-
Notifications
You must be signed in to change notification settings - Fork 2
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
368ca34
commit 6c9752f
Showing
17 changed files
with
1,016 additions
and
4 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,112 @@ | ||
The first session is the Monday session. The second session is the Thursday | ||
session. | ||
|
||
These are the notes for the Monday session. | ||
|
||
We will update them before and after the session, to please keep checking back | ||
for updates. Just refresh the page in your browser to get updates. | ||
|
||
The Zoom link for all sessions is | ||
<https://numfocus-org.zoom.us/j/89458437731?pwd=eTF0V252bHlKOXBucnBUWlVBSm9uUT09>. | ||
|
||
## Recording | ||
|
||
[Recording of Monday Week 1 session | ||
1](https://numfocus-org.zoom.us/rec/share/nxcgD4PGsc-RI3QdTAiR2GBU1xkMrB5CPmf-sPSC52FSqTkXW7T55CPH1gS7lSSZ.PINmaKGVNAmPXOi-) | ||
|
||
## Schedule and plan | ||
|
||
- We will be referring often to the [textbook](https://textbook.nipraxis.org). | ||
- Hello and welcome. | ||
- Thanks to the [Chan Zuckerberg | ||
Initiative](https://chanzuckerberg.com/eoss/proposals/strengthening-community-and-code-foundations-for-brain-imaging/). | ||
- [Surviving the | ||
computer](https://textbook.nipraxis.org/surviving_computers.html). See video link below. | ||
- Machinery: | ||
- <https://textbook.nipraxis.org> | ||
- <https://learn.nipraxis.org> | ||
- <https://hub.nipraxis.org> and the Jupyter notebook. | ||
- <https://github.com/nipraxis> | ||
- About the project. | ||
- We will gradually move away from notebooks. | ||
- [Using Jupyter notebooks](https://textbook.nipraxis.org/using_jupyter.html) | ||
and [more on Jupyter | ||
notebooks](https://textbook.nipraxis.org/more_on_jupyter.html) | ||
- For reference: [Very fast introduction to | ||
Python](https://textbook.nipraxis.org/introducing_python.html) | ||
|
||
|
||
## For homework | ||
|
||
If you need to catch up on Python and Numpy, you have a double-dose of | ||
homework this week. In particular, you really will need to do the second | ||
section here, to get fluent in basic Python and Numpy. If you are already fluent, you only need to do the first section. | ||
|
||
Any problems, email <matthew.brett@gmail.com>, I will point you to someone else | ||
who can help if I can't help you. | ||
|
||
### For everyone: surviving computer, installing on your own machine | ||
|
||
Make sure you have watched: | ||
|
||
<iframe title="Surviving the computer" src="https://player.vimeo.com/video/693542789?h=63ccfc6dfa" width="640" height="360" frameborder="0" allowfullscreen></iframe> | ||
|
||
Next: | ||
|
||
* Check your knowledge with the [fast introduction to | ||
Python](https://textbook.nipraxis.org/brisk_python.html). | ||
* [Install Python and required libraries on your | ||
computer](https://textbook.nipraxis.org/installation.html). Make sure you | ||
have run the install check at the end of that page. | ||
|
||
That's all for those of you who are comfortable with Python and Numpy. See below for those of you who need to catch up. | ||
|
||
### If you need practice with Python or Numpy | ||
|
||
If you don't know Python well, we strongly suggest you do these exercises to | ||
catch up, otherwise the rest of the course will be too fast. Make sure, too, that you've read the fast introduction to Python above. | ||
|
||
#### Python | ||
|
||
If you are new to Python, do the [expressions and statements | ||
exercise](https://hub.nipraxis.org/hub/user-redirect/git-pull?repo=https%3A//github.com/uob-cfd/exprs_states&subPath=exprs_states.ipynb), | ||
to get into the swing of things. | ||
|
||
Next, do these exercises from the [Google Python | ||
class](https://developers.google.com/edu/python/). There are links in the | ||
exercises to the sections to read to revise the ideas you need. | ||
|
||
- [string1 | ||
exercise](https://hub.nipraxis.org/hub/user-redirect/git-pull?repo=https%3A//github.com/nipraxis/google_string1&subPath=string1.ipynb) | ||
- [list1 | ||
