[DOC] Improving clarity of docs and figures #419

dowdlelt · 2019-11-06T20:43:21Z

Closes #83, .

Changes proposed in this pull request:

Adds live plots to the publications page
Publication page is renamed to reflect new focus on reporting average parameters
Reorganized main what is multiecho page
edited outputs to reflect .gz of nifti files
Adding details of output to approach page

codecov · 2019-11-06T21:01:14Z

Codecov Report

Merging #419 into master will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master     #419   +/-   ##
=======================================
  Coverage   82.17%   82.17%           
=======================================
  Files          41       41           
  Lines        2552     2552           
=======================================
  Hits         2097     2097           
  Misses        455      455

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update d2e1fc6...33e4675. Read the comment docs.

docs/considerations.rst

emdupre

This looks great ! A few comments.

The only structural one (and the most nitpicky) is it would be great if we could start new sentences on new lines !!

docs/approach.rst

emdupre · 2019-11-08T14:43:15Z

docs/approach.rst

@@ -165,24 +183,18 @@ These components are subjected to component selection, the specifics of which
 vary according to algorithm.

 In the simplest approach, ``tedana`` uses Minka’s MLE to estimate the
-dimensionality of the data, which disregards low-variance components.
+dimensionality of the data, which disregards low-variance components. (the `mle` option in for `--tedpca`).


Suggested change

dimensionality of the data, which disregards low-variance components. (the `mle` option in for `--tedpca`).

dimensionality of the data, which disregards low-variance components (the `mle` option in for `--tedpca`).

I agree - Unacceptable.

docs/approach.rst

docs/considerations.rst

docs/faq.rst

docs/publications.rst

dowdlelt · 2019-11-08T17:59:17Z

#290 and #336 addressed, I think. lemme know!

This reverts commit 28098e1.

docs/approach.rst

emdupre · 2019-11-08T20:20:53Z

docs/considerations.rst

+
+A minimum of 3 echoes is required for running the current implementation fo TE-dependent denoising in
+``tedana``. 
+While there are successful studies that don’t follow this rule,


Can we invert this sentence ? I'm still a little confused on first read-through, personally 😕

I've removed the not follow language - and just say we need three echoes, but left in the note that dual echo is not what we are talking about here.

docs/faq.rst

Co-Authored-By: Elizabeth DuPre <emd222@cornell.edu>

…rovements

Co-Authored-By: Elizabeth DuPre <emd222@cornell.edu>

emdupre · 2019-11-08T20:51:47Z

I'm so excited !!!!

Final check: Is this ready to merge ?

dowdlelt · 2019-11-08T20:55:59Z

I believe i have addressed all of your concerns - I believe it is ready to go.

emdupre

But why is the math broken ?! 😭

emdupre

Small patches to trigger a new build ?

docs/considerations.rst

Co-Authored-By: Elizabeth DuPre <emd222@cornell.edu>

emdupre · 2019-11-08T21:30:12Z

https://external-builds.readthedocs.io/html/tedana/419/approach.html

emdupre · 2020-07-19T16:20:35Z

@all-contributors please add @mvaziri for documentation !

allcontributors · 2020-07-19T16:20:45Z

@emdupre

I've put up a pull request to add @mvaziri! 🎉

emdupre changed the title ~~[DOC] Improving clarity of docs and figures~~ [WIP, DOC] Improving clarity of docs and figures Nov 6, 2019

tsalo reviewed Nov 6, 2019

View reviewed changes

docs/considerations.rst Show resolved Hide resolved

dowdlelt added documentation issues related to improving documentation for the project hackathon Issues to tackle in the NIH hackathon labels Nov 7, 2019

emdupre reviewed Nov 8, 2019

View reviewed changes

This was referenced Nov 8, 2019

Update docs to make it more beginner friendly #290

Closed

Add documentation page with info linking to other multi-echo denoising software #336

Closed

dowdlelt added 21 commits November 8, 2019 14:42

edited gitignore after testing

0f1fa94

Revert "edited gitignore after testing"

2e327cd

This reverts commit 28098e1.

fixing typo and clarity

42185ef

cleaning up approach introduction

8375c93

more cleanup in approach

21899e2

adding initial plot to pubs page

f742ab7

correcting plots

f6637b6

removing comment parts

d02a2c6

getting live plots working on publication page

9f55ea6

clean up and adding more WIP details

5d0c038

completing live TE plot from spreasheet

64fce83

changing outputs to nii.gz

ecccb9c

adding TR and Vox dim subplots

00a6b07

initial adding of output details

bce67e6

fixing tables

20249de

rearranging to considerations and recomendations

8cd1117

seperating out considerations section

7cd37c1

technically spelling things correct

ef8d4b7

started fixing titles

2efcfa9

addinf figures for what is ME page

ee7008c

title clarification

4688cf3

dowdlelt added 5 commits November 8, 2019 14:42

life by a thousand little edits

d4c82d8

GrAmMaRs

93befb1

other software!

