[REVIEW]: A reproducible benchmark of denoising strategies in resting-state fMRI connectivity

[roboneuro]

Submitting author: !--author-handle-->@htwangtw<!--end-author-handle-- (Hao-Ting Wang) Repository: https://github.com/SIMEXP/fmriprep-denoise-benchmark Branch with paper.md (empty if default branch): main Version: v1.0 Editor: !--editor-->@mathieuboudreau<!--end-editor-- Reviewers: !--reviewers-list-->@agahkarakuzu<!--end-reviewers-list-- Reproducible preprint: https://preprint.neurolibre.org/10.55458/neurolibre.00012 Repository archive: 10.5281/zenodo.7996698 Data archive: 10.5281/zenodo.7764979 Book archive: 10.5281/zenodo.7996696 Docker archive: 10.5281/zenodo.7996700

Status

Status badge code:

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Markdown: [![status](https://neurolibre.org/papers/934e2fe21c1d2bcd4d014f5b03e9a812/status.svg)](https://neurolibre.org/papers/934e2fe21c1d2bcd4d014f5b03e9a812)

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 @mathieuboudreau 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:

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

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[roboneuro]

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

OK DOIs

- 10.1038/s41592-018-0235-4 is OK
- 10.3389/fninf.2014.00014 is OK
- 10.1109/MCSE.2021.3059263 is OK
- 10.31219/osf.io/h89js is OK

MISSING DOIs

- None

INVALID DOIs

- None

[roboneuro]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.52 s (117.6 files/s, 14535.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          26            584            585           2871
Markdown                        15            341              0           1156
TeX                              3            111              0           1121
SVG                              1              0              0            282
Bourne Shell                    10             52             39            240
JSON                             3              0              0             63
YAML                             2              8             13             46
make                             1              7              0             20
-------------------------------------------------------------------------------
SUM:                            61           1103            637           5799
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[roboneuro]

Wordcount for paper.md is 671

[roboneuro]

Failed to discover a Statement of need section in paper

[agahkarakuzu]

@roboneuro commands

[roboneuro]

Hello @agahkarakuzu, here are the things you can ask me to do:

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@roboneuro list editors

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@roboneuro production sync book

[agahkarakuzu]

@roboneuro generate pdf

[roboneuro]

:warning: An error happened when generating the pdf.

[agahkarakuzu]

@roboneuro generate pdf

[roboneuro]

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

[agahkarakuzu]

@roboneuro preview server status

[roboneuro]

🟢 NeuroLibre server is active (running).
🍀 Ready to accept requests from Issue #12
🔗 URL: https://preview.neurolibre.org

[agahkarakuzu]

@roboneuro build book

[roboneuro]

:seedling: I've started building your NeuroLibre reproducible preprint! :seedling:

My close :robot: friend GPT read your paper.md and noted:

"Move over noise, fMRIPrep is here to make brain scans look sharper than a freshly sharpened pencil."

[roboneuro]

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

BinderHub build log

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

Jupyter Book build log

Because the Binder build failed, the book build was not triggered.

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

For guidelines, please see the relevant documentation.

[agahkarakuzu]

@htwangtw the first pass generated the book below:

https://preview.neurolibre.org/book-artifacts/SIMEXP/github.com/fmriprep-denoise-benchmark/ae0c21d8ab87cfbfef76e69a3865a9e568c5b46f/_build/html/

Looks like it is missing the figures. There's a issue with the logs on the server side, I'll check that.

[agahkarakuzu]

@htwangtw can you also change the following:

https://github.com/SIMEXP/fmriprep-denoise-benchmark/blob/f6182097bd15fbdff533bc0b629c44c89e12727d/content/_config.yml#L43

to

launch_buttons:
  notebook_interface        : classic  # The interface interactive links will activate ["classic", "jupyterlab"]
  binderhub_url             : https://test.conp.cloud  # The URL of the Neurolibre BinderHub
  thebe                     : false  # Add a thebe button to pages (requires the repository to run on Binder)

[htwangtw]

@htwangtw the first pass generated the book below:

https://preview.neurolibre.org/book-artifacts/SIMEXP/github.com/fmriprep-denoise-benchmark/ae0c21d8ab87cfbfef76e69a3865a9e568c5b46f/_build/html/

Looks like it is missing the figures. There's a issue with the logs on the server side, I'll check that.