exercise](https://hub.nipraxis.org/hub/user-redirect/git-pull?repo=https%3A//github.com/nipraxis/google_list1&subPath=list1.ipynb) | ||
|
||
We also suggest you try the slightly more advanced exercises: | ||
|
||
- [string2 | ||
exercise](https://hub.nipraxis.org/hub/user-redirect/git-pull?repo=https%3A//github.com/nipraxis/google_string2&subPath=string2.ipynb) | ||
- [list2 | ||
exercise](https://hub.nipraxis.org/hub/user-redirect/git-pull?repo=https%3A//github.com/nipraxis/google_list2&subPath=list2.ipynb) | ||
|
||
#### Numpy | ||
|
||
(Re-)Read the [introduction to | ||
Numpy](https://textbook.nipraxis.org/numpy_intro.html). | ||
|
||
For a fuller introduction to Numpy, please see [the Scientific Python Numpy tutorial](https://lectures.scientific-python.org/intro/numpy/index.html). | ||
|
||
Specifically, see: | ||
|
||
* The [numpy array | ||
object](https://lectures.scientific-python.org/intro/numpy/array_object.html); | ||
* [Array | ||
operations](https://lectures.scientific-python.org/intro/numpy/operations.html). | ||
* If you know Matlab, you might want to look over this page on [Numpy for | ||
Matlab users](https://numpy.org/doc/stable/user/numpy-for-matlab-users.html). | ||
|
||
Make sure you can do the [arrays | ||
exercise](https://hub.nipraxis.org/hub/user-redirect/git-pull?repo=https%3A//github.com/nipraxis/arrays&subPath=arrays.ipynb) | ||
|
||
## The end | ||
|
||
That's it for this session. |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,39 @@ | ||
The *second session* is the Thursday session. | ||
|
||
These are the notes for the second session, for week 1. | ||
|
||
We will update them before and after the session, to please keep checking back for updates. Just refresh the page in your browser to get updates. | ||
|
||
The Zoom link for all sessions is | ||
<https://numfocus-org.zoom.us/j/89458437731?pwd=eTF0V252bHlKOXBucnBUWlVBSm9uUT09>. | ||
|
||
## Recording | ||
|
||
[Week 1 session | ||
2 recording](https://numfocus-org.zoom.us/rec/share/KzZxz_u4kOloz-bjfa9xFwEkxmoR_NknZo9un-wjlpuLnGwLnAqApLgRkyx5-jVk.P-Zk3Vcl31LMqkhq) | ||
|
||
## Schedule and plan | ||
|
||
- Please log on to <https://hub.nipraxis.org>. | ||
- About homework: | ||
- It will appear at the bottom of the session 1 page for each week. | ||
- We will depend on you having done the homework for the _following week_. | ||
- Reminder about the project | ||
- [Surviving the | ||
computer](https://textbook.nipraxis.org/surviving_computers.html). See | ||
[video](https://player.vimeo.com/video/693542789?h=63ccfc6dfa) (also linked from Session 1 page. | ||
- [Pathlib](https://textbook.nipraxis.org/pathlib.html) | ||
- Skip through the [introduction to | ||
Numpy](https://textbook.nipraxis.org/numpy_intro.html) | ||
- The OKpy testing system and a [practice with arrays | ||
exercise](https://hub.nipraxis.org/hub/user-redirect/git-pull?repo=https%3A//github.com/nipraxis/array_practice&subPath=array_practice.ipynb) | ||
|
||
## For homework | ||
|
||
See the [Week 1 session 1 page](https://apps.learn.nipraxis.org/learning/course/course-v1:Nipraxis+NI1+2023_NI1/block-v1:Nipraxis+NI1+2023_NI1+type@sequential+block@a292732b08514bbaa13ca5f862182dcd/block-v1:Nipraxis+NI1+2023_NI1+type@vertical+block@73fc602fe7034cd1913edd805920cf7e) | ||
|
||
In general, look for the homework in the session 1 page for each week. | ||
|
||
## The end | ||
|
||
That's it for this session. |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,43 @@ | ||
## Recording | ||
|
||
[Week 2 session | ||
1](https://numfocus-org.zoom.us/rec/share/4DcuAFZduwAT9b-VllUxYlDnwdPq7air4JSb6y6uMo9wehVwJejysulxj12kQ69F.s8CFqaGB5bwagTsp) | ||
|
||
### Arrays, images and plotting | ||
|
||
* [What is an image?](https://textbook.nipraxis.org/what_is_an_image.html) | ||
* [Boolean arrays](https://textbook.nipraxis.org/boolean_arrays.html) | ||
* [Reshape and 2D](https://textbook.nipraxis.org/reshape_and_2d) | ||
* [Arrays and images](https://textbook.nipraxis.org/arrays_and_images) | ||
* [Camera | ||
exercise](https://hub.nipraxis.org/hub/user-redirect/git-pull?repo=https%3A//github.com/nipraxis/camera&subPath=camera.ipynb) | ||
