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Test data #209

Merged
merged 36 commits into from
Sep 8, 2022
Merged

Test data #209

merged 36 commits into from
Sep 8, 2022

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akhanf
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@akhanf akhanf commented Aug 25, 2022 •
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Adds instructions for using a test dataset (single openneuro subject) to make the getting started instructions more concrete.

Also added an overview of the different ways of running hippunfold, and pros/cons of each

To do:

  • this page is pretty long now, could consider moving the Docker and Singularity sections to sub-pages. Seems natural to have the 4 methods described in 4 separate sub-pages
  • check over instructions to make sure they are reproducible
  • check rendering of docs

akhanf and others added 30 commits August 15, 2022 16:15
@akhanf
WIP: adding test data and updating docs
14fea90
@akhanf
updated installation instructions
2228674
@akhanf
some more updates to include test data in instructions
68e627f
@akhanf
more updates to docs
13437c2
@akhanf
Fixed headings
5e36ee1
@akhanf
Update installation.md
62c61ac
@akhanf
changed from m2r2 to myst parser
d0dd3e3
@akhanf
reorganize docs
d518a64
@akhanf
reorg
0dcb032
@akhanf
added dag visualizations, and scripts to create them
a6df59f
@akhanf
remove old dags
a101403
@akhanf
some cleaning up
716b7b9
@akhanf
started adding dags to docs
9b47c50
@akhanf
updates to pipeline txt
404f02e
@akhanf
more refactoring
8901dbf
@akhanf
refactored dag generation, now creates subgraph visualizations
8871cf4
@akhanf
updated pipeline with new dags
8fd5a07
@akhanf
linting
0686213
@akhanf
add nnunet diagram
14be48b
@akhanf
add more dags
6045f92
@akhanf
unpin docutils to hopefully fix bullets
d94492a
@akhanf
pin to higher version
e4725a3
@akhanf
upgrade sphinx-rtd-theme
d7d6995
@akhanf
updates to singularity instructions
df2ef6e
@akhanf
more refactoring
8a6aa21 
- moved docker and singularity getting started examples to separate pages
- updated standardBIDS to rather describe useful options for running
  hippunfold on your data (since the basic aspects are covered in the
new getting started examples)
@akhanf
added text to each section in pipeline
65c98c2
@akhanf
remove nnunet diagram (added to supp methods instead)
02ef72d
@akhanf
change dags to png, only commit those used in docs
a3b2c68 
commit txt dot files for all others..
@akhanf
fix couple typos
4732eff
@akhanf
updates for title/author for online documentation
96523ce
@akhanf akhanf merged commit 46b42a2 into master Sep 8, 2022
@akhanf akhanf deleted the testdata branch September 8, 2022 16:40
@akhanf akhanf added the documentation Improvements or additions to documentation label Sep 8, 2022
@akhanf akhanf mentioned this pull request Sep 8, 2022
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