@agahkarakuzu The preview here is building an older version of the book. Not sure what's going on...

[agahkarakuzu]

I am on it, no worries.

[agahkarakuzu]

@roboneuro build book

[roboneuro]

:seedling: I've started building your NeuroLibre reproducible preprint! :seedling:

My close :robot: friend GPT read your paper.md and noted:

"fmriprep-denoise-benchmark: making MRI scans clearer than a freshly Windexed window."

[agahkarakuzu]

There is an issue with our binderhub cluster on the preview server today, it is quite slow, plus:

I0513 20:06:50.717521 1634881 request.go:1097] Response Body: {"kind":"Status","apiVersion":"v1","metadata":{},"status":"Failure","message":"container \"notebook\" in pod \"jupyter-simexp-2dfmriprep-2dnoise-2dbenchmark-2dnsy7o4ho\" is waiting to start: PodInitializing","reason":"BadRequest","code":400}
I0513 20:06:50.717810 1634881 helpers.go:216] server response object: [{
  "metadata": {},
  "status": "Failure",
  "message": "container \"notebook\" in pod \"jupyter-simexp-2dfmriprep-2dnoise-2dbenchmark-2dnsy7o4ho\" is waiting to start: PodInitializing",
  "reason": "BadRequest",
  "code": 400
}]

Trying to debug before my flight, but I may need to get to this tomorrow.

Issue is not specific to this submission, happens when the request hits node-1.

[htwangtw]

No worries! Thanks for all the work

[agahkarakuzu]

@roboneuro build book

[roboneuro]

:seedling: I've started building your NeuroLibre reproducible preprint! :seedling:

My close :robot: friend GPT read your paper.md and noted:

"Move over superheroes, fMRIPrep is the new brain saver!"

[roboneuro]

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

BinderHub build log

Found built image, launching...
Launching server...
Server requested
2023-05-15T19:14:11.281782Z [Normal] Successfully assigned binderhub/jupyter-simexp-2dfmriprep-2dnoise-2dbenchmark-2d1cljsy6y to neurolibre-node1
2023-05-15T19:14:15Z [Normal] Container image "jupyterhub/k8s-network-tools:1.1.2" already present on machine
2023-05-15T19:14:18Z [Normal] Created container block-cloud-metadata
2023-05-15T19:14:22Z [Normal] Started container block-cloud-metadata
2023-05-15T19:14:23Z [Normal] Container image "binder-registry.conp.cloud/binder-registry.conp.cloud/binder-simexp-2dfmriprep-2ddenoise-2dbenchmark-d0ef34:5fc1f8b558e76b82574ba5b48edde0cb0eb6ca24" already present on machine
2023-05-15T19:14:26Z [Normal] Created container notebook
2023-05-15T19:14:28Z [Normal] Started container notebook
Server ready at /jupyter/user/simexp-fmriprep-noise-benchmark-1cljsy6y/
server running at https://test.conp.cloud/jupyter/user/simexp-fmriprep-noise-benchmark-1cljsy6y/

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

Jupyter Book build log

Checking if jupyter book build will be done...
     content/_config.yml exists.
     /mnt/books/SIMEXP/github.com/fmriprep-denoise-benchmark/5fc1f8b558e76b82574ba5b48edde0cb0eb6ca24/successfully_built not found.
     Detecting user submission, changing launch_button config to test https://test.conp.cloud and adding jb cache execution.
detect existing binderhub_url

Building jupyter-book for SIMEXP/github.com/fmriprep-denoise-benchmark/5fc1f8b558e76b82574ba5b48edde0cb0eb6ca24

