[REVIEW]: Integrating Structural, Functional, and Biochemical Brain Imaging Data with MRShiny Brain - An Interactive Web Application

[roboneuro]

Submitting author: @arcj-hub (Jessica Archibald)
Repository: https://github.com/arcj-hub/MRShiny-Brain
Branch with paper.md (empty if default branch):
Version: 4.3.2 (Rversion)
Editor: @agahkarakuzu
Reviewers: @agahkarakuzu
Reproducible preprint: https://preprint.neurolibre.org/10.55458/neurolibre.00029
Repository archive: 10.5281/zenodo.14375265
Data archive: N/A
Book archive: 10.5281/zenodo.14375267
Docker archive: N/A

Status

Status badge code:

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Markdown: [![status](https://neurolibre.org/papers/e247b9a6eb73e2cedddff27d25fa8cad/status.svg)](https://neurolibre.org/papers/e247b9a6eb73e2cedddff27d25fa8cad)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@agahkarakuzu, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@roboneuro generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @agahkarakuzu know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

@agahkarakuzu, please create your checklist typing: @roboneuro generate my checklist

[roboneuro]

Hello humans, I'm @roboneuro, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@roboneuro commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@roboneuro generate pdf

[roboneuro]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.01 s (861.4 files/s, 169789.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                                1            145             48            752
TeX                              1             32              0            277
Markdown                         2             45              0            138
YAML                             3              8             17             59
JSON                             1              0              0              3
Jupyter Notebook                 1              3            247              0
-------------------------------------------------------------------------------
SUM:                             9            233            312           1229
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[roboneuro]

Wordcount for paper.md is 2506

[roboneuro]

Failed to discover a Statement of need section in paper

[agahkarakuzu]

@roboneuro build book

[roboneuro]

🔴 Binder build has failed 🥀

Status: Failed 5a80ac4f
Last updated: 2024-07-31 11:47:32 PDT

ℹ️ See details

The next comment will forward the logs

[roboneuro]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1002/jmri.25436 is OK
- 10.1002/mrm.1910330620 is OK
- 10.1002/nbm.3050 is OK

MISSING DOIs

- 10.1152/physrev.00016.2012 may be a valid DOI for title: Metabolism and the circadian clock converge
- 10.1016/j.neuroimage.2018.01.043 may be a valid DOI for title: Sex- and sex hormone-related variations in energy-metabolic frontal brain asymmetries: A magnetic resonance spectroscopy study
- 10.1016/b978-0-444-64196-0.00001-7 may be a valid DOI for title: The cingulate cortex in neurologic diseases: History, Structure, Overview
- 10.1038/s41592-018-0235-4 may be a valid DOI for title: fMRIPrep: a robust preprocessing pipeline for functional MRI
- 10.1038/s41596-020-0327-3 may be a valid DOI for title: Analysis of task-based functional MRI data preprocessed with fMRIPrep
- 10.1016/j.media.2007.06.004 may be a valid DOI for title: Symmetric Diffeomorphic Image Registration with Cross-Correlation: Evaluating Automated Labeling of Elderly and Neurodegenerative Brain
- 10.1109/42.906424 may be a valid DOI for title: Segmentation of brain MR images through a hidden Markov random field model and the expectation-maximization algorithm
- 10.1016/s1053-8119(02)91132-8 may be a valid DOI for title: Improved Optimization for the Robust and Accurate Linear Registration and Motion Correction of Brain Images
- 10.1016/j.mri.2007.07.003 may be a valid DOI for title: Empirical optimization of ASL data analysis using an ASL data processing toolbox: ASLtbx
- 10.1016/s1361-8415(01)00036-6 may be a valid DOI for title: A global optimisation method for robust affine registration of brain images
- 10.1016/j.neuroimage.2009.06.060 may be a valid DOI for title: Accurate and Robust Brain Image Alignment using Boundary-based Registration
- 10.1016/j.neuroimage.2013.08.048 may be a valid DOI for title: Methods to detect, characterize, and remove motion artifact in resting state fMRI
- 10.1002/nbm.4484 may be a valid DOI for title: Minimum Reporting Standards for in vivo Magnetic Resonance Spectroscopy (MRSinMRS): Experts’ consensus recommendations
- 10.4137/mri.s32903 may be a valid DOI for title: Hitchhiker’S Guide to Voxel Segmentation for Partial Volume Correction of in Vivo Magnetic Resonance Spectroscopy
- 10.1002/mrm.20901 may be a valid DOI for title: Use of Tissue Water as a Concentration Reference for Proton Spectroscopic Imaging

