bids-apps/bids-apps.github.io

Portable neuroimaging pipelines that understand BIDS datasets

This is the repository for generating the BIDS Apps website.

See out CONTRIBUTING guidelines to see how you can help.

Want to learn more about working with BIDS? Have a question, comment, or suggestion?

1. Read some introductory material, most likely the very basic problems have already been addressed!

• BIDS Starter Kit for tutorials, wikis, templates, ...

2. Post your question in one of several channels where BIDS members are active

• the NeuroStars discourse forum
• the BrainHack Mattermost, for instant messaging (see also this news item)
• the Google group, for broader discussions surrounding BIDS
• the specification repository issue page, if you found inconsistencies, typos, or other issues with the BIDS specification itself

Dashboard

Status of the default branch of each app.

name	status	ci	last commit	version
bids-apps/afni_proc	active
bids-apps/antsCorticalThickness	active
bids-apps/baracus	active
bids-apps/brainiak-srm	active
bids-apps/BrainSuite	active
bids-apps/BROCCOLI	active
bids-apps/CPAC	active
bids-apps/DPARSF	active
bids-apps/example	active
bids-apps/freesurfer	active
bids-apps/giga_connectome	active
bids-apps/HCPPipelines	active
bids-apps/hyperalignment	active
bids-apps/MAGeTbrain	active
bids-apps/mindboggle	active
bids-apps/MRtrix3_connectome	active
bids-apps/ndmg	active
bids-apps/nipypelines	active
bids-apps/oppni	active
bids-apps/PyMVPA	active
bids-apps/QAP	active
bids-apps/rsHRF	active
bids-apps/SPM	active
bids-apps/tracula	active
bids-apps/aa	unmaintained
bids-apps/FibreDensityAndCrosssection	unmaintained
bids-apps/niak	unmaintained
bids-apps/rs_signal_extract	unmaintained
cpp-lln-lab/bidsMReye	active
cpp-lln-lab/bidspm	active
djarecka/fmriprep-fake	active
khanlab/funcmasker-flex	active
trendscenter/gift-bids	active
khanlab/hippunfold	active
MICA-MNI/micapipe	active
nipreps/fmriprep	active
nipreps/dmriprep	active
nipreps/mriqc	active
nipreps/nibabies	active
nipreps/nirodents	active
nipreps/smriprep	active
PeerHerholz/BIDSonym	active
PennLINC/aslprep	active
PennLINC/xcp_d	active
PennLINC/qsiprep	active
poldracklab/fitlins	active
connectomicslab/connectomemapper3	active
sebastientourbier/multiscalebrainparcellator	active
Medical-Image-Analysis-Laboratory/mialsuperresolutiontoolkit	active

bids-apps.github.io's Issues

[BUG] circle ci failures

Describe your problem in detail.

god knows why it cannot checkout the repo...

Describe what you expected.

No response

Disable DISQUS? Discontinue BIDS-Apps mailing list in favor of other channels?

I'd find it reasonable to move the BIDS Apps website away from the "blog feeling" with the DISQUS widget for making comments. Instead, we should explicitly advise people to use one of our "standard" communication channels:

• mailing list
• neurostars
• brainhack mattermost
• GitHub issues

WDYT?

Note that apart from our standard mailing list (called "bids-discussion"), there is another mailing list: https://groups.google.com/g/bids-apps-dev (last post 2018?)

Personally, I'd like to discontinue that one and re-direct people towards "bids-discussion" or the other channels named above.

again: WDYT?

add BIDS Software Development Guidelines from our google drive?

Not sure if this document may be incorporated here on the BIDS apps website or maybe better in the bids starter kit. I cannot decide.

https://docs.google.com/document/d/1_A1GUHAbczHL6WnEw3b8_8_4PXb1A4wZ4Ckrjgapt5c/edit#heading=h.wru3kew0szzp

Add a separate dash board on the website to see the status of our different "base image" builds

Your idea

Would defo help me at the moment at least.

add a badge with docker image size

Your idea

Automate updating Readme table in Readme when new apps are added.

logo broken on all but landing page

Hi folks,

I just noticed that the BIDS Apps logo doesn't show up on all but the landing page. The working logo points to
https://bids-apps.neuroimaging.io/images/BIDS_apps_logo_black.jpg, while the non-working one points to https://bids-apps.neuroimaging.io/dev_faq/images/BIDS_apps_logo_black.jpg. Happy to submit a small PR for this if no one else wants to/is on it.

