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ENH: Adds notebook and Python package updates #2

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merged 7 commits into from
Jul 14, 2020
Merged

ENH: Adds notebook and Python package updates #2

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b2cdae4
update config template
josephmje Jul 7, 2020
70c5e1f
move figures to central folder for use in jupyter notebooks nad md
josephmje Jul 7, 2020
c36c6ab
Merge remote-tracking branch 'upstream/gh-pages' into gh-pages
josephmje Jul 9, 2020
b72e1ec
Merge remote-tracking branch 'upstream/gh-pages' into gh-pages
josephmje Jul 12, 2020
b9e4d8b
Merge remote-tracking branch 'upstream/gh-pages' into gh-pages
josephmje Jul 13, 2020
732970f
add notebook changes
josephmje Jul 14, 2020
6233da3
update pybids
josephmje Jul 14, 2020
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33 changes: 15 additions & 18 deletions _config.yml
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Expand Up @@ -6,8 +6,8 @@
# swc: Software Carpentry
# dc: Data Carpentry
# lc: Library Carpentry
# cp: Carpentries (to use for instructor traning for instance)
carpentry: "dc"
# cp: Carpentries (to use for instructor training for instance)
carpentry: "incubator"

# Overall title for pages.
title: "Introduction to MRI and BIDS"
Expand All @@ -28,33 +28,27 @@ kind: "lesson"
# Please don't change it: <USERNAME>/<PROJECT> is correct.
repository: <USERNAME>/<PROJECT>

# Email address, no mailto:
email: "[email protected]"

# Sites.
amy_site: "https://amy.software-carpentry.org/workshops"
carpentries_github: "https://github.com/carpentries"
carpentries_pages: "https://carpentries.github.io"
carpentries_site: "https://carpentries.org/"
dc_site: "http://datacarpentry.org"
example_repo: "https://github.com/carpentries/lesson-example"
example_site: "https://carpentries.github.io/lesson-example"
lc_site: "https://librarycarpentry.org/"
example_repo: "https://github.com/swcarpentry/lesson-example"
example_site: "https://swcarpentry.github.com/lesson-example"
lc_site: "https://librarycarpentry.github.io/"
swc_github: "https://github.com/swcarpentry"
swc_pages: "https://swcarpentry.github.io"
swc_site: "https://software-carpentry.org"
template_repo: "https://github.com/carpentries/styles"
training_site: "https://carpentries.github.io/instructor-training"
workshop_repo: "https://github.com/carpentries/workshop-template"
workshop_site: "https://carpentries.github.io/workshop-template"
cc_by_human: "https://creativecommons.org/licenses/by/4.0/"
template_repo: "https://github.com/swcarpentry/styles"
training_site: "https://swcarpentry.github.io/instructor-training"
workshop_repo: "https://github.com/swcarpentry/workshop-template"
workshop_site: "https://swcarpentry.github.io/workshop-template"

# Surveys.
pre_survey: "https://carpentries.typeform.com/to/wi32rS?slug="
post_survey: "https://carpentries.typeform.com/to/UgVdRQ?slug="
instructor_pre_survey: "https://www.surveymonkey.com/r/instructor_training_pre_survey?workshop_id="
instructor_post_survey: "https://www.surveymonkey.com/r/instructor_training_post_survey?workshop_id="

pre_survey: "https://www.surveymonkey.com/r/swc_pre_workshop_v1?workshop_id="
post_survey: "https://www.surveymonkey.com/r/swc_post_workshop_v1?workshop_id="
training_post_survey: "https://www.surveymonkey.com/r/post-instructor-training"

# Start time in minutes (0 to be clock-independent, 540 to show a start at 09:00 am).
start_time: 0
Expand Down Expand Up @@ -94,3 +88,6 @@ exclude:

# Turn on built-in syntax highlighting.
highlighter: rouge

# Remote theme
remote_theme: carpentries/carpentries-theme
10 changes: 5 additions & 5 deletions code/01-neuroimaging-fundamentals/01-neuroimaging-fundamentals.ipynb
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Expand Up @@ -23,17 +23,17 @@
"\n",
"Imagine taking a slice \n",
"\n",
"<img src=\"T1w.gif\" align=\"middle\"/> \n",
"<img src=\"../../fig/T1w.gif\" align=\"middle\"/> \n",
"\n",
"<img src=\"T2w.gif\" align=\"middle\"/>\n",
"<img src=\"../../fig/T2w.gif\" align=\"middle\"/>\n",
"\n",
"- 3D image of anatomy\n",
"- a 3D **pixel** is called a **voxel**\n",
"- T1w is the most common (white matter is white, grey matter is grey, cerebral spinal fluid (CSF) is black\n",
"\n",
"### Functional (fMRI)\n",
"\n",
"<img src=\"bold.gif\" align=\"middle\"/>\n",
"<img src=\"../../fig/bold.gif\" align=\"middle\"/>\n",
"\n",
"- tracks the blood oxygen level dependant (BOLD) signal\n",
"- 4D (x, y, z + time)\n",
Expand All @@ -42,7 +42,7 @@
"\n",
"### Diffusion (DWI)\n",
"\n",
"<img src=\"dwi.gif\" align=\"middle\"/>\n",
"<img src=\"../../fig/dwi.gif\" align=\"middle\"/>\n",
"\n",
"- measures diffusion of water in order to model tissue microstructure\n",
"- 4D (x, y, z + direction of diffusion)\n",
Expand Down Expand Up @@ -109,4 +109,4 @@
},
"nbformat": 4,
"nbformat_minor": 4
}
}
2 changes: 1 addition & 1 deletion code/02-anatomy-of-nifti/02-anatomy-of-nifti.ipynb
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Expand Up @@ -466,7 +466,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.4"
"version": "3.7.7"
}
},
"nbformat": 4,
Expand Down
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