INVALID DOIs

- None

[roboneuro]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[roboneuro]

🥀 We ran into a problem building your book. Please see the log files below.

BinderHub build log

Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2docker59d1yd65'...
HEAD is now at 480bf54 Update paper.md
Building conda environment for python=3.7
Using PythonBuildPack builder
Building conda environment for python=3.7
Building conda environment for python=3.7
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Step 13/51 : RUN groupadd         --gid ${NB_UID}         ${NB_USER} &&     useradd         --comment "Default user"         --create-home         --gid ${NB_UID}         --no-log-init         --shell /bin/bash         --uid ${NB_UID}         ${NB_USER}
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Step 14/51 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        less        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
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Step 26/51 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e9-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-e9bee0 /etc/profile.d/activate-conda.sh
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Building wheels for collected packages: wget
  Building wheel for wget (setup.py): started
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  Created wheel for wget: filename=wget-3.2-py3-none-any.whl size=9657 sha256=bebd1bb1e84ebc1a5b8e9a45a17c9836b58f99f181464e385a4e50b496b90daa
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Installing collected packages: wget, snowballstemmer, patool, msgpack, looseversion, annexremote, uc-micro-py, typing-extensions, tqdm, tenacity, tabulate, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, pyyaml, pyasn1, numpy, more-itertools, mdurl, latexcodec, jmespath, jeepney, iso8601, imagesize, filelock, fasteners, docutils, colorama, chardet, alabaster, scipy, rsa, requests-toolbelt, pybtex, plotly, platformdirs, patsy, pandas, osfclient, markdown-it-py, linkify-it-py, jaraco.classes, botocore, statsmodels, sphinx, SecretStorage, s3transfer, python-gitlab, pybtex-docutils, mdit-py-plugins, keyrings.alt, humanize, gdown, click, sphinxcontrib-bibtex, sphinx_togglebutton, sphinx-thebe, sphinx-multitoc-numbering, sphinx-jupyterbook-latex, sphinx-external-toc, sphinx-design, sphinx-copybutton, sphinx-comments, pydata-sphinx-theme, plotly-express, myst-parser, keyring, boto3, awscli, sphinx-book-theme, nbclient, datalad, repo2data, jupyter-cache, myst-nb, jupyter-book