Running Jupyter-Book v0.13.0
Source Folder: /home/jovyan/content
Config Path: /home/jovyan/content/_config.yml
Output Path: /mnt/books/SIMEXP/github.com/fmriprep-denoise-benchmark/5fc1f8b558e76b82574ba5b48edde0cb0eb6ca24/_build/html
Running Sphinx v4.5.0
Adding copy buttons to code blocks...
Adding copy buttons to code blocks...
[etoc] Excluded 1 extra file(s) not in toc
checking bibtex cache... out of date
parsing bibtex file /home/jovyan/content/references.bib... parsed 68 entries
myst v0.15.2: MdParserConfig(renderer='sphinx', commonmark_only=False, enable_extensions=['colon_fence', 'dollarmath', 'linkify', 'substitution', 'tasklist'], 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', disable_syntax=[], url_schemes=['mailto', 'http', 'https'], heading_anchors=None, heading_slug_func=None, html_meta=[], footnote_transition=True, substitutions=[], sub_delimiters=['{', '}'], words_per_minute=200)
MyST-NB: Excluded Paths: set()
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 11 source files that are out of date
updating environment: MyST-NB: Potential docnames to execute: ['docs/timeseires_metrics', 'index', 'supplementary_materials/CITATION', 'docs/fmriprep', 'research_report/results-atlas', 'research_report/results-group', 'research_report/references', 'supplementary_materials/ohbm2022abstract', 'docs/tldr', 'docs/setup', 'docs/software_implemetation']
executing outdated notebooks... Executing: /home/jovyan/content/supplementary_materials/ohbm2022abstract.md
Executing: /home/jovyan/content/research_report/results-atlas.md
Executing: /home/jovyan/content/research_report/results-group.md
done
[new config] 11 added, 0 changed, 0 removed
reading sources... [  9%] docs/fmriprep
reading sources... [ 18%] docs/setup
reading sources... [ 27%] docs/software_implemetation
reading sources... [ 36%] docs/timeseires_metrics
reading sources... [ 45%] docs/tldr
reading sources... [ 54%] index
Merged cached outputs into content/index.md
reading sources... [ 63%] research_report/references
reading sources... [ 72%] research_report/results-atlas
reading sources... [ 81%] research_report/results-group
reading sources... [ 90%] supplementary_materials/CITATION
reading sources... [100%] supplementary_materials/ohbm2022abstract

ERROR: Execution Failed: /home/jovyan/content/supplementary_materials/ohbm2022abstract.md
ERROR: Execution Failed: /home/jovyan/content/research_report/results-atlas.md
ERROR: Execution Failed: /home/jovyan/content/research_report/results-group.md
ERROR: Couldn't find cache key for notebook file content/research_report/results-atlas.md. Outputs will not be inserted.
  Last execution failed with traceback saved in /mnt/books/SIMEXP/github.com/fmriprep-denoise-benchmark/5fc1f8b558e76b82574ba5b48edde0cb0eb6ca24/_build/html/reports/results-atlas.log
ERROR: Couldn't find cache key for notebook file content/research_report/results-group.md. Outputs will not be inserted.
  Last execution failed with traceback saved in /mnt/books/SIMEXP/github.com/fmriprep-denoise-benchmark/5fc1f8b558e76b82574ba5b48edde0cb0eb6ca24/_build/html/reports/results-group.log
ERROR: Couldn't find cache key for notebook file content/supplementary_materials/ohbm2022abstract.md. Outputs will not be inserted.
  Last execution failed with traceback saved in /mnt/books/SIMEXP/github.com/fmriprep-denoise-benchmark/5fc1f8b558e76b82574ba5b48edde0cb0eb6ca24/_build/html/reports/ohbm2022abstract.log
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [  9%] docs/fmriprep
writing output... [ 18%] docs/setup
writing output... [ 27%] docs/software_implemetation
writing output... [ 36%] docs/timeseires_metrics
writing output... [ 45%] docs/tldr
writing output... [ 54%] index
writing output... [ 63%] research_report/references
writing output... [ 72%] research_report/results-atlas
writing output... [ 81%] research_report/results-group
writing output... [ 90%] supplementary_materials/CITATION
writing output... [100%] supplementary_materials/ohbm2022abstract

