Citation boilerplate #779

chrisgorgo · 2017-10-19T00:24:08Z

Closes #713 and #600

chrisgorgo · 2017-10-19T04:02:41Z

https://427-66973489-gh.circle-artifacts.com/0/home/ubuntu/docs/citing.html

effigies

Looks nice. Here are some comments on the links. Found DOIs where possible, a shorter link for Huntenburg 2014. And suggest switching to https://doi.org.

effigies · 2017-10-19T13:47:18Z

docs/citing.rst

+  For more details of the pipeline see <a href="http://fmriprep.readthedocs.io/en/1.0.0-rc6/workflows.html">http://fmriprep.readthedocs.io/en/1.0.0-rc6/workflows.html</a>.
+  </p>
+  <p>
+  1. 	Esteban O, Blair R, Markiewicz CJ, Berleant SL, Moodie C, Ma F, Isik AI, Erramuzpe A, Kent JD, Goncalves M, Poldrack RA, Gorgolewski KJ. poldracklab/fmriprep: 1.0.0-rc6 [Internet]. 2017. Available from: <a href="https://zenodo.org/record/1009184">https://zenodo.org/record/1009184</a>


I think most people will prefer to cite DOIs: https://doi.org/10.5281/zenodo.1009184

effigies · 2017-10-19T13:47:57Z

docs/citing.rst

+  1. 	Esteban O, Blair R, Markiewicz CJ, Berleant SL, Moodie C, Ma F, Isik AI, Erramuzpe A, Kent JD, Goncalves M, Poldrack RA, Gorgolewski KJ. poldracklab/fmriprep: 1.0.0-rc6 [Internet]. 2017. Available from: <a href="https://zenodo.org/record/1009184">https://zenodo.org/record/1009184</a>
+  </p>
+  <p>
+  2. 	Gorgolewski K, Burns CD, Madison C, Clark D, Halchenko YO, Waskom ML, Ghosh SS. Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in python. Front Neuroinform [Internet]. 2011 Aug 22;5(August):13. Available from: <a href="http://dx.doi.org/10.3389/fninf.2011.00013">http://dx.doi.org/10.3389/fninf.2011.00013</a>


I would generally prefer https://doi.org/ to http://dx.doi.org. (Applies to several entries.)

effigies · 2017-10-19T13:48:22Z

docs/citing.rst

+  5. 	Dale A, Fischl B, Sereno MI. Cortical Surface-Based Analysis: I. Segmentation and Surface Reconstruction. Neuroimage. 1999;9(2):179–94.
+  </p>
+  <p>
+  6. 	Fonov VS, Evans AC, McKinstry RC, Almli CR, Collins DL. Unbiased nonlinear average age-appropriate brain templates from birth to adulthood. NeuroImage; Amsterdam [Internet]. 2009 Jul 1;47:S102. Available from: <a href="https://search.proquest.com/docview/1833173019">https://search.proquest.com/docview/1833173019</a>


DOI: https://doi.org/10.1016/S1053-8119(09)70884-5

effigies · 2017-10-19T13:48:43Z

docs/citing.rst

+  4. 	Tustison NJ, Avants BB, Cook PA, Zheng Y, Egan A, Yushkevich PA, Gee JC. N4ITK: improved N3 bias correction. IEEE Trans Med Imaging [Internet]. 2010 Jun;29(6):1310–20. Available from: <a href="http://dx.doi.org/10.1109/TMI.2010.2046908">http://dx.doi.org/10.1109/TMI.2010.2046908</a>
+  </p>
+  <p>
+  5. 	Dale A, Fischl B, Sereno MI. Cortical Surface-Based Analysis: I. Segmentation and Surface Reconstruction. Neuroimage. 1999;9(2):179–94.