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Successfully installed SecretStorage-3.3.3 alabaster-0.7.13 annexremote-1.6.5 awscli-1.31.13 boto3-1.33.13 botocore-1.33.13 chardet-5.2.0 click-8.1.7 colorama-0.4.4 datalad-1.1.0 docutils-0.16 fasteners-0.19 filelock-3.12.2 gdown-4.7.3 humanize-4.6.0 imagesize-1.4.1 iso8601-2.1.0 jaraco.classes-3.2.3 jeepney-0.8.0 jmespath-1.0.1 jupyter-book-0.14.0 jupyter-cache-0.5.0 keyring-24.1.1 keyrings.alt-4.2.0 latexcodec-3.0.0 linkify-it-py-2.0.3 looseversion-1.3.0 markdown-it-py-2.2.0 mdit-py-plugins-0.3.5 mdurl-0.1.2 more-itertools-9.1.0 msgpack-1.0.5 myst-nb-0.17.2 myst-parser-0.18.1 nbclient-0.5.13 numpy-1.21.6 osfclient-0.0.5 pandas-1.3.5 patool-1.12 patsy-0.5.6 platformdirs-4.0.0 plotly-5.14.1 plotly-express-0.4.1 pyasn1-0.5.1 pybtex-0.24.0 pybtex-docutils-1.0.3 pydata-sphinx-theme-0.12.0 python-gitlab-3.15.0 pyyaml-6.0.1 repo2data-2.6.0 requests-toolbelt-1.0.0 rsa-4.7.2 s3transfer-0.8.2 scipy-1.7.3 snowballstemmer-2.2.0 sphinx-5.0.2 sphinx-book-theme-0.4.0rc1 sphinx-comments-0.0.3 sphinx-copybutton-0.5.2 sphinx-design-0.3.0 sphinx-external-toc-0.3.1 sphinx-jupyterbook-latex-0.5.2 sphinx-multitoc-numbering-0.1.3 sphinx-thebe-0.2.1 sphinx_togglebutton-0.3.2 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-bibtex-2.5.0 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 statsmodels-0.13.5 tabulate-0.9.0 tenacity-8.2.3 tqdm-4.66.4 typing-extensions-4.7.1 uc-micro-py-1.0.3 wget-3.2
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{"aux": {"ID": "sha256:054ff568f43910b590e9b783cf8c30bbb5d17166ca4fd7293d1cb80ab6ff63e7"}}Successfully built 054ff568f439
Successfully tagged binder-registry.conp.cloud/binder-registry.conp.cloud/binder-arcj-2dhub-2dmrshiny-2dbrain-452d63:480bf5412bff30f0c34e0935d89598cc3b24b625
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Successfully pushed binder-registry.conp.cloud/binder-registry.conp.cloud/binder-arcj-2dhub-2dmrshiny-2dbrain-452d63:480bf5412bff30f0c34e0935d89598cc3b24b625Built image, launching...
Launching server...
Server requested
2024-07-31T18:44:49.322194Z [Normal] Successfully assigned binderhub/jupyter-arcj-2dhub-2dmrshiny-2dbrain-2dmtqb0qo6 to neurolibre-master
2024-07-31T18:44:52Z [Normal] Container image "jupyterhub/k8s-network-tools:3.0.0-beta.3" already present on machine
2024-07-31T18:44:54Z [Normal] Created container block-cloud-metadata
2024-07-31T18:44:54Z [Normal] Started container block-cloud-metadata
2024-07-31T18:44:55Z [Normal] Pulling image "binder-registry.conp.cloud/binder-registry.conp.cloud/binder-arcj-2dhub-2dmrshiny-2dbrain-452d63:480bf5412bff30f0c34e0935d89598cc3b24b625"
2024-07-31T18:46:16Z [Normal] Successfully pulled image "binder-registry.conp.cloud/binder-registry.conp.cloud/binder-arcj-2dhub-2dmrshiny-2dbrain-452d63:480bf5412bff30f0c34e0935d89598cc3b24b625" in 1m21.73s (1m21.73s including waiting)
2024-07-31T18:46:17Z [Normal] Created container notebook
2024-07-31T18:46:18Z [Normal] Started container notebook
Server ready at /jupyter/user/arcj-hub-mrshiny-brain-mtqb0qo6/
server running at https://test.conp.cloud/jupyter/user/arcj-hub-mrshiny-brain-mtqb0qo6/

