# Lunch and Learn Q&A

## Helpful Links

Binder: https://mybinder.org/v2/gh/carpentries-incubator/SDC-BIDS-IntroMRI/gh-pages?filepath=code%2F

Carpentries Notes: https://carpentries-incubator.github.io/SDC-BIDS-IntroMRI/

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/

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

Gather.town password: BrainHackON

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/

## Questions & Answers

**Question**: Do I need python to learn from this course?

No, you can learn more about how MRI scans are organized and what kinds of files you are working with in the lesson!

**Question**: Where can I find the terminal?

Go to the dashboard of the jupyter notebook and click new on the top right. Terminal will be one of the four options.

**Question**: Where do I find the notebooks for the lesson inside the binder instance?

The notebooks are sitting inside the `code/` folder

**Question**: Do I need %%bash for each cell in the notebook?

Each cell you want to run bash in needs the %%bash tag. Outside of this lesson you could install a bask kernel for jupyter using the command `pip install bash_kernel`

**Question**: Where can I find solutions?

Each notebook has an accompanying `*_solutions` notebook in the `code/` folder.

**Question**: Does the anaconda terminal allow you to use bash commands on Windows?

We believe so!

**Question**: Did anyone have the code to remove the scout files?

`rm ./*scout*` rm is the linux command to remove something. Be careful using it with wildcards (`*`).

**Question**: How do you auto-complete in Python code?

You can use tab and it will auto-complete if the initial string is specific enough.

**Question**: Is the “header” information being extracted is from both the intrinsic NIfTI header and the .json sidecar?

In nibabel - the header - is the NifTI header. The json is a concept added by the BIDS standard to log things that are missing from the Nifti header. We look at it in a later notebook, so stay tuned.

**Question**: Why I can't see the OUT?

OUT can be toggled on and off two ways. First the o shortcut on a specific cell or using the All Output -> Toggle option from the Cell menu.

**Question**: Can you have negative nifti coordinates?

You cannot as they are locations in memory. They are not the scanner coordinates which can be negative (measured from isocenter).

**Question**: Is `slices = [x_slice, y_slice, z_slice]` same as -> `slice =t1_data[9,19,2]`?

Not quite, it would be

x_slice = 9
y_slice = 19
z_slice = 2
slice = t1_data[x_slice, y_slice, z_slice]

As you need to say what data to pull from and additionally you would have had to initialize x_slice, etc.

**Question**: Does BIDS support multi-shell diffusion data?

Yes, you could label different shell protocols with the `acq-*` label.
Also, yes - BIDS requires you to add `.bvec` and `.bval` files so that future users can understand the shells and directions

**Question**: Where should we keep the task.tsv for task imaging, or does it belong to part of the BIDS format?

Due to BIDS inheritance they could go several places. Alongside each file is totally great but if they have shared info across a group they can go higher in the folder structure and everything below them inherits the task info from that file.

**Question**: If you use the UNIDEN image from MP2RAGE as your T1-weighted anatomical, would you have to label this differently from an acquired T1w?

Example of how UWO handles MP2RAGE images. This is an animal subject, don't put your subjects name in there.

## Miscellanea

The notebooks are available for download from https://github.com/carpentries-incubator/SDC-BIDS-IntroMRI (in the code folder) if you want to explore them outside of class.