✍️ Academic Writing




Impact Factor


Nature Communications

Dr. Heather Partner, Associate Editor (correspondence with JCA)


Nature Communications Biology

Editor: yomayra.guzman “at” nature “dot” com





Nature Scientific Reports


Nature Scientific Data


Nature Methods


Nature Protocols


Journal of Neuroscience Methods


Frontiers in Neuroinformatics





Organizing Folders

Recommended file structure:

     |- 2017_MRM/
           |- fig/
               |- figures.key (or pptx) --> all your figures, one per slide
           |- r0/
               |- cover_letter_r0_v0.docx
               |- manuscript_r0_v0.docx
               |- manuscript_r0_v1.docx
               |- manuscript_r0_v1_JCA.docx
               |- manuscript_r0_v2.docx
               |- reviewer_suggestions.docx
           |- r1/
               |- manuscript_r1_v0.docx
               |- manuscript_r1_v1.docx

You can start from this template.

  • First version: my_paper_r0_v0.docx

  • Version Corrected by Paul Smith: my_paper_r0_v0_PS.docx

  • Then your new version (accept all Track Changes otherwise it’s messy!): my_paper_r0_v1.docx

  • After first submission to the journal, you receive comments. New name: my_paper_r1_v0.docx

  • and so on…

Cover letter

Excellent recommendations from Michael Breakspear on how to write a cover letter.

Addressing Reviewer Comments

  • Copy/paste comments in a new file responses_to_reviews

  • Address comments point-by-point

  • For most comments, the manuscript will need to be updated and the modified text copied in the responses. Please do not duplicate this text during the review process, because the manuscript might be edited later by another coauthor, and there will be discrepancies between the manuscript and the responses. Therefore, edit the manuscript first, and in the responses, indicate a placeholder with a comment “will be copy/pasted when final version of the manuscript is ready”.

  • Please read these ten simple rules for writing a response to reviewers.

Managing References

We recommend using Paperpile for managing your bibliography.

We have a Paperpile account for the lab. For login please use the Google account neuropolylab "at" gmail "dot" com

If you prefer to have your own Paperpile license please request it to your supervisor.


Paperpile on Google Docs works only with Google Chrome.

Install Paperpile

  1. Connect to Paperpile website with the NeuroPoly Google account (or with your account if you have a license). Sometimes if you only have a single Google account logged in, you will have to add another account here: https://accounts.google.com/AccountChooser?service=lso

  2. Install Paperpile chrome extension on the browser (Google Chrome)

  3. Use your personal account to connect on Google Docs, start a new document page. Insert citations, when you do Paperpile/Format citations/ it will require you to authorize Paperpile into Google docs.

  4. Authorize Paperpile on Google using your personal account.

Figures (in vectorial format)

Create and manage figures:

  • make your figure in Keynote (or Power Point)

  • keep only one keynote file

  • number the slide for a specific fig, eg.: slide 1 –> fig 1, slide 2 –> fig 2. The material/old slides go after a big slide called “OLD”.

  • when using phantom and MRI data please indicate the session number, slice, TE, etc. anything so we can reproduce the figure in the future.

Incorporate figure in article:

  • Export all your figures into a single PDF document (select: best quality).

  • Open PDF with Preview

  • Tools > Rectangular selection

  • CMD+c, CMD+n

  • Save figure

  • Import your figure into Word and use “crop” tool.


For everyone:

NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal, Montreal, QC, Canada

Affiliation for Julien Cohen-Adad:

Functional Neuroimaging Unit, CRIUGM, Université de Montréal, Montreal, QC, Canada

Mila - Quebec AI Institute, Montreal, QC, Canada

Affiliation for Nikola Stikov:

Montreal Heart Institute, Montreal, QC, Canada


For all articles/abstracts, please add the following:

Funded by the Canada Research Chair in Quantitative Magnetic Resonance Imaging [950-230815], the Canadian Institute of Health Research [CIHR FDN-143263], the Canada Foundation for Innovation [32454, 34824], the Fonds de Recherche du Québec - Santé [28826], the Natural Sciences and Engineering Research Council of Canada [RGPIN-2019-07244], the Canada First Research Excellence Fund (IVADO and TransMedTech), the Courtois NeuroMod project and the Quebec BioImaging Network [5886, 35450], INSPIRED (Spinal Research, UK; Wings for Life, Austria; Craig H. Neilsen Foundation, USA).

For projects involving SEM, please add:

the Center for Characterization and Microscopy of Materials (CM)² for electron microscopy scanning

If using the GPU on Bireli, add:

NVIDIA Corporation for the donation of a Titan X GPU

For those with the Polytechnique MEDITIS fellowship and other fellowships, please don’t forget to mention them.

Writing Platforms/Software

Google Docs

We recommend you install (and use) the following Adds-on:



Cross Reference

Cross-referencing figures on Google Docs

Markdown Tools

Enables adding heading numbers and the creation of a table of contents for markdown.


  1. We have a lab account for Overleaf. It is important to use it, otherwise you won’t be able to share the document with all collaborators.

  2. Connect to Overleaf with the NeuroPoly Google account. Sometimes if you only have a single Google account logged in, you will have to add another account here: https://accounts.google.com/AccountChooser?service=lso