diff --git a/data/tools/apps.yml b/data/tools/apps.yml index 39b9afa5..d135ee3c 100644 --- a/data/tools/apps.yml +++ b/data/tools/apps.yml @@ -173,7 +173,7 @@ apps: - derivative datatype: - dwi - description: Generate subject connectomes from raw BIDS data & perform inter-subject connection density normalisation, using the MRtrix3 software package. + description: Generate subject connectomes from raw BIDS data & perform inter-subject connection density normalization, using the MRtrix3 software package. - gh: bids-apps/ndmg status: active diff --git a/docs/collaboration/reports/google_summer/2018-gsoc.md b/docs/collaboration/reports/google_summer/2018-gsoc.md index 0524098f..eb86e52c 100644 --- a/docs/collaboration/reports/google_summer/2018-gsoc.md +++ b/docs/collaboration/reports/google_summer/2018-gsoc.md @@ -19,7 +19,7 @@ reproducibility to foster collaboration. sharing-pot Imagine you are a carrot farmer trying to make dinner. You could make carrot -soup by yourself, but you could also share ingredients with the neighbours to +soup by yourself, but you could also share ingredients with the neighbors to make a much tastier soup with onions, greens, and some salt. Some people may be able to contribute more than others -- but everyone benefits. @@ -98,7 +98,7 @@ We include how to get in touch, write in markdown, [submit a pull request](../../bids_github/CONTRIBUTING.md#making-a-change-with-a-pull-request) and explanations of where to put useful code or links in the wiki. -The licence on our repository is CC-BY and these guidelines have already been +The license on our repository is CC-BY and these guidelines have already been incorporated into other open source neuroimaging projects such as [NiBetaSeries](https://nibetaseries.readthedocs.io/en/stable/). We also used the @@ -121,7 +121,7 @@ Canada ([Elizabeth DuPre](https://github.com/emdupre)), Britain ([Chris Gorgolewski](https://github.com/chrisgorgo) and [Chris Holdgraf](https://github.com/choldgraf/)), as well as a collaborator from India ([Madhur Tandon](https://github.com/madhur-tandon)). The strategy for this -problem was to work publicly and to demonstrate best practise in open source +problem was to work publicly and to demonstrate best practice in open source project leadership. This meant rather than waiting until completion to share something, we would continuously post our work in progress and incorporate feedback. Specifically, Github milestones and “closing soon” tags on issues were diff --git a/docs/getting_started/resources/glossary.md b/docs/getting_started/resources/glossary.md index e25e2a99..62bdbcc9 100644 --- a/docs/getting_started/resources/glossary.md +++ b/docs/getting_started/resources/glossary.md @@ -33,7 +33,7 @@ One continuous block of a scan. #### BIDS -Brain Imaging Data Structure - a standardised way to organise your neuroimaging data. +Brain Imaging Data Structure - a standardized way to organize your neuroimaging data. ### C diff --git a/docs/getting_started/resources/talks.md b/docs/getting_started/resources/talks.md index a3840332..7486dd25 100644 --- a/docs/getting_started/resources/talks.md +++ b/docs/getting_started/resources/talks.md @@ -22,7 +22,7 @@ Two great resources for curated lists of talks and slides are: | Title | Speaker | Year | Occasion | Location | Video | Slides | | -------------------------------------------------------------------------------- | ----------------------------------- | ---- | ------------------------------------------------------------------------| ------------------------------------ | -------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------- | -| BIDS: underlying data management principles | Remi Gau | 2022 | Open Research at the Wellcome Centre for Integrative Neuroimaging (WIN) | Online | [link](https://vimeo.com/showcase/7645853/video/668642973) | [link](https://osf.io/h6gsr/) | +| BIDS: underlying data management principles | Remi Gau | 2022 | Open Research at the Wellcome Center for