Cheers, Peer

Remove Gemfile.lock?

I don't we need this file: https://github.com/BIDS-Apps/bids-apps.github.io/blob/c881455dec3cfa966e70b64b8bb8b595d93ca52d/Gemfile.lock#L1

do we? This just contains the "fixed" versions that are to be installed when deploying to GH pages ... but for a simple setup such as this one (or bids-website), just the Gemfile should be enough: https://github.com/BIDS-Apps/bids-apps.github.io/blob/c881455dec3cfa966e70b64b8bb8b595d93ca52d/Gemfile#L1

I think that removing the lock file will also get rid of the security warning.

[BUG] some circle.ci config are too antiquated to even run

Describe your problem in detail.

For example:

https://app.circleci.com/pipelines/github/bids-apps/BROCCOLI

Describe what you expected.

No response

Add Brainsuite to the app dashboard

I'm not sure why it's not on there, but we would love to be part of the board!

Originally posted by @yeunkim in #95 (comment)

[BUG] fix invalid docker badges on the dashboard

Describe your problem in detail.

Describe what you expected.

No response

Add fmri data to brainsuite in _config.yml

Hi @Remi-Gau

Sorry for the barrage of requests. One more thing - could you add "- func" to the datatype in the _config.yml (line 137) for brainsuite?

• gh: "bids-apps/BrainSuite"
  status: active
  dh: "bids/brainsuite"
  ds_type:
  - raw
  datatype:
  - anat
  - dwi
  - func

Thank you!

add smriprep and other nipreps to the list

ref: datalad/datalad-container#157 (attn @m-petersen)

apparently only good old fmriprep is listed

$> git grep mriprep
_config.yml:  - gh: 'nipreps/fmriprep'
_config.yml:    dh: 'nipreps/fmriprep'

and none of the other nipreps bids-apps. Would be nice to see them added. context: I use this listing to populate/update (well -- yet to account for shub:// going read-only, so outdated ATM) https://github.com/ReproNim/containers/

Pushing bids app with stable tag

Hi @Remi-Gau

I made a new release today of BrainSuite BIDS App (with CircleCI tests passed) but I still only see the unstable tag on DockerHub. Could you let me know any additional steps I should take in order to push the "stable" tag version?

To clarify - I've tried making a git tag (v21a in this case) and pushing the tag with new commits to trigger the circleci tests. I don't know how the $CIRCLE_TAG variable gets set in https://raw.githubusercontent.com/bids-apps/maintenance-tools/main/circleci/push_docker.sh.

Thank you!

Add fitlins to the list of bids apps

Rename "BIDS-Apps" org --> "bids-apps" ... capitalization for consistency with bids-standard

The title says what I'd like to do. What are your opinions? Can you think of potential caveats that we need to check first?

Add snake bids example to the list of bids apps

Possibly split example and snake bids example into a different subsection.

"images" for some apps are "not found", although seems to be there all correct

but if we go to qsiprep (just click on badge) -- they are on docker hub.
not sure yet where to dig

A bit more text about Singularity?

I had a some bit of trouble with figuring out the appropriate paths that would be available to the Singularity container. Do you think that adding a bit more text after the example to explain that, when running the Singularity container version, the paths to the data and the output need to be determined specifically for the cluster being used, but that using paths from /home/ are a good bet?

As you note, different folders will be accessible in different places, and I got confused about which to use.

I can write some text and submit via PR if this seems a good idea.

Add more prominent link to BIDS and example data

http://bids.neuroimaging.io
https://github.com/INCF/bids-examples

adding new app to the site?

Hello!

I am hoping to have a new app added to the list? Please let me know if there is anything I need do to, it is already set up on circleci.