If the BinderHub build looks OK, please see the Jupyter Book build log(s) below.

Jupyter Book build log

Running Jupyter-Book v0.14.0
Source Folder: /home/jovyan/content
Config Path: /home/jovyan/content/_config.yml
Output Path: /mnt/books/arcj-hub/github.com/MRShiny-Brain/480bf5412bff30f0c34e0935d89598cc3b24b625/_build/html
�[01mRunning Sphinx v5.0.2�[39;49;00m
Adding copy buttons to code blocks...
Adding copy buttons to code blocks...
�[01mmaking output directory... �[39;49;00mdone
[etoc] Changing master_doc to '00-simple_markdown'
locale_dir /home/jovyan/content/locales/en/LC_MESSAGES does not exists
�[01mmyst v0.18.1:�[39;49;00m MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=['colon_fence', 'dollarmath', 'linkify', 'substitution', 'tasklist'], disable_syntax=[], all_links_external=False, url_schemes=['mailto', 'http', 'https'], ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=None, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area')
�[01mmyst-nb v0.17.2:�[39;49;00m NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, execution_mode='cache', execution_cache_path='/mnt/books/arcj-hub/github.com/MRShiny-Brain/480bf5412bff30f0c34e0935d89598cc3b24b625/_build/.jupyter_cache', execution_excludepatterns=[], execution_timeout=-1, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=False, merge_streams=False, render_plugin='default', remove_code_source=False, remove_code_outputs=False, code_prompt_show='Show code cell {type}', code_prompt_hide='Hide code cell {type}', number_source_lines=False, output_stderr='show', render_text_lexer='myst-ansi', render_error_lexer='ipythontb', render_image_options={}, render_figure_options={}, render_markdown_format='commonmark', output_folder='build', append_css=True, metadata_to_fm=False)
Using jupyter-cache at: /mnt/books/arcj-hub/github.com/MRShiny-Brain/480bf5412bff30f0c34e0935d89598cc3b24b625/_build/.jupyter_cache
locale_dir /home/jovyan/content/locales/en/LC_MESSAGES does not exists
�[01mbuilding [mo]: �[39;49;00mtargets for 0 po files that are out of date
�[01mbuilding [html]: �[39;49;00mtargets for 1 source files that are out of date
�[01mupdating environment: �[39;49;00mlocale_dir /home/jovyan/content/locales/en/LC_MESSAGES does not exists
[new config] 1 added, 0 changed, 0 removed
�[01mreading sources... �[39;49;00m[100%] �[35mnotebook�[39;49;00m
/home/jovyan/content/notebook.ipynb: Executing notebook using local CWD [mystnb]
/home/jovyan/content/notebook.ipynb: Executed notebook in 1.34 seconds [mystnb]
/home/jovyan/content/notebook.ipynb: Cached executed notebook: ID=1 [mystnb]
�[91m/home/jovyan/content/notebook.ipynb:100004: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header]�[39;49;00m

�[91m/home/jovyan/content/notebook.ipynb:100010: WARNING: Non-consecutive header level increase; H1 to H3 [myst.header]�[39;49;00m

�[31m/home/jovyan/content/notebook.ipynb:130004: ERROR: Unknown directive type "bibliography".�[39;49;00m
�[91mSphinx error:�[39;49;00m

root file /home/jovyan/content/00-simple_markdown.rst not found

Traceback (most recent call last):

File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/sphinx.py", line 171, in build_sphinx

app.build(force_all, filenames)

File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/application.py", line 329, in build

self.builder.build_update()

File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/init.py", line 290, in build_update

len(to_build))

File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/init.py", line 302, in build

updated_docnames = set(self.read())

File "/srv/conda/envs/notebook/lib/python3.7/site-packages/sphinx/builders/init.py", line 413, in read

self.env.doc2path(self.config.root_doc))

sphinx.errors.SphinxError: root file /home/jovyan/content/00-simple_markdown.rst not found
The above exception was the direct cause of the following exception:
Traceback (most recent call last):

File "/srv/conda/envs/notebook/bin/jupyter-book", line 8, in 

sys.exit(main())

File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1157, in call

return self.main(*args, **kwargs)

File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1078, in main

rv = self.invoke(ctx)

File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1688, in invoke

return _process_result(sub_ctx.command.invoke(sub_ctx))

File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 1434, in invoke

return ctx.invoke(self.callback, **ctx.params)

File "/srv/conda/envs/notebook/lib/python3.7/site-packages/click/core.py", line 783, in invoke

return __callback(*args, **kwargs)

File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/cli/main.py", line 318, in build

result, builder, OUTPUT_PATH, build_type, PAGE_NAME, click.echo

File "/srv/conda/envs/notebook/lib/python3.7/site-packages/jupyter_book/cli/main.py", line 525, in builder_specific_actions

raise RuntimeError(_message_box(msg, color="red", doprint=False)) from result

RuntimeError:

�[91m===============================================================================�[0m
There was an error in building your book. Look above for the cause.
�[91m===============================================================================�[0m
Jupyter-book exit code: 1

Jupyter-book build failed!