/home/jovyan/content/supplementary_materials/ohbm2022abstract.md.rst:121: WARNING: Couldn't find key `ohbm-qcfc-fig` in keys defined across all pages.
/home/jovyan/content/supplementary_materials/ohbm2022abstract.md.rst:137: WARNING: Couldn't find key `ohbm-dist-fig` in keys defined across all pages.
/home/jovyan/content/supplementary_materials/ohbm2022abstract.md.rst:155: WARNING: Couldn't find key `ohbm-network-fig` in keys defined across all pages.
generating indices... genindex done
writing additional pages... search done
copying images... [ 25%] images/fig-1-masker.png
copying images... [ 50%] images/fig2-benchmark.png
copying images... [ 75%] images/api_summary.png
copying images... [100%] images/ohbm2022_abstract_head.png

copying static files... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 9 warnings.

The HTML pages are in ../../mnt/books/SIMEXP/github.com/fmriprep-denoise-benchmark/5fc1f8b558e76b82574ba5b48edde0cb0eb6ca24/_build/html.

===============================================================================

Finished generating HTML for book.
Your book's HTML pages are here:
    ../../mnt/books/SIMEXP/github.com/fmriprep-denoise-benchmark/5fc1f8b558e76b82574ba5b48edde0cb0eb6ca24/_build/html/
You can look at your book by opening this file in a browser:
    ../../mnt/books/SIMEXP/github.com/fmriprep-denoise-benchmark/5fc1f8b558e76b82574ba5b48edde0cb0eb6ca24/_build/html/index.html
Or paste this line directly into your browser bar:
    file:///mnt/books/SIMEXP/github.com/fmriprep-denoise-benchmark/5fc1f8b558e76b82574ba5b48edde0cb0eb6ca24/_build/html/index.html            

===============================================================================

Jupyter-book execution failed!

Execution error log for ohbm2022abstract notebook (ohbm2022abstract.ipynb) or MyST (ohbm2022abstract.md)).

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
    executenb(
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/nbclient/client.py", line 1112, in execute
    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/nbclient/util.py", line 74, in wrapped
    return just_run(coro(*args, **kwargs))
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/nbclient/util.py", line 53, in just_run
    return loop.run_until_complete(coro)
  File "/srv/conda/envs/notebook/lib/python3.8/asyncio/base_events.py", line 616, in run_until_complete
    return future.result()
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/nbclient/client.py", line 553, in async_execute
    await self.async_execute_cell(
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/nbclient/client.py", line 857, in async_execute_cell
    self._check_raise_for_error(cell, exec_reply)
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/nbclient/client.py", line 760, in _check_raise_for_error
    raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
------------------
import warnings

warnings.filterwarnings('ignore')
from fmriprep_denoise.visualization import figures, utils
from myst_nb import glue

path_root = utils.get_data_root() / "denoise-metrics"

# Load metric data
dataset = 'ds000228'
fmriprep_version = 'fmriprep-20.2.1lts'

atlas_name = 'schaefer7networks'
dimension = 400
------------------

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
/tmp/ipykernel_121/3984434378.py in 
      2 
      3 warnings.filterwarnings('ignore')
----> 4 from fmriprep_denoise.visualization import figures, utils
      5 from myst_nb import glue
      6 

ModuleNotFoundError: No module named 'fmriprep_denoise'
ModuleNotFoundError: No module named 'fmriprep_denoise'

Execution error log for results-atlas notebook (results-atlas.ipynb) or MyST (results-atlas.md)).