Docker: khanlab/hippunfold:v0.4.1
Docs: https://hippunfold.readthedocs.io/en/latest/
Github: https://github.com/khanlab/hippunfold

Thanks!
Ali

"No usable temporary directory found in ['/tmp', '/var/tmp', '/usr/tmp', '/']" CircleCI error during testing

I'm running tests on CircleCI for BrainSuite BIDS App and I have been running into this error:

test: print version
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
#!/bin/bash -eo pipefail
docker load -i /tmp/workspace/docker/image.tar
docker run -ti --rm --read-only \
  -v /tmp/workspace/data/ds114_test1:/bids_dataset \
  -v ${HOME}/outputs02:/outputs \
    bids/${CIRCLE_PROJECT_REPONAME,,} \
      /bids_dataset \
      /outputs participant --version

Loaded image: bids-apps/brainsuite:latest
Unable to find image 'bids/brainsuite:latest' locally
latest: Pulling from bids/brainsuite
Image docker.io/bids/brainsuite:latest uses outdated schema1 manifest format. Please upgrade to a schema2 image for better future compatibility. More information at https://docs.docker.com/registry/spec/deprecated-schema-v1/

beaf4746: Pulling fs layer 
f24b2f04: Pulling fs layer 
ad169b64: Pulling fs layer 
c6d5adc7: Pulling fs layer 
ab9f2a29: Pulling fs layer 
4b4059e9: Pulling fs layer 
1a21da73: Pulling fs layer 
95caeb02: Pulling fs layer 
e5bc09e8: Pulling fs layer 
3589680c: Pulling fs layer 
bba3cada: Pulling fs layer 
f6521379: Pulling fs layer 
e4a4baa8: Pulling fs layer 
cfbeee3a: Pulling fs layer 
03d7defc: Pulling fs layer 
dc8e2ad7: Pulling fs layer 
db59422b: Pulling fs layer 
Digest: sha256:8487b132383863d077361f0c31030efbce31eecdea77933f9908ef7c2c86eebe
Status: Downloaded newer image for bids/brainsuite:latest
^@^@Traceback (most recent call last):
  File "./qc-system/run.py", line 9, in <module>
    import nibabel
  File "/opt/conda/lib/python2.7/site-packages/nibabel/__init__.py", line 45, in <module>
    from .loadsave import load, save
  File "/opt/conda/lib/python2.7/site-packages/nibabel/loadsave.py", line 18, in <module>
    from .imageclasses import all_image_classes
  File "/opt/conda/lib/python2.7/site-packages/nibabel/imageclasses.py", line 15, in <module>
    from .minc2 import Minc2Image
  File "/opt/conda/lib/python2.7/site-packages/nibabel/minc2.py", line 31, in <module>
    h5py, have_h5py, setup_module = optional_package('h5py')
  File "/opt/conda/lib/python2.7/site-packages/nibabel/optpkg.py", line 98, in optional_package
    pkg = __import__(name, fromlist=fromlist)
  File "/opt/conda/lib/python2.7/site-packages/h5py/__init__.py", line 60, in <module>
    from .tests import run_tests
  File "/opt/conda/lib/python2.7/site-packages/h5py/tests/__init__.py", line 13, in <module>
    from .common import ut
  File "/opt/conda/lib/python2.7/site-packages/h5py/tests/common.py", line 40, in <module>
    testfile, fname = tempfile.mkstemp(unichr(0x03b7))
  File "/opt/conda/lib/python2.7/tempfile.py", line 307, in mkstemp
    dir = gettempdir()
  File "/opt/conda/lib/python2.7/tempfile.py", line 275, in gettempdir
    tempdir = _get_default_tempdir()
  File "/opt/conda/lib/python2.7/tempfile.py", line 217, in _get_default_tempdir
    ("No usable temporary directory found in %s" % dirlist))
IOError: [Errno 2] No usable temporary directory found in ['/tmp', '/var/tmp', '/usr/tmp', '/']
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

I believe it can't find the /tmp directory inside the CircleCI container (not the bids app container). Do you have any suggestions? Current config.yml is located in bids-apps/BrainSuite/.circleci/config.yml (https://github.com/bids-apps/BrainSuite/blob/master/.circleci/config.yml).

