etc., as well as age groups (peds, elderly, etc.). I’m not sure these are all available in one place, though. You might have to ask the creators for access.
[Paule-J]:There is one developed by Fonov et al based on ADNI data, in particular. (https://hal.archives-ouvertes.fr/hal-00645521/document)

**Question**: Could all this be done with a different type of surface mesh file? For example .obj?

Some of the file loading
**Question**:



