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WIP - Task notebooks#9

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Commits

Commits on Nov 12, 2018

• first commit

  jerdra

  committed
  8135e99

• rename first notebook

  jerdra

  committed
  0554574

• update tutorials and gitignore

  

  Jerry Jeyachandra

  committed
  018f3ad

• remove images

  

  Jerry Jeyachandra

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  b900154

• Create README.md

  jerdra

  authored
  30f651c

• Finish up first draft of README.md

  jerdra

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  88f1d0e

• Update README.md

  jerdra

  authored
  009a4f2

• clean up README a bit

  jerdra

  authored
  1668b77

• Update README.md

  jerdra

  authored
  a3bc4e2

• Update README.md

  jerdra

  authored
  41508e2

• Update README.md

  jerdra

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  7ba8991

• Update README.md

  jerdra

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  2057b10

• Update README.md

  jerdra

  authored
  5ad48f9

• Update README.md

  jerdra

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  71ddda0

• Update README.md

  jerdra

  authored
  5e57705

• Update README.md

  jerdra

  authored
  87f2708

• add fmri signal cleaning notebook

  

  Jerry Jeyachandra

  committed
  1f14786

• Merge branch 'master' of https://github.com/jerdra/scwg2018_python_neuroimaging

  

  Jerry Jeyachandra

  committed
  b55ab42

• added rough (not correct) confound regression notebook

  

  Jerry Jeyachandra

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  09c4ce9

Commits on Nov 13, 2018

• update confounds and some text in intro

  jerdra

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  3ef0f98

• remove test notebook

  jerdra

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  e470067

• renamed files and added new section

  jerdra

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  1eafb6e

Commits on Nov 14, 2018

• Merge pull request carpentries-incubator#1 from jerdra/master

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  josephmje

  authored
  d8138b1

• nibabel and pybids updates

  josephmje

  committed
  ea1e4aa

• minor updates

  josephmje

  committed
  2d02a69

• updated part4

  

  Jerry Jeyachandra

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  29d2ff4

Commits on Nov 19, 2018

• finished low-level connectivity

  

  Jerry Jeyachandra

  committed
  c0d3877

Commits on Nov 20, 2018

• fpolish out the notebooks

  

  Jerry Jeyachandra

  committed
  fc27d49

• clear outputs

  

  Jerry Jeyachandra

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  70ceea3

Commits on Nov 21, 2018

• update intro notebook

  josephmje

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  652d631

• add dataset READMEs and jsons

  josephmje

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  f1fd1df

• Add static images embedded in notebooks

  josephmje

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  9474cdf

• Delete 01_nibabel.ipynb

  josephmje

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  ec19d5a

• Delete 03_intro_dataset.ipynb

  josephmje

  authored
  9e82123

• wip on introducing dataset and downloading preprocessed data

  josephmje

  committed
  78f4e94

• Merge branch 'master' of https://github.com/josephmje/scwg2018_python_neuroimaging

  josephmje

  committed
  37af958

• Add more notebooks and clear kernel

  josephmje

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  a156cb2

Commits on Nov 22, 2018

• Merge pull request carpentries-incubator#2 from jerdra/master

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  josephmje

  authored
  281701b

• Delete .python-version

  josephmje

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Commits on Nov 23, 2018

• renamed notebooks, changed filepaths and download list

  josephmje

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• remove renamed notebooks

  josephmje

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  91beddd

• more changes

  josephmje

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  3fe327d

• Remove duplicated files in resources folder

  josephmje

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  924a0ea

• finessed preprocessing notebook, my functional connectivity still to come

  josephmje

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• Delete ._ADHD200_parcellate_200.nii.gz

  josephmje

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• remove hidden files

  josephmje

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  949abca

• Merge branch 'master' of https://github.com/josephmje/scwg2018_python_neuroimaging

  josephmje

  committed
  b7a9285

• update README instructions for downloading data

  josephmje

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  7841de7

• more content updates

  josephmje

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  204397b

• cleaning up intro

  josephmje

  committed
  7a953f3

• Merge pull request carpentries-incubator#1 from josephmje/master

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  jerdra

  authored
  62f8644

• Update README.md

  jerdra

  authored
  9dfe577

• Update README.md

  jerdra

  authored
  397d712

• Update README.md

  jerdra

  authored
  ac5091d

Commits on Nov 24, 2018

• Update README.md

  jerdra

  authored
  037474a

• fix security flaw

  jerdra

  committed
  cac5a69

• Merge branch 'master' of https://github.com/jerdra/scwg2018_python_neuroimaging

