[REVIEW]: Integrating Structural, Functional, and Biochemical Brain Imaging Data with MRShiny Brain - An Interactive Web Application #29

roboneuro · 2024-07-31T18:40:19Z

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: Pending
Repository archive: Pending
Data archive: Pending
Book archive: Pending
Docker archive: Pending

Status

Status badge code:

HTML: <a href="https://neurolibre.org/papers/e247b9a6eb73e2cedddff27d25fa8cad"><img src="https://neurolibre.org/papers/e247b9a6eb73e2cedddff27d25fa8cad/status.svg"></a>
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

The text was updated successfully, but these errors were encountered:

roboneuro · 2024-07-31T18:40:22Z

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 · 2024-07-31T18:40:23Z

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 · 2024-07-31T18:40:25Z

Wordcount for paper.md is 2506

roboneuro · 2024-07-31T18:40:25Z

Failed to discover a Statement of need section in paper

agahkarakuzu · 2024-07-31T18:40:34Z

@roboneuro build book

roboneuro · 2024-07-31T18:40:38Z

🔴 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 · 2024-07-31T18:40:39Z

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 · 2024-07-31T18:41:10Z

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

roboneuro · 2024-07-31T18:47:35Z

🥀 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 4/51 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
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Step 12/51 : ENV HOME /home/${NB_USER}
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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 18/51 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
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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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Step 28/51 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e9-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dbase-2denv-2ebash-41d468 /tmp/install-base-env.bash
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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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{"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 · 2024-07-31T20:21:54Z

@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 · 2024-08-01T02:26:21Z

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 · 2024-08-01T03:13:18Z

@roboneuro build book

roboneuro · 2024-08-01T03:13:22Z

🟢 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 · 2024-08-01T03:16:19Z

🎊🎊🎊 Good news!

🌺 Take a look at the latest version of your NRP

arcj-hub · 2024-08-01T15:13:31Z

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 · 2024-08-01T15:16:10Z

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 · 2024-08-01T15:26:35Z

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 · 2024-08-01T15:44:59Z

@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 · 2024-08-01T15:46:17Z

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 · 2024-08-01T15:48:06Z

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

agahkarakuzu · 2024-08-01T16:30:04Z

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

agahkarakuzu · 2024-08-01T16:31:17Z

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 · 2024-08-01T16:36:13Z

@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.

arcj-hub · 2024-08-01T18:56:09Z

Hey, I think we do need the library(shinyWidgets) for the slider to be gray. But in the spectroscopy tab of this version: https://shinybrain.db.neurolibre.org/ It says it will be deprecated in a future release. Let me see what I can add to make this gray without Shiny Widgets. ***@***.*** And please, if you don’t mind looking at my notebook to see what the issue is. I do not use VS or jupyter. I’ve added you as a collab. Also if I need to make changes to the app in the future, say add more subjects or data can I do this on Git and then you would redeploy? Zero downtime it’s so cool! From: Agah ***@***.***> Reply-To: neurolibre/neurolibre-reviews ***@***.***> Date: Thursday, August 1, 2024 at 10:30 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] @arcj-hub<https://github.com/arcj-hub> https://shinybrain.db.neurolibre.org should be now fully functional. Please let me know if there's something not working. — Reply to this email directly, view it on GitHub<#29 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ATSCAELZ7V3RCGALIACHV23ZPJPCHAVCNFSM6AAAAABLZBJAWWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRTGQ4DCMJXGM>. You are receiving this because you were mentioned.Message ID: ***@***.***>

agahkarakuzu · 2024-08-01T18:59:54Z

ShinyWidgets is already included, I deployed it from my fork of your repo (https://github.com/agahkarakuzu/MRShiny-Brain)

arcj-hub · 2024-08-01T20:11:01Z

Hey, I can’t replicate the slidercolour issue on my end. I am using the latest R Studio version and have added the source code (setSliderColor.R) to the repo. It is used in line 227. If this does not work, do you mind just commenting that out? And we can leave them all blue. From: Agah ***@***.***> Reply-To: neurolibre/neurolibre-reviews ***@***.***> Date: Thursday, August 1, 2024 at 1:00 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] ShinyWidgets is already included, I deployed it from my fork of your repo (https://github.com/agahkarakuzu/MRShiny-Brain) — Reply to this email directly, view it on GitHub<#29 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ATSCAENWWOVNN3EHA5QP23DZPKAT7AVCNFSM6AAAAABLZBJAWWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRTG43DENZXGA>. You are receiving this because you were mentioned.Message ID: ***@***.***>

agahkarakuzu · 2024-08-01T20:49:41Z

@arcj-hub I added a custom.css to set slider color darkgray and commented out the line in app.R.

Also if I need to make changes to the app in the future, say add more subjects or data can I do this on Git and then you would redeploy?

You can open an issue using the dashboard template to ping us.