Integrative Neuroimaging (WIN) | Online | [link](https://vimeo.com/showcase/7645853/video/668642973) | [link](https://osf.io/h6gsr/) | | BIDS: a recipe for success | Patricia Clement | 2021 | [GlimR](https://glimr.eu/) BIDS workshop | | [link](https://www.youtube.com/watch?v=ukgiAP2Hn3E) | [link](https://osf.io/nu24a) | | BIDS conversion | Remi Gau & Guiomar Niso | 2021 | ACCS & OHBM Webinar and Workshop Series | online | [link](https://www.youtube.com/watch?v=m7vEHGpqQIw) | [link](https://remi-gau.github.io/bids_cookbook/) | | The BIDS Ecosystem | Chris Markiewicz | 2020 | Neuro Data Science School | Online | n/a | [link](https://effigies.github.io/bids-ecosystem/) | diff --git a/docs/getting_started/tutorials/conversion/pet.md b/docs/getting_started/tutorials/conversion/pet.md index f9392449..a33d737d 100644 --- a/docs/getting_started/tutorials/conversion/pet.md +++ b/docs/getting_started/tutorials/conversion/pet.md @@ -503,7 +503,7 @@ we're going to make sure we have images to place in them. #### Collecting and installing TPCCLIB Since our raw imaging files are in ECAT format, -we'll be using the `ecat2nii` tool it the Turku PET Centre C library (`TPCCLIIB`) +we'll be using the `ecat2nii` tool it the Turku PET Center C library (`TPCCLIIB`) as it's very handy at converting PET ECAT images into the more BIDS friendly nifti format. If you're imaging files are in `.IMG` you can use \*\*<\insert converter>\*\* or if they're in DICOM `dcm2niix` is an excellent tool to transform `.dcm` files into `.nii`. @@ -536,7 +536,7 @@ machine:Downloads user$ echo "export PATH=$PATH:/some/directory/you/are/fond/of/ machine:Downloads user$ source ~/.bashrc machine:Downloads user$ ecat2nii - ecat2nii - tpcclib 0.7.6 (c) 2020 by Turku PET Centre + ecat2nii - tpcclib 0.7.6 (c) 2020 by Turku PET Center Converts PET images from ECAT 6.3 or 7 to NIfTI-1 format. Conversion can also be done using ImageConverter (.NET application). @@ -1141,7 +1141,7 @@ follows: - [TPCCLIIB](https://gitlab.utu.fi/vesoik/tpcclib) is a command line library containing (among many others) PET tools such as `ecat2nii` that will be used below to convert the imaging data from a PET dataset into nifti format. - The Turku PET Centre site can be found [here](https://turkupetcentre.fi/) + The Turku PET Center site can be found [here](https://turkupetcentre.fi/) for additional information on anything PET. - a [BIDS PET Template](https://github.com/bids-standard/bids-starter-kit/tree/main/templates) diff --git a/includes/abbreviations.md b/includes/abbreviations.md index f242b826..8af1b81a 100644 --- a/includes/abbreviations.md +++ b/includes/abbreviations.md @@ -12,7 +12,7 @@ -*[ASL]: Arterial Spin Labelling +*[ASL]: Arterial Spin Labeling *[BEP]: BIDS Extension Proposal *[BEPs]: BIDS Extension Proposals *[BIDS]: Brain Imaging Data Structure diff --git a/pyproject.toml b/pyproject.toml index f8aa36d1..d9480f2c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,7 +15,7 @@ line-length = 79 [tool.codespell] builtin = "clear,rare,en-GB_to_en-US" -ignore-words-list = "Acknowledgements,als,ans,asai,nd,manuel,te" +ignore-words-list = "Acknowledgements,als,ans,asai,nd,manuel,te,acknowledgements" skip = ".git,env,specification,starter_kit,examples,apps,execution,pyproject.toml,data/**.tsv,data/**.json,docs/collaboration/contributors.md" [tool.hatch.build.hooks.vcs] diff --git a/templates/README.md b/templates/README.md index 1a4de270..a5b75a17 100644 --- a/templates/README.md +++ b/templates/README.md @@ -9,7 +9,7 @@ files in the BIDS dataset (dataset_description.json, events.tsv, ...). It can also be useful to also include information that might already be present in another file of the dataset but might be important for users to be aware of -before preprocessing or analysing the data. +before preprocessing or analyzing the data. If the README gets too long you have the possibility to create a `/doc` folder and add it to the `.bidsignore` file to make sure it is ignored by the BIDS validator.