🐞 After inspecting the logs above, you can interactively debug your notebooks on our BinderHub server.

For guidelines, please see the relevant documentation.

🐞 After inspecting the logs above, you can interactively debug your notebooks on our BinderHub server.

For guidelines, please see the relevant documentation.

[agahkarakuzu]

@arcj-hub the error above is because your content/_toc.yml is not modified after cloning the template:

format: jb-book
root: 00-simple_markdown
parts:
  - caption: Ipynb
    chapters:
    - file: 01-simple_notebook
  - caption: MyST
    chapters:
    - file: 02-simple-myst

Here are the steps you can follow to fix it:

Step 1:

• Create a content/summary.md file and move the abstract of your article there (from the notebook).

Step 2:

• Update content/_toc.yml

format: jb-book
root: summary
parts:
  - caption: MRShiny Brain
    chapters:
    - file: notebook

Thank you!

[arcj-hub]

Done! From: Agah ***@***.***> Reply-To: neurolibre/neurolibre-reviews ***@***.***> Date: Wednesday, July 31, 2024 at 2:22 PM To: neurolibre/neurolibre-reviews ***@***.***> Cc: "Archibald, Jessica" ***@***.***>, Mention ***@***.***> Subject: Re: [neurolibre/neurolibre-reviews] [REVIEW]: Integrating Structural, Functional, and Biochemical Brain Imaging Data with MRShiny Brain - An Interactive Web Application (Issue #29) [CAUTION: Non-UBC Email] @arcj-hub<https://github.com/arcj-hub> the error above is because your content/_toc.yml is not modified after cloning the template: format: jb-book root: 00-simple_markdown parts: - caption: Ipynb chapters: - file: 01-simple_notebook - caption: MyST chapters: - file: 02-simple-myst Here are the steps you can follow to fix it: Step 1: * Create a content/summary.md file and move the abstract of your article there (from the notebook). Step 2: * Update content/_toc.yml format: jb-book root: summary parts: - caption: MRShiny Brain chapters: - file: notebook Thank you! — Reply to this email directly, view it on GitHub<#29 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ATSCAELYWYBKUJZD2JWBX5DZPFBPRAVCNFSM6AAAAABLZBJAWWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRRGM4DINBRGM>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[agahkarakuzu]

@roboneuro build book

[roboneuro]

🟢 Successfully built

Status: Success 2466b4db
Last updated: 2024-07-31 20:16:15 PDT

ℹ️ See details

:confetti_ball: Roboneuro will send you the book URL.

[roboneuro]

🎊🎊🎊 Good news!

🌺 Take a look at the latest version of your NRP

[arcj-hub]

Hey Agah, Just noticed on this most recent version there is some text missing. Is this made from the paper.md? Specifically, the thermometry info is missing. And the visual of the dashboard is cut off. Let me know what form I can edit to fix this 😊 Thanks! From: roboneuro ***@***.***> Reply-To: neurolibre/neurolibre-reviews ***@***.***> Date: Wednesday, July 31, 2024 at 9:16 PM To: neurolibre/neurolibre-reviews ***@***.***> Cc: "Archibald, Jessica" ***@***.***>, Mention ***@***.***> Subject: Re: [neurolibre/neurolibre-reviews] [REVIEW]: Integrating Structural, Functional, and Biochemical Brain Imaging Data with MRShiny Brain - An Interactive Web Application (Issue #29) [CAUTION: Non-UBC Email] 🎊🎊🎊 Good news! 🌺 Take a look at the latest version of your NRP<https://preview.neurolibre.org/book-artifacts/arcj-hub/github.com/MRShiny-Brain/caeb60c5fcec333393ac089943ee04348bd1b0e3/_build/html/> — Reply to this email directly, view it on GitHub<#29 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ATSCAEJBQXH775G6W2OHN6DZPGSBVAVCNFSM6AAAAABLZBJAWWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRRHA4DANZSGI>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[agahkarakuzu]

Hi @arcj-hub, this was built from two files:

• abstract.md
• notebook.ipynb

You can add the text in (I guess notebook.ipynb) and they will appear here as well.