DOI: https://doi.org/10.1006/nimg.1998.0395

effigies · 2017-10-19T13:49:28Z

docs/citing.rst

+  7. 	Avants BB, Epstein CL, Grossman M, Gee JC. Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain. Med Image Anal [Internet]. 2008 Feb;12(1):26–41. Available from: <a href="http://dx.doi.org/10.1016/j.media.2007.06.004">http://dx.doi.org/10.1016/j.media.2007.06.004</a>
+  </p>
+  <p>
+  8. 	Jenkinson M, Bannister P, Brady M, Smith S. Improved optimization for the robust and accurate linear registration and motion correction of brain images. Neuroimage [Internet]. 2002 Oct;17(2):825–41. Available from: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12377157">https://www.ncbi.nlm.nih.gov/pubmed/12377157</a>


DOI: https://doi.org/10.1006/nimg.2002.1132

effigies · 2017-10-19T13:50:18Z

docs/citing.rst

+  9. 	Andersson JLR, Skare S, Ashburner J. How to correct susceptibility distortions in spin-echo echo-planar images: application to diffusion tensor imaging. Neuroimage [Internet]. 2003 Oct;20(2):870–88. Available from: <a href="http://dx.doi.org/10.1016/S1053-8119(03)00336-7">http://dx.doi.org/10.1016/S1053-8119(03)00336-7</a>
+  </p>
+  <p>
+  10. 	Cox RW. AFNI: software for analysis and visualization of functional magnetic resonance neuroimages. Comput Biomed Res [Internet]. 1996 Jun;29(3):162–73. Available from: <a href="http://www.ncbi.nlm.nih.gov/pubmed/8812068">http://www.ncbi.nlm.nih.gov/pubmed/8812068</a>


DOI: https://doi.org/10.1006/cbmr.1996.0014

effigies · 2017-10-19T13:51:56Z

docs/citing.rst

+  11. 	Jenkinson M. Fast, automated, N-dimensional phase-unwrapping algorithm. Magn Reson Med [Internet]. 2003 Jan;49(1):193–7. Available from: <a href="http://dx.doi.org/10.1002/mrm.10354">http://dx.doi.org/10.1002/mrm.10354</a>
+  </p>
+  <p>
+  12. 	Huntenburg JM. Evaluating nonlinear coregistration of BOLD EPI and T1w images [Internet]. Freie Universität Berlin; 2014. Available from: <a href="http://pubman.mpdl.mpg.de/pubman/item/escidoc:2327525/component/escidoc:2327523/master_thesis_huntenburg_4686947.pdf">http://pubman.mpdl.mpg.de/pubman/item/escidoc:2327525/component/escidoc:2327523/master_thesis_huntenburg_4686947.pdf</a>


This appears to be the preferred link (one click away from the actual PDF): http://hdl.handle.net/11858/00-001M-0000-002B-1CB5-A

effigies · 2017-10-19T13:52:22Z

docs/citing.rst

+  12. 	Huntenburg JM. Evaluating nonlinear coregistration of BOLD EPI and T1w images [Internet]. Freie Universität Berlin; 2014. Available from: <a href="http://pubman.mpdl.mpg.de/pubman/item/escidoc:2327525/component/escidoc:2327523/master_thesis_huntenburg_4686947.pdf">http://pubman.mpdl.mpg.de/pubman/item/escidoc:2327525/component/escidoc:2327523/master_thesis_huntenburg_4686947.pdf</a>
+  </p>
+  <p>
+  13. 	Wang S, Peterson DJ, Gatenby JC, Li W, Grabowski TJ, Madhyastha TM. Evaluation of Field Map and Nonlinear Registration Methods for Correction of Susceptibility Artifacts in Diffusion MRI. Front Neuroinform [Internet]. 2017 [cited 2017 Feb 21];11. Available from: <a href="http://journal.frontiersin.org/article/10.3389/fninf.2017.00017/full">http://journal.frontiersin.org/article/10.3389/fninf.2017.00017/full</a>


DOI: https://doi.org/10.3389/fninf.2017.00017

chrisgorgo · 2017-10-20T00:05:42Z

Ok - this is ready for review. I added dynamic fetching of the Zenodo reference (made a small library for it - planning to reuse it in other projects).

chrisgorgo · 2017-10-20T00:19:39Z

Library: https://github.com/chrisfilo/zenodo.js

effigies

Code looks good. Couple minor comments, mostly involving HTTPS.