I hope this is the correct place to post this issue, but if not, please let me know where the appropriate place is would be to post CircleCI testing issues for bids apps.

Thank you!

Please pin this repo on the BIDS-Apps organization page

so it would be easier to find it to discuss/file generic issues

bidsmreye

Your BIDS app

  - gh: "cpp-lln-lab/bidsMReye"
    dh: "cpplab/bidsmreye"
    ci: "gh"
    branch: "main"
    workflow: "test"
    ds_type:
      - raw
    datatype:
      - func

Submission checklist

• complies to the BIDS app API
• has a system-test workflow set up
• test dataset is validated before processing

Further requirements for new bids apps

Looking through a lot of the CI tests we have, many apps are tested against at least 2 datasets:

• one with no session level folder
• one with session level folder
• that tests are run regularly
• that docker builds are run regularly

I would say that this should be a requirement in the test suite that new bids apps must have.

Of course only if relevant.

Add more details about each app

Your idea

At then moment the names of each app may not be transparent enough to know what the app does.

Should at least be added to the yml for each app:

• does it act on raw and/or derivatives BIDS dataset?
• what datatype does it accept (func, eeg, anat...)?

Where does the logo come from? -- and: revamping of background image + logo?

There is currently this logo for the BIDS-Apps organization:

• https://github.com/BIDS-Apps/bids-apps.github.io/blob/master/images/gear.jpg

I wonder where it comes from, how it is licensed, and whether we should change it to just the BIDS logo.

---

Furthermore, there is currently this background image on the website:

• https://github.com/BIDS-Apps/bids-apps.github.io/blob/master/images/cover.jpg

I think we can probably do without it -- it's okay to have it, but it's not really related to "anything BIDS-Apps".

Mention bids app execution specification

When the website is finalized.

add short description in the metadata of each app

useful for creating lists of apps in other repo with a blurb of what each app does

Make a BIDS-Apps org README

similar to: https://github.com/bids-standard/

but note #47 (needs to be done first, perhaps)

Clarify license and authors

The license currently says:

https://github.com/BIDS-Apps/bids-apps.github.io/blob/c881455dec3cfa966e70b64b8bb8b595d93ca52d/LICENSE#L3

And the author currently says:

https://github.com/BIDS-Apps/bids-apps.github.io/blob/c881455dec3cfa966e70b64b8bb8b595d93ca52d/_config.yml#L21

I think we should:

1. clarify the role of "Josh Gerdes" ... was he the author of the template used for the website? If yes, we should just make our license more specific: The contents belong to bids contributors, the website template belongs to josh gerdes
2. Make the "author" (currently Chris G) more inclusive --> this should also be bids contributors, given that more people than Chris G have contributed by now (and -- more importantly -- will do so in the future)

What are your opinions?

failing to get proper github badges on dashboard

@sappelhoff

any idea where this could be coming from?

I have not looked into it yet. Just in case you have a better hunch than me.

I could help

please invite me to the organization ;-)

site not displaying correctly!

I fear some change I made broke things! The beautiful formatting is gone.

Add to contributing guide

#25 was a first pass at our contributing guide. During the process, we found additional headings that would helpful to add to the contributing guide. Please feel free to suggest more topics on this issue!

• Adding an app to this repository
• table of contents
• Joining the community (like in our bids-specification contributing)

[wishlist] defacer BIDS-app

Given a "raw" BIDS dataset, but which was not defaced yet, should deface anatomicals for all subjects/sessions, and move non-defaced under sourcedata/. Could be any of the https://open-brain-consent.readthedocs.io/en/stable/anon_tools.html#faces-dental-stripping but probably ideally the one used by OpenNeuro folks themselves. Note also that the https://github.com/mih/mridefacer/blob/master/mridefacer also has "datalad support" in that it takes care about annotating non-defaced anatomicals as having distribution restrictions.

tags to add: good for a hackathon

A few badges broken

Hey BIDS apps team! It looks like a column of badges are 404-ing on https://bids-apps.neuroimaging.io/apps/:

I suspect a circle workflow was removed, changed, or something along those lines, it looks like the Circle URL that is linked to is 404 along with the badge. https://circleci.com/gh/BIDS-Apps/aa.svg?style=shield

Just wanted to let you know!

