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Paper: Developing a Graph Convolution-Based Analysis Pipeline for Multi-Modal Neuroimage Data: An Application to Parkinson's Disease #477

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commented May 23, 2019

If you are creating this PR in order to submit a draft of your paper,
see http://procbuild.scipy.org/ for logs generated by the build
process.

See the project readme
for more information.

xtianmcd added some commits May 13, 2019

Rename papers/neuro_analy_pipeline_scipy2019.rst to papers/christian_…
…mcdaniel/neuro_analy_pipeline_scipy2019.rst
@deniederhut

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commented May 23, 2019

Hm... looks like you might have a bibtex issue. Here's the message from the server:

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xtianmcd added some commits May 23, 2019

@xtianmcd

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commented May 23, 2019

@deniederhut thanks for your comments. Where did you find that server output? My .log output and the output printed to Terminal wasn't showing the error regarding the alpha character in my .bib file.

Anyway, I've fixed that error, and I figured out the push issue (needed to specify to push to origin 2019). However, I still cannot get a successful build. FYI, I have verified my .bib file using the BibLatex-Check package (although I know BibLatex is technically different from a bibfile), I have tried running make clean before the build, and have tried repeating the build twice to get the .bib file to build (these were all suggestions from you last year when I encountered similar problems). I get a successful pdf locally (except for citations), and I don't see any errors in my .log file (I can provide it if that helps), but I do see warnings.

I didn't expect the warnings to prevent a build (else I figured they would be errors), but I'm trying to fix them now. I've resolved all but a few Warning types that I don't know how to resolve. E.g.:

Package hyperref Warning: Ignoring empty anchor on input line 419

I've checked my footnotes and they are all entered according to the docs.

LaTeX Warning: Citation `KW2017' on page 6 undefined on input line 406.

The citation is in the .bib file as

@Proceedings{KW2017,
  author = "Thomas N Kipf and Max Welling",
  title = "Semi-Supervised Classification with Graph Convolutional Networks",
  year = "2017",
  publisher = "ICLR",
}

and the .bib file is noted in my .rst file using :bibliography: <bibfile_name_without_extension> at the top. There is a Warning like this for most or all of my citations, indicating there's still an issue in my .bib file. Finding the location you got that other error from may be what I need.

Underfull \hbox (badness 3343) in paragraph at lines ... 

and

Package caption Warning: Unsupported document class (or package) detected,
(caption)                usage of the caption package is not recommended.
See the caption package documentation for explanation.

seem related to the translation between .rst and Latex, and I couldn't find fixes for them from my end (in my .rst file).

Anyway, these are my thoughts... pls let me know if you have any other suggestions, and where you got the output from the server that you posted earlier. Thanks so much!! I'm learning a lot

@cbcunc

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commented May 23, 2019

That last commit did it. It builds on procbuild now.

@xtianmcd

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commented May 23, 2019

Success! Thanks for the help and patience. FYI, I got my references to appear by adding the lines

.. raw:: latex

   \bibliographystyle{plain}

to my .rst file. Initial answer here although I did not need the lines from the first code block or the bottom line of the last block to make the References appear (likely because of the :bibliography: <bibfile_name_without_extenstion> line already in the .rst file).

I added the lines before my Appendix section to try and put the References before the Appendix, but the References still inserted at the end. Any idea how to "append" an Appendix to the very end, after References?.

These lines also caused helpful errors to appear in my .log file and print to Terminal (I had a problematic hyphen in my .bib file). I tried building without the raw latex lines after fixing the hyphen and the References did not show up, so I confirmed that these lines are the reason for the References appearing in my case.

@deniederhut

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commented May 24, 2019

I stopped by to look at the error logs but it looks like you've already got it figured out - congrats!

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commented May 28, 2019

Dear @xtianmcd,

I am one of the reviewers of your paper. Would you prefer me to list my comments in a comment box or on the rst file?

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commented May 28, 2019

Hi @AngelosPsy, thanks for checking in! I would say, if you have some comments that point to specific words/sentences, then on the rst file will be best. Otherwise, more general comments about a section, etc may be better to leave here To keep more of a record.

Also FYI, I will be adding more to the results later this week. I have the results but am currently out of town. Thanks!

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commented May 29, 2019

Hi @xtianmcd,

OK, since from what I understand the paper is not 100% ready yet (i.e., the results are missing) I will just place my general comments here. After revisions, I can go through the paper sentence by sentence and make more specific comments. I understand that you are out of town so I do not expect and immediate answer. Also, if you are on vacation, please feel free to ignore my message until you return – it is good to have real vacation 😃

Copyright

  • Why not just write “Christian McDaniel, Shannon Quinn” rather than “Christian McDaniel et al.” ?

Abstract

  • “resulting in progressively worsening motor, cognitive, and psychological symptoms.” What do you mean with “worsening…psychological symptoms”?
  • The abstract may turn out to be too long after you insert the results. Maybe you should rewrite the abstract a bit so it is not too long.

