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

roboneuro commented 3 months ago

Submitting author: !--author-handle-->@arcj-hub@agahkarakuzu@agahkarakuzu<!--end-reviewers-list-- Reproducible preprint: Pending Repository archive: Pending Data archive: N/A Book archive: Pending Docker archive: N/A

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

roboneuro commented 3 months ago

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 commented 3 months ago

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 commented 3 months ago

Wordcount for paper.md is 2506

roboneuro commented 3 months ago

Failed to discover a Statement of need section in paper

agahkarakuzu commented 3 months ago

@roboneuro build book

roboneuro commented 3 months ago

🔴 Binder build has failed 🥀

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

:information_source: See details

The next comment will forward the logs

roboneuro commented 3 months ago

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 commented 3 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

roboneuro commented 3 months ago

🥀 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 2/51 : ENV DEBIAN_FRONTEND=noninteractive
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Step 3/51 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends locales > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
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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 5/51 : ENV LC_ALL en_US.UTF-8
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Step 6/51 : ENV LANG en_US.UTF-8
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Step 7/51 : ENV LANGUAGE en_US.UTF-8
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Step 8/51 : ENV SHELL /bin/bash
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Step 9/51 : ARG NB_USER
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Step 10/51 : ARG NB_UID
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Step 11/51 : ENV USER ${NB_USER}
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Step 12/51 : ENV HOME /home/${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 15/51 : EXPOSE 8888
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Step 16/51 : ENV APP_BASE /srv
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Step 17/51 : ENV CONDA_DIR ${APP_BASE}/conda
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Step 18/51 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
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Step 19/51 : ENV NPM_DIR ${APP_BASE}/npm
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Step 20/51 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
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Step 21/51 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
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Step 22/51 : ENV MAMBA_ROOT_PREFIX ${CONDA_DIR}
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Step 23/51 : ENV MAMBA_EXE ${CONDA_DIR}/bin/mamba
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Step 24/51 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
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Step 25/51 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
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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 27/51 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e9-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e7-2elock-d12193 /tmp/env/environment.lock
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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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Step 29/51 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-base-env.bash' && rm -rf /tmp/install-base-env.bash /tmp/env
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Step 30/51 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
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Step 31/51 : USER root
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Step 32/51 : ARG REPO_DIR=${HOME}
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Step 36/51 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
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Step 37/51 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
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Step 38/51 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt
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Step 39/51 : USER ${NB_USER}
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Step 40/51 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "binder/requirements.txt"
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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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Successfully built wget
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 commented 3 months ago

@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 commented 3 months ago

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-hubhttps://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 GitHubhttps://github.com/neurolibre/neurolibre-reviews/issues/29#issuecomment-2261384413, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ATSCAELYWYBKUJZD2JWBX5DZPFBPRAVCNFSM6AAAAABLZBJAWWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRRGM4DINBRGM. You are receiving this because you were mentioned.Message ID: @.***>

agahkarakuzu commented 3 months ago

@roboneuro build book

roboneuro commented 3 months ago

🟢 Successfully built

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

:information_source: See details

:confetti_ball: Roboneuro will send you the book URL.

roboneuro commented 3 months ago

:confetti_ball::confetti_ball::confetti_ball: Good news!

:hibiscus: Take a look at the latest version of your NRP

arcj-hub commented 3 months ago

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 NRPhttps://preview.neurolibre.org/book-artifacts/arcj-hub/github.com/MRShiny-Brain/caeb60c5fcec333393ac089943ee04348bd1b0e3/_build/html/

— Reply to this email directly, view it on GitHubhttps://github.com/neurolibre/neurolibre-reviews/issues/29#issuecomment-2261880722, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ATSCAEJBQXH775G6W2OHN6DZPGSBVAVCNFSM6AAAAABLZBJAWWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRRHA4DANZSGI. You are receiving this because you were mentioned.Message ID: @.***>

agahkarakuzu commented 3 months ago

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 commented 3 months ago

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 commented 3 months ago

@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 commented 3 months ago

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 GitHubhttps://github.com/neurolibre/neurolibre-reviews/issues/29#issuecomment-2263354173, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ATSCAELDHJFRU2LZXKAIIHLZPJHUDAVCNFSM6AAAAABLZBJAWWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRTGM2TIMJXGM. You are receiving this because you were mentioned.Message ID: @.***>