Add CONTRIBUTING.md

Describe how one can contribute to this repository (the bids-apps.neuroimaging.io website)

https://opensource.guide/how-to-contribute/#how-to-submit-a-contribution
https://github.com/emdupre/me-ica/blob/py3/CONTRIBUTING.md

Add link to the paper

http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005209

Add "last updated" badge to list of BIDS Apps

Your idea

similar to how it's currently done in bids-standard/bids-website#261

knowing when an app was last updated gives an indication of how actively it is developed, as a heuristic for reliability and whether or not it's worth looking into.

Add validation that all gh/dh exist as specified in _config.yml

Your idea

Inspired by

• #121

which broke our cron job in https://github.com/ReproNim/containers . So would be nice if _config.yml records were checked for presence on gh/dh. For dh it is just https://registry.hub.docker.com/v2/repositories/bids/{dh} away AFAIK.

allow apps to run their CI on any CI provider

Your idea

Currently we can only show CI badges on our app page if the app runs its CI on circle-CI.

This is too restrictive.

We should probably allow apps to run their CI anywhere and adapt how those badges are grabbed for each case.

We could cover:

• travis (see bidsonym #66)
• github action (fitlins could be a candidate)

fmriprep badge is out of date (says 1.5.0 when there is 1.5.9 now)

might be related to #2

CI: Upload html build artifacts for inspection of website based on PR build

The only CI check we currently have (recently migrated from Travis to GH actions) is a quick "build test": https://github.com/BIDS-Apps/bids-apps.github.io/blob/c881455dec3cfa966e70b64b8bb8b595d93ca52d/.github/workflows/ruby_tests.yml#L1

I think it'd be cool to extend this by uploading the html artifacts for inspection. Doing this on GH Actions is slightly inconvenient, because one always has to download a zip file and then look at it.

With circleci and https://github.com/larsoner/circleci-artifacts-redirector, this can be made much more convenient (just click on the check, and view artifacts in the browser)

bidspm

Your BIDS app

  - gh: "cpp-lln-lab/bidspm"
    dh: "cpplab/bidspm"
    ci: "gh"
    branch: "main"
    workflow: "test"
    ds_type:
      - raw
      - derivative
    datatype:
      - anat
      - func

Submission checklist

• complies to the BIDS app API
• has a system-test workflow set up
• test dataset is validated before processing

dashboard should show the status of the latest stable image instead of master

In light of
bids-apps/maintenance-tools#7

it seems that it maybe be more useful to have our dashboard show the status of how the latest version of an app is running rather than the status of the default branch of the repo.

We could keep those on a separate page that could more useful for us or anyone who would like to try the bleeding edge version of an app.

Link to BIDS Apps paper, link to "BIDS Apps" BEP027 (aka "BIDS Apps spec"?)

I didn't find a link to either of those two important resources:

• https://doi.org/10.1371/journal.pcbi.1005209
• https://bids.neuroimaging.io/bep027

Get rid of superfluous files?

I think there may be some files in this repository that:

1. either shouldn't be here (there are better places)
2. or are not needed

Candidates for 1.

• OHBM2017_poster.afdesign --> this should rather be a PDF on Zenodo or similar
• ...?

Candidates for 2.

• categories.md
• tags.md
• ... ?

Is everyone fine with removing these files? If somebody really needs the poster, it'll be in the git history.

badges not updating

The badges for build success and issue count do not appear to be updating. CPAC now has no issues and several passed circleCI tests, but it still says that its build is a failure and that there is an issue. Do I need to do something to trigger the web page to be rebuilt or something?

Check that website is responsive on different view ports.

Was getting some awkward behavior on my phone.

Nav bar was hard to locate.