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
    executenb(
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/nbclient/client.py", line 1112, in execute
    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/nbclient/util.py", line 74, in wrapped
    return just_run(coro(*args, **kwargs))
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/nbclient/util.py", line 53, in just_run
    return loop.run_until_complete(coro)
  File "/srv/conda/envs/notebook/lib/python3.8/asyncio/base_events.py", line 616, in run_until_complete
    return future.result()
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/nbclient/client.py", line 553, in async_execute
    await self.async_execute_cell(
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/nbclient/client.py", line 857, in async_execute_cell
    self._check_raise_for_error(cell, exec_reply)
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/nbclient/client.py", line 760, in _check_raise_for_error
    raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
------------------
import warnings

warnings.filterwarnings("ignore")
from fmriprep_denoise.dataset.atlas import ATLAS_METADATA
from fmriprep_denoise.visualization import figures, utils

import ipywidgets as widgets
from ipywidgets import interactive, interact

path_root = utils.get_data_root() / "denoise-metrics"
------------------

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
/tmp/ipykernel_141/2250748336.py in 
      2 
      3 warnings.filterwarnings("ignore")
----> 4 from fmriprep_denoise.dataset.atlas import ATLAS_METADATA
      5 from fmriprep_denoise.visualization import figures, utils
      6 

ModuleNotFoundError: No module named 'fmriprep_denoise'
ModuleNotFoundError: No module named 'fmriprep_denoise'

Execution error log for results-group notebook (results-group.ipynb) or MyST (results-group.md)).

Traceback (most recent call last):
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
    executenb(
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/nbclient/client.py", line 1112, in execute
    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/nbclient/util.py", line 74, in wrapped
    return just_run(coro(*args, **kwargs))
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/nbclient/util.py", line 53, in just_run
    return loop.run_until_complete(coro)
  File "/srv/conda/envs/notebook/lib/python3.8/asyncio/base_events.py", line 616, in run_until_complete
    return future.result()
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/nbclient/client.py", line 553, in async_execute
    await self.async_execute_cell(
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/nbclient/client.py", line 857, in async_execute_cell
    self._check_raise_for_error(cell, exec_reply)
  File "/srv/conda/envs/notebook/lib/python3.8/site-packages/nbclient/client.py", line 760, in _check_raise_for_error
    raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
------------------
import warnings

warnings.filterwarnings("ignore")

import ipywidgets as widgets
from ipywidgets import interactive
from fmriprep_denoise.visualization import utils

path_root = utils.get_data_root() / "denoise-metrics"
strategy_order = list(utils.GRID_LOCATION.values())
group_order = {
    "ds000228": ["adult", "child"],
    "ds000030": ["control", "ADHD", "bipolar", "schizophrenia"],
}
datasets = ["ds000228", "ds000030"]
datasets_baseline = {"ds000228": "adult", "ds000030": "control"}
------------------

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
/tmp/ipykernel_161/1204424769.py in 
      5 import ipywidgets as widgets
      6 from ipywidgets import interactive
----> 7 from fmriprep_denoise.visualization import utils
      8 
      9 path_root = utils.get_data_root() / "denoise-metrics"

ModuleNotFoundError: No module named 'fmriprep_denoise'
ModuleNotFoundError: No module named 'fmriprep_denoise'

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

For guidelines, please see the relevant documentation.

[htwangtw]

@roboneuro build book

[roboneuro]

:seedling: I've started building your NeuroLibre reproducible preprint! :seedling:

My close :robot: friend GPT read your paper.md and noted:

"fmriprep-denoise-benchmark: making brain waves and cleaning up the mess, one scan at a time."

[htwangtw]

@roboneuro preprint server status

[roboneuro]

I'm sorry @htwangtw, I'm afraid I can't do that. That's something only editors are allowed to do.

[htwangtw]

@roboneuro build book

[roboneuro]

:seedling: I've started building your NeuroLibre reproducible preprint! :seedling:

My close :robot: friend GPT read your paper.md and noted:

"Move over Iron Man, fMRIPrep-Denoise Benchmark is the new superhero of brain imaging!"