agahkarakuzu commented 3 months ago

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

agahkarakuzu commented 3 months ago

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

agahkarakuzu commented 3 months ago

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 commented 3 months ago

@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 commented 3 months ago

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-hubhttps://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 GitHubhttps://github.com/neurolibre/neurolibre-reviews/issues/29#issuecomment-2263481173, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ATSCAELZ7V3RCGALIACHV23ZPJPCHAVCNFSM6AAAAABLZBJAWWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRTGQ4DCMJXGM. You are receiving this because you were mentioned.Message ID: @.***>

agahkarakuzu commented 3 months ago

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

arcj-hub commented 3 months ago

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 GitHubhttps://github.com/neurolibre/neurolibre-reviews/issues/29#issuecomment-2263762770, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ATSCAENWWOVNN3EHA5QP23DZPKAT7AVCNFSM6AAAAABLZBJAWWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRTG43DENZXGA. You are receiving this because you were mentioned.Message ID: @.***>

agahkarakuzu commented 3 months ago

@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 commented 3 months ago

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-hubhttps://github.com/arcj-hub I added a custom.csshttps://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 templatehttps://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 GitHubhttps://github.com/neurolibre/neurolibre-reviews/issues/29#issuecomment-2263960290, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ATSCAEIQGR37TJYCWMYCUADZPKNPXAVCNFSM6AAAAABLZBJAWWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRTHE3DAMRZGA. You are receiving this because you were mentioned.Message ID: @.***>

agahkarakuzu commented 3 months ago

@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 commented 3 months ago

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-hubhttps://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 GitHubhttps://github.com/neurolibre/neurolibre-reviews/issues/29#issuecomment-2265981196, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ATSCAENODW3N2FFKKTTI7QDZPPKKJAVCNFSM6AAAAABLZBJAWWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRVHE4DCMJZGY. You are receiving this because you were mentioned.Message ID: @.***>

arcj-hub commented 3 months ago

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-hubhttps://github.com/arcj-hub I added a custom.csshttps://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 templatehttps://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 GitHubhttps://github.com/neurolibre/neurolibre-reviews/issues/29#issuecomment-2263960290, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ATSCAEIQGR37TJYCWMYCUADZPKNPXAVCNFSM6AAAAABLZBJAWWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRTHE3DAMRZGA. You are receiving this because you were mentioned.Message ID: @.***>

agahkarakuzu commented 2 months ago

@roboneuro cache data

agahkarakuzu commented 2 months ago

@roboneuro cache data

agahkarakuzu commented 2 months ago

@roboneuro cache data

agahkarakuzu commented 2 months ago

@roboneuro cache data

roboneuro commented 2 months ago

⚪ DOWNLOAD DATA

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

:information_source: See details

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

:recycle: Refresh

agahkarakuzu commented 2 months ago

@roboneuro cache data

roboneuro commented 2 months ago

🟠 DOWNLOAD DATA

Status: In progress 41bc499f Last updated: 2024-09-02 22:10:20 PDT

:information_source: See details

Started downloading the data.

:recycle: Refresh

agahkarakuzu commented 2 months ago

@roboneuro cache data

roboneuro commented 2 months ago

🔴 DOWNLOAD DATA

Status: Failed c70dfdbc Last updated: 2024-09-03 19:02:13 PDT

:information_source: See details

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

agahkarakuzu commented 2 months ago

@roboneuro cache data

roboneuro commented 2 months ago

🟢 DOWNLOAD DATA

Status: Success 20ae599b Last updated: 2024-09-03 21:58:09 PDT

:information_source: See details

Downloaded data in /DATA/mr_shiny_brain (48.7 kB).
- data.csv (48.5 kB)
- repo2data_cache_record.json (126 Bytes)

agahkarakuzu commented 2 months ago

@roboneuro cache data

roboneuro commented 2 months ago

🟢 DOWNLOAD DATA

Status: Success b8e2c7f6 Last updated: 2024-09-13 14:39:14 PDT

:information_source: See details

Downloaded data in /DATA/mr_shiny_brain (48.7 kB).
- repo2data_cache_record.json (126 Bytes)
- data.csv (48.5 kB)

agahkarakuzu commented 3 weeks ago

@roboneuro set N/A as docker archive

roboneuro commented 3 weeks ago

Done, docker archive is now N/A

agahkarakuzu commented 3 weeks ago

@roboneuro set N/A as data archive

roboneuro commented 3 weeks ago

Done, data archive is now N/A

agahkarakuzu commented 3 weeks ago

@roboneuro zenodo status

agahkarakuzu commented 3 weeks ago

@roboneuro commands

neurolibre / neurolibre-reviews