|
||
## Homework | ||
|
||
Make sure you've done the exercises from the sessions: | ||
|
||
* Session 1: | ||
* [Camera](https://hub.nipraxis.org/hub/user-redirect/git-pull?repo=https%3A//github.com/nipraxis/camera&subPath=camera.ipynb) | ||
* Session 2: | ||
* [Anatomical | ||
exercise](https://hub.nipraxis.org/hub/user-redirect/git-pull?repo=https%3A//github.com/nipraxis/anatomical&subPath=anatomical.ipynb) | ||
* Consider also: [Arteries | ||
exercise](https://hub.nipraxis.org/hub/user-redirect/git-pull?repo=https%3A//github.com/nipraxis/arteries&subPath=arteries.ipynb) | ||
|
||
In the next session, we will be starting with Git, and to work on your own | ||
computer. | ||
|
||
Read, mark, learn and inwardly digest the [curious | ||
git](https://matthew-brett.github.io/curious-git/) tutorial. | ||
|
||
We think this will take you 90 minutes, at a careful read, and you will need | ||
to read it carefully, in order to benefit from it. | ||
|
||
If you do read it carefully, you will be investing in your own future | ||
productivity — Git version control is a powerful way to work more efficiently, | ||
especially in collaboration, and you need to understand the way that Git | ||
**thinks**, in order to use Git with fluency and efficiency. | ||
|
||
## That's it. | ||
|
||
That's it for this session. |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,25 @@ | ||
## Recording | ||
|
||
[Week 2 session | ||
2 recording](https://numfocus-org.zoom.us/rec/share/dG612zhE7qU4sE_Wo2oyOmFnkjxqY3sBcrF7kijixQ3zoVRST4__StpYv47bBQ.EsD2R2-D6ZCERmoj) | ||
|
||
## Schedule | ||
|
||
## Three-dimensional arrays | ||
|
||
* [Arrays in 3D](https://textbook.nipraxis.org/arrays_3d) | ||
* [Images in 3D](https://textbook.nipraxis.org/images_3d) | ||
* [Reshaping and three | ||
dimensions](https://textbook.nipraxis.org/reshape_and_3d.html) | ||
* [Anatomical | ||
exercise](https://hub.nipraxis.org/hub/user-redirect/git-pull?repo=https%3A//github.com/nipraxis/anatomical&subPath=anatomical.ipynb) | ||
* If you have time: [Arteries | ||
exercise](https://hub.nipraxis.org/hub/user-redirect/git-pull?repo=https%3A//github.com/nipraxis/arteries&subPath=arteries.ipynb) | ||
|
||
## For homework | ||
|
||
See the page for session 1. | ||
|
||
## That's it. | ||
|
||
That's it for this session. |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,102 @@ | ||
## Recording | ||
|
||
[Week 3 session 1 | ||
recording](https://numfocus-org.zoom.us/rec/share/1DWWt27ub3hc7RX4rj4dy6yn8iFDPKHQxYr8rvInUvl_zwycUIwqvKWMTE0CSdXc.Xvs5ZTX5xE0D3TgK?startTime=1692022041000) | ||
|
||
## Schedule | ||
|
||
* Again, towards the project. | ||
* Bracketing Git, Github and working on your own computer. | ||
|
||
### Some background | ||
|
||
You will need to have followed the [installation | ||
instructions](https://textbook.nipraxis.org/installation.html). | ||
|
||
In particular, you are about to use your terminal application: | ||
|
||
* [Powershell on | ||
Windows](https://textbook.nipraxis.org/installation_on_windows.html#powershell) | ||
* [Powshell on | ||
Mac](https://textbook.nipraxis.org/installation_on_mac.html#terminal-app) | ||
|
||
### Modules and functions | ||
|
||
We start with the laptop way. | ||
|
||
* [on_modules](https://textbook.nipraxis.org/on_modules). | ||
|
||
### FMRI artifacts | ||
|
||
* [Principles of FMRI video](https://www.youtube.com/watch?v=7Kk_RsGycHs) | ||
* [Radiopedia article in MRI | ||
artifacts](https://radiopaedia.org/articles/mri-artifacts-1) | ||
* [Common MRI artifacts and how to fix | ||
them](https://gate.nmr.mgh.harvard.edu/wiki/whynhow/images/3/39/Artifacts_why_n_how_dec_14_2017_V7.pdf) | ||
|
||
The above don't focus much on fMRI (some coverage of susceptibility | ||
distortion), but here are some MRI quality control runs that show some | ||
interesting effects: | ||
|
||
* [Spin history artifact, motion spike, AP | ||
ghosting](https://mriqc.s3.amazonaws.com/artifacts/sub-ds045s409874_task-machinegame_run-04_bold.html) | ||
* [Ringing, bands in | ||