  jerdra

  committed
  1063b57

• Update README.md

  jerdra

  authored
  6e88286

• Update README.md

  jerdra

  authored
  902a863

• Update README.md

  jerdra

  authored
  f96fdd6

• Update README.md

  jerdra

  authored
  f6f42f7

• Update README.md

  jerdra

  authored
  98b3a9b

• Update README.md

  jerdra

  authored
  7e65588

Commits on Nov 25, 2018

• Update README.md

  jerdra

  authored
  2735ce3

Commits on Nov 26, 2018

• updates

  josephmje

  committed
  5eeb92a

• Merge pull request carpentries-incubator#3 from jerdra/master

  Show description for 5c28a01
  josephmje

  authored
  5c28a01

• add numpy image

  josephmje

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  5cf4e17

• final changes

  josephmje

  committed
  b135d32

• Merge pull request carpentries-incubator#2 from josephmje/master

  Show description for 07721d0
  jerdra

  authored
  07721d0

• added yeo parcellation

  josephmje

  committed
  c664afd

• Merge pull request carpentries-incubator#3 from josephmje/master

  Show description for 1411f7d
  jerdra

  authored
  1411f7d

• Update README.md

  jerdra

  authored
  92aef67

• Update README.md

  jerdra

  authored
  ec47dff

• yeo atlas mods

  josephmje

  committed
  6a134c8

• use first subject + yeo

  

  Jerry Jeyachandra

  committed
  c906898

• Merge branch 'master' of https://github.com/jerdra/scwg2018_python_neuroimaging

  

  Jerry Jeyachandra

  committed
  40c1149

Commits on Nov 27, 2018

• remove relative path for download_list

  josephmje

  committed
  f74e5d7

• changed to intranetwork connectivity using yeo

  jerdra

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  4726c62

• Merge branch 'yeo_networks'

  jerdra

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  1e2e0bc

• cleaned notebooks and update functional connectivity

  josephmje

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  3ca7019

• Merge branch 'master' into master

  josephmje

  authored
  3df7927

• clear up final notebook

  jerdra

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  271c663

• integrate Michaels updates and add simple visualization

  jerdra

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  4515ddc

• integrate Michaels parcellation changes

  jerdra

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  1faddb4

• final updates

  josephmje

  committed
  619d943

• create solutions book + code-along books

  

  Jerry Jeyachandra

  committed
  cd8dcac

• Update README.md

  jerdra

  authored
  95ee372

• final changes

  

  Jerry Jeyachandra

  committed
  50b1eb8

• Merge branch 'master' of https://github.com/jerdra/scwg2018_python_neuroimaging

  

  Jerry Jeyachandra

  committed
  beafa14

• added binder link

  josephmje

  authored
  f9595be

• Update README.md

  jerdra

  authored
  95a5ce9

• Update README.md

  jerdra

  authored
  10e0f5a

Commits on Dec 16, 2018

• Merge branch 'master' into master

  josephmje

  authored
  b06b85b

• Merge pull request carpentries-incubator#5 from jerdra/master

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  josephmje

  authored
  95d491c

Commits on Feb 28, 2019

• initial commit of GLM notebook

  ostanley

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  12bafb5

Commits on Mar 1, 2019

• finished outline

  ostanley

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Commits on Mar 14, 2019

• preliminary OLS with permutations, need better design extraction

  ostanley

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Commits on Mar 15, 2019

• Added basic OLS example using bht task from sub-10788

  ostanley

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Commits on Jun 14, 2019

• Rename 04_intro-nilearn-and-image-manipulation.ipynb to 02_intro-nilearn-and-image-manipulation.ipynb

  josephmje

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  34428ad

• Rename 04_intro-nilearn-and-image-manipulation_solutions.ipynb to 02_intro-nilearn-and-image-manipulation_solutions.ipynb

  josephmje

  authored
  805cb2c

• Rename 02_intro-dataset.ipynb to 03_intro-dataset.ipynb

  josephmje

  authored
  328eed2

• Rename 02_intro-dataset_solutions.ipynb to 03_intro-dataset_solutions.ipynb

  josephmje

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  1a5dbb0

• Rename 03_preprocessing.ipynb to 04_preprocessing.ipynb

  josephmje

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Commits on Jun 16, 2019

• more detail to exercise 1 solutions, will need to update workshop notebook accordingly, changed subject cause my comp has no space, but well move the download component anyway