Introduction

  • Maybe when there are multiple references you can include them within brackets.
  • In general, I think the introduction assumes too much knowledge from the readers. For example, I do not think many would know what “T1-weighted images” are. The same goes for some statements such as the following: “The edges of the graph offer an explicit metric for establishing meaningful neighborhoods of nodes and the features offer meaningful descriptors with which to group them.” It should be clear what it is meant with “meaningful descriptors” etc.
  • Please also check throughout the manuscript and remove some bits that seem like residual notes (e.g., “[and functional data??]” or “[If functional data is used, insert info re: fMRI acquisition/preprocessing]”).

Background

  • I absolutely understand why there is such extensive explanation of, for example, the Graph Convolutional Networks etc. However, I soon got lost in that section and I think the way this part is written targets more of a specialized audience rather than the broader audience of scipy. I would kindly suggest that big parts of the background section are reduced so that the paper focuses more on the programming part (see Methods section). To repeat, I absolutely agree that a good background will make it easier to understand the methods but I do think that the background part is written for more of a general, rather than a specialized, audience.

Discussions and Conclusions

  • This part needs to be rewritten as it is neither a discussion or a conclusion section. It is more of a one-line summary of the paper.

References

  • There is a mix up of the footones with the references. I would suggest that the footnoes are placed before the references.
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commented Jun 10, 2019

Hi @AngelosPsy,

Thanks for your helpful feedback, and patience regarding my travels! I have addressed your points, and have made some comments below.

In general, I reduced the Background and combined it with the Methods section, and reworded/revised a lot of the paper. My goal is to include enough technical background for neuroimaging and deep learning so that an outsider to the fields could understand and implement the methods, in line with the "pipeline" format. However, that's easier said than done and if things are still too wordy or verbose please let me know!

Copyright

Why not just write “Christian McDaniel, Shannon Quinn” rather than “Christian McDaniel et al.” ?

This is generated by the build system of SciPy. Do you know if there is a way for me to change it? If so, I'll look into it!

Abstract

“resulting in progressively worsening motor, cognitive, and psychological symptoms.” What do you mean with “worsening…psychological symptoms”?

I changed this to 'psychiatric symptoms (i.e., depression)'. I am referring to issues such as depression. Hopefully that makes it more clear; otherwise I can try something else.

The abstract may turn out to be too long after you insert the results. Maybe you should rewrite the abstract a bit so it is not too long.

Do you know the limit? I believe newly updated abstract is currently exactly 150 words.

There is a mix up of the footones with the references. I would suggest that the footnoes are placed before the references.

This is also a result of the build process. I tried moving the footnotes but they were still inserted in the same place. (I have also tried putting the Appendices after the Results, but the build process seems to always put the Results at the very end)

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commented Jun 13, 2019

Thank you for your responses to my answers. Could you maybe fix the file as it fails to build (see here http://procbuild.scipy.org/# ). After that I can continue with my review.

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commented Jun 13, 2019

Thanks @AngelosPsy for catching that... Try now!

@cbcunc cbcunc self-requested a review Jun 19, 2019

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@xtianmcd This paper renders to 10 pages. Our review guidelines state, "The compiled version should be no longer than 8 pages, including figures, source code, appendices, etc.."

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commented Jun 23, 2019

Hi @xtianmcd,

I do not know how the text would look like after you have reduced it to fit in the 8-page limit but here are some additional comment to the present version of the ms.

  • “Parkinson’s disease (PD) is a highly prevalent neurodegenerative disease” : Disease is a … disease. Please rephrase.

  • Figure 4: Increase label size, do you need colors? Is not the the importance obvious via the length of the bar. You may also consider decreasing the width of the bars to save space.

  • Please fix the gap on page 8

  • “MRI data requires extensive artifact correction and removal before it can be used. MRI signals are acquired through the application of precisely coordinated magnetic fields and radiofrequency (RF) pulses.”: Please combine sentences

  • The standard software for preprocessing anatomical MRI (aMRI1) data is Freesurfer9. Freesurfer is an actively developed software with responsive technical support and rich forums. The software is dense and the documentation is lacking in some areas, so training may still be helpful, although not available in our case.: Please reduce redundancy here so that the text is shortened.

  • Discussions and Conclusions: I think it should be ‘Discussion and Conclusion’

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commented Jun 24, 2019

@AngelosPsy I have made the suggested changes.

@cbcunc Is it okay if the Footnotes and References exceed the 8-page limit? If so, then the paper is now 8 pages, except that it insists on keeping the last line on page 9. When I shorten sections, the build process just widens that gaps of the math sections to keep the last line on page 9. Any advice?

I am not seeing the changes in the build server. Do you I need to create a pull request, or was that done when I pushed to my fork and the changes are just waiting to be approved?

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commented Jun 25, 2019

I am not seeing the changes in the build server.

Builds can be triggered by hand by pressing the refresh button on the right side of your PR listing on procbuild.scipy.org

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