And the visual of the dashboard is cut off.

I am in the process of deploying your dashboard to our server, once that's done, we can deal with the respective settings.

On that note, it seems that most of the library() commands in the app.R are redundant. For example, I cannot see why RNifti is loaded. Can you confirm the list of packages your dashboard is actively using?

[agahkarakuzu]

From what I can tell your dashboard only needs the following:

library(shiny)
library(shinythemes)
library(plotly)
library(dplyr)
library(ggplot2)
library(DT)

do you confirm, or is there something else I am missing?

[agahkarakuzu]

@arcj-hub nevermind, here's the dashboard :)

https://shinybrain.db.neurolibre.org/

As you can see, no need to wait as we deployed with zero downtime!

Right now images are missing, but will fix it quickly.

[arcj-hub]

I just updated the notebook.ipynb sorry! I forgot the text was in two places. And that is correct, I just updated the code for the dashboard From: Agah ***@***.***> Reply-To: neurolibre/neurolibre-reviews ***@***.***> Date: Thursday, August 1, 2024 at 9:26 AM To: neurolibre/neurolibre-reviews ***@***.***> Cc: "Archibald, Jessica" ***@***.***>, Mention ***@***.***> Subject: Re: [neurolibre/neurolibre-reviews] [REVIEW]: Integrating Structural, Functional, and Biochemical Brain Imaging Data with MRShiny Brain - An Interactive Web Application (Issue #29) [CAUTION: Non-UBC Email] From what I can tell your dashboard only needs the following: library(shiny) library(shinythemes) library(plotly) library(dplyr) library(ggplot2) library(DT) do you confirm, or is there something else I am missing? — Reply to this email directly, view it on GitHub<#29 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ATSCAELDHJFRU2LZXKAIIHLZPJHUDAVCNFSM6AAAAABLZBJAWWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRTGM2TIMJXGM>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[agahkarakuzu]

OK perfect, I'll update the dashboard to make it fully functional, but we are almost there.

[agahkarakuzu]

@arcj-hub https://shinybrain.db.neurolibre.org should be now fully functional. Please let me know if there's something not working.

[agahkarakuzu]

Also for completeness, these are the libraries needed:

library(shiny)
library(shinythemes)
library(shinyWidgets)
library(plotly)
library(dplyr)
library(ggplot2)
library(DT)
library(reshape2)

the previous post was missing shinyWidgets and reshape2 (for melt function).

[agahkarakuzu]

@arcj-hub I also noticed that your latest change to notebook.ipynb broke the notebook. I guess you are using a text editor to make changes, which is often the reason why this happens.

Can you revert your latest commit and re-edit the notebook using VScode or jupyter? If you are not comfortable, happy to deal with it for you if you give me access to your repository.

[agahkarakuzu]

@roboneuro recommend-accept

[roboneuro]

Attempting dry run of processing paper acceptance...

[roboneuro]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1177/0271678X211004150 is OK
- 10.1152/physrev.00016.2012 is OK
- 10.1016/j.neuroimage.2018.01.043 is OK
- 10.1016/b978-0-444-64196-0.00001-7 is OK
- 10.1038/s41592-022-01458-7 is OK
- 10.5281/zenodo.7809101 is OK
- 10.1038/s41592-018-0235-4 is OK
- 10.1038/s41596-020-0327-3 is OK
- 10.54294/uvnhin is OK
- 10.1016/j.media.2007.06.004 is OK
- 10.1109/42.906424 is OK
- 10.1006/nimg.2002.1132 is OK
- 10.1016/j.mri.2007.07.003 is OK
- 10.1016/s1361-8415(01)00036-6 is OK
- 10.1016/j.neuroimage.2009.06.060 is OK
- 10.1002/jmri.25436 is OK
- 10.1016/j.neuroimage.2013.08.048 is OK
- 10.1002/mrm.1910400308 is OK
- 10.3389/fninf.2014.00014 is OK
- 10.1002/nbm.4257 is OK
- 10.1002/nbm.4484 is OK
- 10.1002/mrm.26091 is OK
- 10.4137/mri.s32903 is OK
- 10.1002/mrm.20901 is OK
- 10.1002/mrm.1910330620 is OK
- 10.1002/nbm.3050 is OK
- 10.31219/osf.io/h89js is OK
- 10.1371/journal.pcbi.1011230 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[roboneuro]