I'll check the generated docs when they build. (Possibly in the morning.)

effigies · 2017-10-20T00:28:22Z

docs/citing.rst

+   function fillCitation(){
+      $('#fmriprep_version').text(version);
+      $('#workflow_url').text('http://fmriprep.readthedocs.io/en/' + version + '/workflows.html');
+      $('#workflow_url').attr('href', 'http://fmriprep.readthedocs.io/en/' + version + '/workflows.html');


effigies · 2017-10-20T00:28:32Z

docs/citing.rst

+         });
+         getDOI(zenodoID, function(err, DOI) {
+            $('#fmriprep_doi_url').text('http://doi.org/' + DOI);
+            $('#fmriprep_doi_url').attr('href', 'http://doi.org/' + DOI);


effigies · 2017-10-20T00:30:41Z

docs/citing.rst

+        for (var i = 0; i < controlElementsIdsLength; i++) {
+        	controlElement = document.getElementById(controlElementsIds[i])
+
+        	if (controlElement.checked == null){


Mixed tabs and spaces in this line and the one above it.

effigies · 2017-10-20T00:33:03Z

docs/citing.rst

+.. raw:: html
+
+   <script language="javascript">
+   var version = '1.0.0-rc6';


I'd be inclined to leave this as 'latest'. Anybody who's building docs manually is likely to be near HEAD and putting in a specific version makes this a place that needs updating.

effigies · 2017-10-20T00:34:52Z

docs/citing.rst

+  <img src onerror='fillCitation()'>
+  </p>
+  <p>
+  2. 	Gorgolewski K, Burns CD, Madison C, Clark D, Halchenko YO, Waskom ML, Ghosh SS. Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in python. Front Neuroinform [Internet]. 2011 Aug 22;5(August):13. Available from: <a href="http://doi.org/10.3389/fninf.2011.00013">http://doi.org/10.3389/fninf.2011.00013</a>


Sorry, wasn't clear. The main thing I was suggesting with the DOI URLs was the s in https, more than just dropping the dx. (I suspect https://dx.doi.org works, but figure shorter URLs are better.)

effigies · 2017-10-20T00:35:13Z

docs/conf.py

+
+def setup(app):
+    # We need this for the boilerplate script
+    app.add_javascript("https://cdn.rawgit.com/chrisfilo/zenodo.js/v0.1/zenodo.js")


Newline at end of file.

chrisgorgo · 2017-10-20T14:55:41Z

For some reason GitHub does not display the new line, but this should be done now.

oesteban

The PR got merged before I finished the review.

oesteban · 2017-10-20T15:52:39Z

circle.yml

@@ -35,6 +35,7 @@ dependencies:
  override:
    - sed -i -E "s/(__version__ = )'[A-Za-z0-9.-]+'/\1'$CIRCLE_TAG'/" fmriprep/info.py


Can we join together these 3 replacements in only one?:

- | if [[ "$CIRCLE_TAG" != "" ]]; then sed -i -E "s/(__version__ = )'[A-Za-z0-9.-]+'/\1'$CIRCLE_TAG'/" fmriprep/info.py sed -i -E "s/(__version__ = )'[A-Za-z0-9.-]+'/\1'$CIRCLE_TAG'/" wrapper/fmriprep_docker.py sed -i -E "s/(var version = )'[A-Za-z0-9.-]+'/\1'$CIRCLE_TAG'/" docs/citing.rst fi

oesteban · 2017-10-20T15:55:13Z

docs/citing.rst

+            $('#fmriprep_citation').text(citation);
+         });
+         getDOI(zenodoID, function(err, DOI) {
+            $('#fmriprep_doi_url').text('https://doi.org/' + DOI);