916729b

links to api in approach

709a166

white space?

e28447a

dowdlelt force-pushed the doc_improvements branch from 2e90d29 to e28447a Compare November 8, 2019 19:42

emdupre changed the title ~~[WIP, DOC] Improving clarity of docs and figures~~ [DOC] Improving clarity of docs and figures Nov 8, 2019

emdupre reviewed Nov 8, 2019

View reviewed changes

dowdlelt and others added 9 commits November 8, 2019 15:23

Update docs/faq.rst

9634b71

Co-Authored-By: Elizabeth DuPre <emd222@cornell.edu>

MRI scanners != BBQ

85a5f06

Merge remote-tracking branch 'dowdlelt/doc_improvements' into doc_imp…

420593d

…rovements

Update docs/approach.rst

563e643

Co-Authored-By: Elizabeth DuPre <emd222@cornell.edu>

Update docs/approach.rst

0782967

Co-Authored-By: Elizabeth DuPre <emd222@cornell.edu>

Apply suggestions from code review, thanks a million

cad87a9

Co-Authored-By: Elizabeth DuPre <emd222@cornell.edu>

echo cleanup, and kundu 3 banish

6977bd5

noted png default

d7e4598

completely changed the QC section

90718ed

emdupre approved these changes Nov 8, 2019

View reviewed changes

emdupre requested changes Nov 8, 2019

View reviewed changes

emdupre reviewed Nov 8, 2019

View reviewed changes

docs/considerations.rst Outdated Show resolved Hide resolved

docs/considerations.rst Outdated Show resolved Hide resolved

pls wrk

33e4675

Co-Authored-By: Elizabeth DuPre <emd222@cornell.edu>

emdupre self-requested a review November 8, 2019 21:29

emdupre approved these changes Nov 8, 2019

View reviewed changes

dowdlelt merged commit 9f62169 into ME-ICA:master Nov 8, 2019

allcontributors bot mentioned this pull request Jul 19, 2020

docs: add mvaziri as a contributor #587

Merged

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

[DOC] Improving clarity of docs and figures #419

[DOC] Improving clarity of docs and figures #419

dowdlelt commented Nov 6, 2019

codecov bot commented Nov 6, 2019 •

edited

Loading

emdupre left a comment

emdupre Nov 8, 2019

dowdlelt Nov 8, 2019

dowdlelt commented Nov 8, 2019

emdupre Nov 8, 2019

dowdlelt Nov 8, 2019

emdupre commented Nov 8, 2019

dowdlelt commented Nov 8, 2019

emdupre left a comment

emdupre left a comment

emdupre commented Nov 8, 2019 •

edited

Loading

emdupre commented Jul 19, 2020

allcontributors bot commented Jul 19, 2020

	dimensionality of the data, which disregards low-variance components. (the `mle` option in for `--tedpca`).
	dimensionality of the data, which disregards low-variance components (the `mle` option in for `--tedpca`).

[DOC] Improving clarity of docs and figures #419

[DOC] Improving clarity of docs and figures #419

Conversation

dowdlelt commented Nov 6, 2019

codecov bot commented Nov 6, 2019 • edited Loading

Codecov Report

emdupre left a comment

Choose a reason for hiding this comment

emdupre Nov 8, 2019

Choose a reason for hiding this comment

dowdlelt Nov 8, 2019

Choose a reason for hiding this comment

dowdlelt commented Nov 8, 2019

emdupre Nov 8, 2019

Choose a reason for hiding this comment

dowdlelt Nov 8, 2019

Choose a reason for hiding this comment

emdupre commented Nov 8, 2019

dowdlelt commented Nov 8, 2019

emdupre left a comment

Choose a reason for hiding this comment

emdupre left a comment

Choose a reason for hiding this comment

emdupre commented Nov 8, 2019 • edited Loading

emdupre commented Jul 19, 2020

allcontributors bot commented Jul 19, 2020

codecov bot commented Nov 6, 2019 •

edited

Loading

emdupre commented Nov 8, 2019 •

edited

Loading