⚠️ Error preparing paper acceptance. The generated XML metadata file is invalid.

Element abstract content does not follow the DTD, expecting (object-id* , label? , title? , p* , sec*), got (CDATA)

[agahkarakuzu]

@roboneuro recommend-accept

[roboneuro]

Attempting dry run of processing paper acceptance...

[roboneuro]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1177/0271678X211004150 is OK
- 10.1152/physrev.00016.2012 is OK
- 10.1016/j.neuroimage.2018.01.043 is OK
- 10.1016/b978-0-444-64196-0.00001-7 is OK
- 10.1038/s41592-022-01458-7 is OK
- 10.5281/zenodo.7809101 is OK
- 10.1038/s41592-018-0235-4 is OK
- 10.1038/s41596-020-0327-3 is OK
- 10.54294/uvnhin is OK
- 10.1016/j.media.2007.06.004 is OK
- 10.1109/42.906424 is OK
- 10.1006/nimg.2002.1132 is OK
- 10.1016/j.mri.2007.07.003 is OK
- 10.1016/s1361-8415(01)00036-6 is OK
- 10.1016/j.neuroimage.2009.06.060 is OK
- 10.1002/jmri.25436 is OK
- 10.1016/j.neuroimage.2013.08.048 is OK
- 10.1002/mrm.1910400308 is OK
- 10.3389/fninf.2014.00014 is OK
- 10.1002/nbm.4257 is OK
- 10.1002/nbm.4484 is OK
- 10.1002/mrm.26091 is OK
- 10.4137/mri.s32903 is OK
- 10.1002/mrm.20901 is OK
- 10.1002/mrm.1910330620 is OK
- 10.1002/nbm.3050 is OK
- 10.31219/osf.io/h89js is OK
- 10.1371/journal.pcbi.1011230 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[roboneuro]

👋 @neurolibre/executable-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in neurolibre/preprints#85, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[agahkarakuzu]

@roboneuro recommend-accept

[roboneuro]

Attempting dry run of processing paper acceptance...

[roboneuro]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1177/0271678X211004150 is OK
- 10.1152/physrev.00016.2012 is OK
- 10.1016/j.neuroimage.2018.01.043 is OK
- 10.1016/b978-0-444-64196-0.00001-7 is OK
- 10.1038/s41592-022-01458-7 is OK
- 10.5281/zenodo.7809101 is OK
- 10.1038/s41592-018-0235-4 is OK
- 10.1038/s41596-020-0327-3 is OK
- 10.54294/uvnhin is OK
- 10.1016/j.media.2007.06.004 is OK
- 10.1109/42.906424 is OK
- 10.1006/nimg.2002.1132 is OK
- 10.1016/j.mri.2007.07.003 is OK
- 10.1016/s1361-8415(01)00036-6 is OK
- 10.1016/j.neuroimage.2009.06.060 is OK
- 10.1002/jmri.25436 is OK
- 10.1016/j.neuroimage.2013.08.048 is OK
- 10.1002/mrm.1910400308 is OK
- 10.3389/fninf.2014.00014 is OK
- 10.1002/nbm.4257 is OK
- 10.1002/nbm.4484 is OK
- 10.1002/mrm.26091 is OK
- 10.4137/mri.s32903 is OK
- 10.1002/mrm.20901 is OK
- 10.1002/mrm.1910330620 is OK
- 10.1002/nbm.3050 is OK
- 10.31219/osf.io/h89js is OK
- 10.1371/journal.pcbi.1011230 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[roboneuro]

👋 @neurolibre/executable-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in neurolibre/preprints#86, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[agahkarakuzu]

@roboneuro production sync pdf

[roboneuro]

🌱♻️📄 Synced the summary PDF from the source, should be now available at https://preprint.neurolibre.org/10.55458/neurolibre.00029.pdf?no-cache

[agahkarakuzu]

@roboneuro accept

[roboneuro]

Doing it live! Attempting automated processing of paper acceptance...