I usually prefer to hide the https://doi.org/ on DOIs and just show doi:some-doi-without-http-doi-org. But it is only a preference.

oesteban · 2017-10-20T15:57:58Z

docs/citing.rst

+  <img src onerror='fillCitation()'>
+  </p>
+  <p>
+  2. 	Gorgolewski K, Burns CD, Madison C, Clark D, Halchenko YO, Waskom ML, Ghosh SS. Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in python. Front Neuroinform [Internet]. 2011 Aug 22;5(August):13. Available from: <a href="https://doi.org/10.3389/fninf.2011.00013">https://doi.org/10.3389/fninf.2011.00013</a>


As before, I usually prefer:

doi:<a href="https://doi.org/10.3389/fninf.2011.00013">10.3389/fninf.2011.00013</a>

over:

Available from: <a href="https://doi.org/10.3389/fninf.2011.00013">https://doi.org/10.3389/fninf.2011.00013</a>

oesteban · 2017-10-20T15:59:29Z

docs/citing.rst

+   With slicetime correction: <input id="slicetime" type="checkbox" checked="true" onclick="toggle();"/><br />
+   </p>
+
+   <p style="font-style: italic;">Results included in this manuscript come from preprocessing performed using FMRIPREP version <span id="fmriprep_version">latest</span> [1] a Nipype [2,3] based tool. Each T1 weighted volume was corrected for bias field using N4BiasFieldCorrection v2.1.0 [4] and skullstripped using antsBrainExtraction.sh v2.1.0 (using


Can we add links to the references? ([1, 2, etc])

effigies · 2017-10-20T16:14:13Z

Ah, sorry. I'm okay with all of those changes, if you want to make a new PR.

effigies · 2017-10-20T16:20:44Z

If you do make a new one, we may want to add DOI:10.1016/j.neuroimage.2007.12.025 for T2-based pial refinement (possibly another checkbox next to FreeSurfer?).

This was just posted on the mailing list this morning. I wasn't aware there was any citation for T2 refinement before.

chrisgorgo · 2017-10-20T16:43:33Z

Please open issues for all the fixes/enhancements you mentioned.

chrisgorgo added 3 commits October 18, 2017 17:19

added boilerplate [docs only]

8e2af2f

removing authors [docs only]

233adf9

removing authors [docs only]

5f5f37e

making links more linky [docs only]

c3a1ffe

effigies reviewed Oct 19, 2017

View reviewed changes

chrisgorgo added 4 commits October 19, 2017 09:48

clean up [docs only]

4042cbf

dynamic generation of Zenodo references [docs only]

717bd7e

simplify code [docs only]

e96ae33

new URLs [docs only]

7a7a9fa

chrisgorgo changed the title ~~[WIP] Citation boilerplate~~ Citation boilerplate Oct 19, 2017

effigies reviewed Oct 20, 2017

View reviewed changes

chrisgorgo added 3 commits October 19, 2017 21:51

https [docs only]

fdcb3e8

minor fixes [docs only]

fae883d

extra new line [docs only]

046969d

effigies merged commit e95c6d7 into nipreps:master Oct 20, 2017

oesteban reviewed Oct 20, 2017

View reviewed changes

oesteban added this to the 1.0.0-rc7 milestone Oct 20, 2017

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Citation boilerplate #779

Citation boilerplate #779

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chrisgorgo commented Oct 20, 2017

		@@ -35,6 +35,7 @@ dependencies:
		override:
		- sed -i -E "s/(__version__ = )'[A-Za-z0-9.-]+'/\1'$CIRCLE_TAG'/" fmriprep/info.py

Citation boilerplate #779

Citation boilerplate #779

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chrisgorgo commented Oct 19, 2017

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chrisgorgo commented Oct 20, 2017

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effigies commented Oct 20, 2017

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