  jerdra

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  308517b

• re-do exercise with answer templating to assist learning

  jerdra

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  70ea0e1

• simplify visualization section

  jerdra

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  d913870

Commits on Jun 17, 2019

• redo slicing section

  jerdra

  committed
  980e3a4

• Merge branch 'master' of https://github.com/josephmje/scwg2018_python_neuroimaging

  josephmje

  committed
  e30de76

Commits on Jun 18, 2019

• Resolving issue carpentries-incubator#12 change file input to pybids

  ostanley

  committed
  49f4ee4

• Nibabel veiwer prototype, re issue carpentries-incubator#13

  ostanley

  committed
  9f39ab4

• inital gif production, need axis labels fixed and centering

  ostanley

  committed
  aa7f8af

• simplify requirements.txt

  josephmje

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• more explanation and simpler language

  josephmje

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  b357680

• run through

  josephmje

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Commits on Jun 19, 2019

• Rename 03_intro-dataset.ipynb to 02_intro-dataset.ipynb

  josephmje

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  e311091

• Rename 03_intro-dataset_solutions.ipynb to 02_intro-dataset_solutions.ipynb

  josephmje

  authored
  bd094fc

• Rename 04_preprocessing.ipynb to 03_preprocessing.ipynb

  josephmje

  authored
  5638893

• Rename 02_intro-nilearn-and-image-manipulation.ipynb to 04_intro-nilearn-and-image-manipulation.ipynb

  josephmje

  authored
  52ecc2c

• Rename 02_intro-nilearn-and-image-manipulation_solutions.ipynb to 04_intro-nilearn-and-image-manipulation_solutions.ipynb

  josephmje

  authored
  1ffb46c

• Merge remote-tracking branch 'upstream/master'

  josephmje

  committed
  0427521

• multiple changes, primarily pybids

  Show description for 559c32b
  kaitj

  committed
  559c32b

• changes to ex 6

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  kaitj

  committed
  7e37d2a

• Merge pull request carpentries-incubator#21 from josephmje/master

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  jerdra

  authored
  ec74aa6

Commits on Jun 20, 2019

• add image

  josephmje

  committed
  09ef616

Commits on Jun 21, 2019

• fixes to nibabel OrthoVeiwer example

  ostanley

  committed
  2a96439

• finished resampling gif with two options, display over old T1 or over functional mask

  ostanley

  committed
  ef1d1e1

• fixed declaration bug where gif was before functional was loaded

  ostanley

  committed
  cb08de2

• Merge remote-tracking branch 'jerdra/master' into scinetchanges

  ostanley

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Commits on Jun 23, 2019

• updates to 07 notebook

  jerdra

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Commits on Jun 24, 2019

• add functional image manipulation to intro to nilearn

  jerdra

  committed
  709b3d9

• Merge pull request carpentries-incubator#25 from jerdra/scinetchanges

  Show description for 9b433d8
  jerdra

  authored
  9b433d8

• Merge branch 'master' of https://github.com/jerdra/scwg2018_python_neuroimaging into scinetchanges

  jerdra

  committed
  f42aadb

• remove functional bit in nibabel intro

  jerdra

  committed
  5c5e162

• Merge pull request carpentries-incubator#26 from jerdra/scinetchanges

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  jerdra

  authored
  4f48fc5

• add better explantion of confound_df

  jerdra

  committed
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• explanation of temporal derivatives"

  jerdra

  committed
  bc6c9e1

• add separator between both signal cleaning methods

  jerdra

  committed
  c90808a

• Merge pull request carpentries-incubator#27 from jerdra/05_updates

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  jerdra

  authored
  9d257a6

• Merge remote-tracking branch 'upstream/master'

  josephmje

  committed
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• forgot pandas

  josephmje

  committed
  51bf219

• finished pandas explanation and exercises

  josephmje

  committed
  fd1dc30

• Merge pull request carpentries-incubator#28 from josephmje/master

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  josephmje

  authored
  ce42905

• add line showing all pybids entities

  josephmje

  committed
  909a4e3

• updating pybids lines after new version

  josephmje

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Commits on Jun 25, 2019

• Merge branch 'master' of https://github.com/jerdra/scwg2018_python_neuroimaging into 07_updates