[roboneuro]

⚠️ Couldn't acccept/publish paper. An error happened. Could not deposit with Crossref.

[agahkarakuzu]

@roboneuro accept

[roboneuro]

Doing it live! Attempting automated processing of paper acceptance...

[roboneuro]

⚠️ Couldn't acccept/publish paper. An error happened.

[agahkarakuzu]

@roboneuro accept

[roboneuro]

Doing it live! Attempting automated processing of paper acceptance...

[roboneuro]

⚠️ Couldn't acccept/publish paper. An error happened. Could not deposit with Crossref.

[agahkarakuzu]

@roboneuro accept

[roboneuro]

Doing it live! Attempting automated processing of paper acceptance...

[roboneuro]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Archibald
  given-names: Jessica
  orcid: "https://orcid.org/0000-0001-6651-183X"
- family-names: Weber
  given-names: Alexander Mark
  orcid: "https://orcid.org/0000-0001-7295-0775"
- family-names: Scheuren
  given-names: Paulina S.
  orcid: "https://orcid.org/0000-0001-7568-0133"
- family-names: Ortiz
  given-names: Oscar
  orcid: "https://orcid.org/0000-0001-5872-2434"
- family-names: Choles
  given-names: Cassandra
- family-names: Lee
  given-names: Jaimie J.
  orcid: "https://orcid.org/0009-0009-6246-2773"
- family-names: Zölch
  given-names: Niklaus
- family-names: MacMillan
  given-names: Erin L.
  orcid: "https://orcid.org/0000-0002-8515-5858"
- family-names: Kramer
  given-names: John L. K
doi: 10.55458
message: To reference this work, please cite our reproducible preprint
  in NeuroLibre.
preferred-citation:
  authors:
  - family-names: Archibald
    given-names: Jessica
    orcid: "https://orcid.org/0000-0001-6651-183X"
  - family-names: Weber
    given-names: Alexander Mark
    orcid: "https://orcid.org/0000-0001-7295-0775"
  - family-names: Scheuren
    given-names: Paulina S.
    orcid: "https://orcid.org/0000-0001-7568-0133"
  - family-names: Ortiz
    given-names: Oscar
    orcid: "https://orcid.org/0000-0001-5872-2434"
  - family-names: Choles
    given-names: Cassandra
  - family-names: Lee
    given-names: Jaimie J.
    orcid: "https://orcid.org/0009-0009-6246-2773"
  - family-names: Zölch
    given-names: Niklaus
  - family-names: MacMillan
    given-names: Erin L.
    orcid: "https://orcid.org/0000-0002-8515-5858"
  - family-names: Kramer
    given-names: John L. K
  date-published: 2024-12-12
  doi: 10.55458/neurolibre.00029
  journal: NeuroLibre Reproducible Preprints
  publisher:
    name: NeuroLibre
  start: 29
  title: Integrating Structural, Functional, and Biochemical Brain
    Imaging Data with MRShiny Brain - An Interactive Web Application
  type: preprint
  url: "https://neurolibre.org/papers/10.55458/neurolibre.00029"
title: Integrating Structural, Functional, and Biochemical Brain Imaging
  Data with MRShiny Brain - An Interactive Web Application

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[roboneuro]

🌰🌱🌺 THIS IS NOT A DRILL, YOU HAVE JUST PUBLISHED A NEUROLIBRE REPRODUCIBLE PREPRINT! 🌺🌸🍀

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.55458.neurolibre.00029 preprints#89
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.55458/neurolibre.00029
2. If everything looks good, then close this review issue.
3. Party like you just published more than a PDF! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...