[agahkarakuzu]

@roboneuro build book

[roboneuro]

:seedling: I've started building your NeuroLibre reproducible preprint! :seedling:

My close :robot: friend GPT read your paper.md and noted:

"FMRIPrep-Denoise-Benchmark: Making fMRI analysis a breeze, so you can finally take a break from staring at brain scans all day!"

[agahkarakuzu]

@roboneuro preview server status

[roboneuro]

🟢 NeuroLibre server is active (running).
🍀 Ready to accept requests from Issue #12
🔗 URL: https://preview.neurolibre.org

[agahkarakuzu]

@roboneuro build book

[roboneuro]

:seedling: I've started building your NeuroLibre reproducible preprint! :seedling:

My close :robot: friend GPT read your paper.md and noted:

"fmriprep-denoise-benchmark: Making your brain scans so clear, even your grandma can see your thoughts!"

[agahkarakuzu]

I checked it on the server side, build for the latest commit https://github.com/SIMEXP/fmriprep-denoise-benchmark/commit/b505548949b88a273625c1b4b22f2684a3ff5a85 has started.

Currently it is timing out for roboneuro to catch the response as the wait time after binderhub stops sending keepalive (container started) is longer than 100 seconds for this submission. I will fix it by moving this to a background task, till then, I can manually return the results.

[agahkarakuzu]

@htwangtw results-atlas.log and results-group.log throwing the same error at commit b505548

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
/tmp/ipykernel_161/3241172364.py in <module>
      2 
      3 warnings.filterwarnings("ignore")
----> 4 from fmriprep_denoise.dataset.atlas import ATLAS_METADATA
      5 from fmriprep_denoise.visualization import figures, utils
      6 

ModuleNotFoundError: No module named 'fmriprep_denoise'
ModuleNotFoundError: No module named 'fmriprep_denoise'

You can take a look at the partial build.

So far a fully successful build happened at https://github.com/SIMEXP/fmriprep-denoise-benchmark/commit/ed1758b425a1f6ec3d4566a7730b9edc3a68a31d which was actually before removing -e. from requirements.txt.

For some reason, it takes too long for binderhub to start the session for this book build, I am trying to understand why.

[htwangtw]

Yeah I have encountered that for my local build as well, but the note book runs fine...

Now the binder documentation on setup.py really confuses me :sweat_smile:

[agahkarakuzu]

So far the easiest option is to work with pip packages for Python. I would say postBuild is the best bet to call setup.py. As it is not in the binder folder, repo2data would not pick it up.

[htwangtw]

yeah i have realised that after rolling things up. Also repo2data would redownload things with the directory layout with https://github.com/SIMEXP/fmriprep-denoise-benchmark/commit/ed1758b425a1f6ec3d4566a7730b9edc3a68a31d, but not the latest in the local build. I am not certain why

[agahkarakuzu]

I am not sure if there's a mechanism in place to check changes made to the repo2data manifest. I can flush the existing data from the server, and the new one should be downloaded upon the next build. Do you want me to proceed with that?

[htwangtw]

Let's try that and I will roll back main to https://github.com/SIMEXP/fmriprep-denoise-benchmark/commit/ed1758b425a1f6ec3d4566a7730b9edc3a68a31d as well as simplify the notebook organisation

[htwangtw]

Let's build 1193ba2

[htwangtw]

@roboneuro build book

[roboneuro]

:seedling: I've started building your NeuroLibre reproducible preprint! :seedling:

My close :robot: friend GPT read your paper.md and noted:

"Reading the fmriprep-denoise benchmark paper was like watching a symphony of brain waves - beautiful, complex, and surprisingly entertaining!"

[agahkarakuzu]

@htwangtw I was in a meeting, so that request went before I could delete the data. Can you push a dummy commit (you can just edit readme) and let me know, so that I can send a new request?