carpetplot](https://mriqc.s3.amazonaws.com/abide/sub-50039_task-rest_bold.html) | ||
* [Ghosting, possible hardware | ||
failure](https://mriqc.s3.amazonaws.com/abide/sub-51489_task-rest_bold.html) | ||
* [LR ghosting evident in background | ||
noise](https://mriqc.s3.amazonaws.com/abide/sub-51146_task-rest_bold.html) | ||
* [Hardware | ||
failures](https://mriqc.s3.amazonaws.com/artifacts/sub-arielle02_task-uknown_bold.html) | ||
* [Electromagnetic | ||
spikes](https://mriqc.s3.amazonaws.com/artifacts/sub-ben01_task-unknown_bold.html) | ||
|
||
## For homework | ||
|
||
### Using Git | ||
|
||
Watch the following two videos introducing Git in use, but relating what you | ||
see to the terms in the [curious | ||
git](https://matthew-brett.github.io/curious-git/) tutorial from last week. | ||
|
||
I'm referring to the "Git parable" in the videos, which is a similar | ||
introduction to the [Curious Git | ||
tutorial](https://matthew-brett.github.io/curious-git) from last week's | ||
homework — but the two tutorials take a very similar track, so you can | ||
consider them interchangeable. | ||
|
||
<iframe src="https://player.vimeo.com/video/121579300?h=ed8db39d7e" width="640" height="438" frameborder="0" allow="autoplay; fullscreen; picture-in-picture" allowfullscreen></iframe> | ||
<p><a href="https://vimeo.com/121579300">Introduction to the git working tree, repository and staging area</a> from <a href="https://vimeo.com/matthewbrett">Matthew Brett</a> on <a href="https://vimeo.com">Vimeo</a>.</p> | ||
|
||
The next video is a little out of date, in that the default branch name in Git | ||
has changed from "master" to "main". You will likely find your copy of Git | ||
calls the default branch "main". For "master" read "main" throughout. | ||
|
||
<iframe src="https://player.vimeo.com/video/121579601?h=5b937ff9ff" width="640" height="436" frameborder="0" allow="autoplay; fullscreen; picture-in-picture" allowfullscreen></iframe> | ||
<p><a href="https://vimeo.com/121579601">The links between git commits, and git branches.</a> from <a href="https://vimeo.com/matthewbrett">Matthew Brett</a> on <a href="https://vimeo.com">Vimeo</a>.</p> | ||
|
||
### Choosing a text editor | ||
|
||
Your second job for this week is to assess and [choose a text | ||
editor](https://textbook.nipraxis.org/choosing_editor.html). | ||
|
||
Here we a list of videos on choosing text editors: | ||
|
||
* Edited version of [Stéfan van der Walt on | ||
Emacs](https://vimeo.com/740066780) (16 minutes). You might prefer the [full | ||
24 minute version of the conversation here](https://vimeo.com/702404210). | ||
* [Pamphile Roy on PyCharm](https://vimeo.com/702001724) (16 minutes). | ||
* Edited version of [Ilhan Polat on Spyder](https://vimeo.com/702215618) (14 | ||
minutes). You can also watch the [54 minute full conversation with Ilhan](https://vimeo.com/706101324). | ||
* [Bhuvak Kalra on VSCode](https://vimeo.com/702402879) (16 minutes). | ||
* Edited version of [Paul Ivanov on | ||
Vim](https://vimeo.com/740121174) (15 minutes). You can watch the [full 43 | ||
minute conversation with Paul Ivanov here](https://vimeo.com/704733982). You | ||
might watch the full version if you interested in more on how you know when | ||
you have the right editor, how long it takes to get going with Vim. | ||
|
||
Please take time for this task, and investigate your options. | ||
|
||
## That's it. | ||
|
||
That's it for this session. |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,20 @@ | ||
## Recording | ||
|
||
[Week 3 session 2 recording](https://numfocus-org.zoom.us/rec/share/YIQUaJjjBQg2HCLm1VbXJ4hPE2T3EeGuMjSMYBw--VajunFmm_PWXKuZwAEiUuVj.8GMzoJ6lXQZHsrMj) | ||
|
||
## Schedule and plan | ||
|
||
* More towards the first project. | ||
* Bracketing Git, Github and working on your own computer. | ||
|
||
### Modules and functions | ||
|
||
More on the laptop way. | ||
|
||
* [on_modules](https://textbook.nipraxis.org/on_modules). | ||
|
||
We will come to the practice later (week 4). | ||
|
||
## That's it. | ||
|
||
That's it for this session. |
Oops, something went wrong.