I also noticed that the dashboard grays out after a waiting a while with no activity. Is this expected?

arcj-hub · 2024-08-02T16:03:57Z

Amazing. And thanks for the info on how to update the dashboard! From: Agah ***@***.***> Reply-To: neurolibre/neurolibre-reviews ***@***.***> Date: Thursday, August 1, 2024 at 2:50 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> I added a custom.css<https://github.com/agahkarakuzu/MRShiny-Brain/blob/main/www/custom.css> to set slider color darkgray and commented out the line in app.R. Also if I need to make changes to the app in the future, say add more subjects or data can I do this on Git and then you would redeploy? You can open an issue using the dashboard template<https://github.com/neurolibre/info/issues/new?assignees=&labels=dashboard&projects=&template=update-an-existing-dashboard.md&title=%5BDASHBOARD%5D> to ping us. I also noticed that the dashboard grays out after a waiting a while with no activity. Is this expected? — Reply to this email directly, view it on GitHub<#29 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ATSCAEIQGR37TJYCWMYCUADZPKNPXAVCNFSM6AAAAABLZBJAWWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRTHE3DAMRZGA>. You are receiving this because you were mentioned.Message ID: ***@***.***>

agahkarakuzu · 2024-08-02T19:07:59Z

@arcj-hub as the first preprint submission with its own dashboard, I wanted to give you the MyST formatted version of your article as a gift (including a header image design):

https://preview.neurolibre.org/book-artifacts/arcj-hub/github.com/MRShiny-Brain/myst/_build/html/

If you like this version, I can push necessary changes to your repository.

arcj-hub · 2024-08-02T19:31:07Z

Wow. I love it 🥹 thank you. Yes, please push those changes to my repository! From: Agah ***@***.***> Reply-To: neurolibre/neurolibre-reviews ***@***.***> Date: Friday, August 2, 2024 at 1:08 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> as the first preprint submission with its own dashboard, I wanted to give you the MyST formatted version of your article as a gift (including a header image design): https://preview.neurolibre.org/book-artifacts/arcj-hub/github.com/MRShiny-Brain/myst/_build/html/ If you like this version, I can push necessary changes to your repository. — Reply to this email directly, view it on GitHub<#29 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ATSCAENODW3N2FFKKTTI7QDZPPKKJAVCNFSM6AAAAABLZBJAWWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRVHE4DCMJZGY>. You are receiving this because you were mentioned.Message ID: ***@***.***>

arcj-hub · 2024-08-02T19:52:28Z

Sorry I forgot to respond to this I also noticed that the dashboard grays out after a waiting a while with no activity. Is this expected? Not expected… From: Agah ***@***.***> Reply-To: neurolibre/neurolibre-reviews ***@***.***> Date: Thursday, August 1, 2024 at 2:50 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> I added a custom.css<https://github.com/agahkarakuzu/MRShiny-Brain/blob/main/www/custom.css> to set slider color darkgray and commented out the line in app.R. Also if I need to make changes to the app in the future, say add more subjects or data can I do this on Git and then you would redeploy? You can open an issue using the dashboard template<https://github.com/neurolibre/info/issues/new?assignees=&labels=dashboard&projects=&template=update-an-existing-dashboard.md&title=%5BDASHBOARD%5D> to ping us. I also noticed that the dashboard grays out after a waiting a while with no activity. Is this expected? — Reply to this email directly, view it on GitHub<#29 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ATSCAEIQGR37TJYCWMYCUADZPKNPXAVCNFSM6AAAAABLZBJAWWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRTHE3DAMRZGA>. You are receiving this because you were mentioned.Message ID: ***@***.***>

agahkarakuzu · 2024-09-03T03:35:10Z

@roboneuro cache data

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@roboneuro cache data

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agahkarakuzu · 2024-09-03T04:22:06Z

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roboneuro · 2024-09-03T04:22:09Z

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Status: Assigned to task 47af0b7d
Last updated: 2024-09-02 21:22:09 PDT

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Celery task assigned successfully. Task ID: 47af0b7d-1d3f-440c-aaed-ae2f3f9559b1

♻️ [Refresh](https://github.com//issues/29#issuecomment-2325576674)

agahkarakuzu · 2024-09-03T05:10:15Z

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roboneuro · 2024-09-03T05:10:19Z

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agahkarakuzu · 2024-09-04T02:02:06Z

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roboneuro · 2024-09-04T02:02:09Z

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Data exists for mr_shiny_brain already downloaded to /DATA/mr_shiny_brain;                   not overwriting by default! Please set overwrite=True.

agahkarakuzu · 2024-09-04T04:57:58Z

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roboneuro · 2024-09-04T04:58:02Z

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agahkarakuzu · 2024-09-13T21:39:02Z

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roboneuro · 2024-09-13T21:39:06Z

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Downloaded data in /DATA/mr_shiny_brain (48.7 kB).
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roboneuro added review Track: 1 (executable) labels Jul 31, 2024

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[PRE REVIEW]: Integrating Structural, Functional, and Biochemical Brain Imaging Data with MRShiny Brain - An Interactive Web Application #28

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[REVIEW]: Integrating Structural, Functional, and Biochemical Brain Imaging Data with MRShiny Brain - An Interactive Web Application #29

[REVIEW]: Integrating Structural, Functional, and Biochemical Brain Imaging Data with MRShiny Brain - An Interactive Web Application #29

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