  jerdra

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  88e399b

• make exercises for 07 and improve explanations + flow

  jerdra

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  2be4fdd

• fixed wording

  jerdra

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  25028f2

• fixed pybids typo for selecting files

  jerdra

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  6a8232e

• fixed typos, added caveat on ConnectivityMeasure with lists

  jerdra

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  d16ac07

• add return type note

  jerdra

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• remove .path in workshop notebook for confounds

  jerdra

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• added missing commas in solutions

  jerdra

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• added missing commas in workshop loop

  jerdra

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• add heatmap visualization using seaborn, and exercise for list indexing

  jerdra

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• finished 07

  jerdra

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• clear solutions output, until all data is avaiable

  jerdra

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  8976991

• Merge pull request carpentries-incubator#29 from jerdra/07_updates

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  jerdra

  authored
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• add setup workshop script

  jerdra

  committed
  7652494

• fixed setup_workshop script

  jerdra

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• Merge remote-tracking branch 'upstream/master'

  josephmje

  committed
  0ba0dfd

• removed .git from binder path

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  josephmje

  authored
  f830913

• Merge remote-tracking branch 'upstream/master'

  josephmje

  committed
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Commits on Jun 26, 2019

• use pybids

  jerdra

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• Merge branch 'master' of https://github.com/jerdra/scwg2018_python_neuroimaging

  jerdra

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  ffe40cd

• Merge remote-tracking branch 'upstream/master'

  josephmje

  committed
  d167d27

• fix pathing in 07

  jerdra

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• update notebook 01

  josephmje

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• Merge remote-tracking branch 'upstream/master'

  josephmje

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  2c10491

• remove former pybids commit

  josephmje

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  4a00cbf

• Merge pull request carpentries-incubator#30 from josephmje/master

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  josephmje

  authored
  7177816

• Update README.md

  jerdra

  authored
  27117af

• Update README.md

  jerdra

  authored
  6bf5c64

• remove solutions

  josephmje

  committed
  e04b05f

• Merge pull request carpentries-incubator#31 from josephmje/master

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  josephmje

  authored
  1337837

• Update README.md

  jerdra

  authored
  27f78cf

• Update README.md

  jerdra

  authored
  f7c968a

• remove solutions again

  josephmje

  committed
  966f087

• Merge pull request carpentries-incubator#32 from josephmje/master

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  josephmje

  authored
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Commits on Sep 11, 2019

• restructure first notebook

  jerdra

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• added result plot

  ostanley

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  c2bc953

• Merge branch 'master' of https://github.com/jerdra/scwg2018_python_neuroimaging

  ostanley

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Commits on Sep 12, 2019

• finished new version of introductory material using nilearn instead of nibabel

  jerdra

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• start reworking 4th notebook

  jerdra

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• updates and more writing for OLS

  ostanley

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Commits on Sep 20, 2019

• switch pybids to pull files

  kaitj

  committed
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Commits on Sep 23, 2019

• Merge branch 'master' of https://github.com/jerdra/scwg2018_python_neuroimaging

  ostanley

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  97b8611

• Merge branch 'master' of https://github.com/ostanley/scwg2018_python_neuroimaging

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Commits on Sep 26, 2019

• continued updates to first level notebook

  ostanley

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• initial commit of permutation notebook

  ostanley

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• update section 4, and add a separate fMRI section to break down content into digestible chunks

  jerdra

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Commits on Oct 4, 2019

• resolved Ekuinder issues

  ostanley

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  9c7d518

• added residual plots working towards issue carpentries-incubator#1

  ostanley

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Commits on Oct 16, 2019

• finish fMRI notebook

  jerdra

  committed
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Commits on Nov 7, 2019

• update notebooks

  jerdra

  committed
  b2a50ad

• reorganize notebooks, add fmriprep output exploration notebook

  jerdra

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• final reorganization

  jerdra

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Commits on Nov 8, 2019

• updated .gitignore

  ostanley

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• updated task based notebook with solutions

  ostanley

  committed
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Commits on Nov 9, 2019

• Merge pull request carpentries-incubator#33 from jerdra/reorg

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  jerdra

  authored
  eef3858

Commits on Nov 11, 2019

• Update README.md

  jerdra

  authored
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Commits on Nov 12, 2019

• no longer download original BIDS dataset

  jerdra

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• upgrade packages

  jerdra

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• removed extra notebooks

  ostanley

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• Merge branch 'master' of https://github.com/jerdra/scwg2018_python_neuroimaging

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  committed
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Commits on Jul 3, 2020

• Merge remote-tracking branch 'carpentries/gh-pages' into tasknotebooks

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  ostanley

  committed
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