diff --git a/README.md b/README.md index 1677904..e0ecf08 100644 --- a/README.md +++ b/README.md @@ -2,4 +2,4 @@ ## The full documentation lives here: [https://collection3165.readthedocs.io/](https://collection3165.readthedocs.io/) -## Use [this GitHub repository's Issues page](https://github.com/DCAN-Labs/nda-abcd-collection-3165/issues) to request documentation changes and to request features or additional data be added into the NDA collection. +## Use [this GitHub repository's Issues page](https://github.com/ABCD-STUDY/nda-abcd-collection-3165/issues) to request documentation changes and to request features or additional data be added into the NDA collection. diff --git a/docs/index.md b/docs/index.md index 518d9b3..ac5debc 100644 --- a/docs/index.md +++ b/docs/index.md @@ -2,8 +2,8 @@ ## Release 1.0.0 -- 2/17/2020: The NDA confirmed for us last week that the re-uploaded data is all released. This brings our data counts to **10,038 MRI sessions worth of NDA imagingcollection01 data** and **9,647 MRI sessions worth of NDA fmriresults01 data**. -- 12/20/2019: We downloaded from NDA and checked every derivative file against our originally uploaded data for being binary identical files. We found some discrepancies which we excluded for the first rolling release, bringing our subject count of derivative files down a little. Please anticipate our next rolling release to be soon after the first rolling release and to include enough subjects to make the total exceed 10,000 MRI sessions of derivative data. +- 4/14/2020: We have uploaded raw fMRI task event files to the NDA for sessions among the 9,647 with task-based fMRI data. We are working with the NDA to get that data released publicly prior to 5/15/2020. +- 2/17/2020: The NDA confirmed for us last week that the uploaded data is all released. This brings our subject counts to **10,038 MRI sessions worth of NDA imagingcollection01 data** and **9,647 MRI sessions worth of NDA fmriresults01 data**. ## Table of Contents @@ -11,7 +11,7 @@ Clicking any link within the readthedocs site will not open a new web browser ta --- -These documents are generated from [GitHub](https://github.com/DCAN-Labs/nda-abcd-collection-3165) as a live readthedocs.org website describing various aspects of [the NDA data in collection 3165](https://nda.nih.gov/edit_collection.html?id=3165). +These documents are generated from [GitHub](https://github.com/ABCD-STUDY/nda-abcd-collection-3165) as a live readthedocs.org website describing various aspects of [the NDA data in collection 3165](https://nda.nih.gov/edit_collection.html?id=3165). 1. [**Release Notes**](https://collection3165.readthedocs.io/en/stable/release_notes/) diff --git a/docs/recommendations.md b/docs/recommendations.md index 5a6674f..f1f4764 100644 --- a/docs/recommendations.md +++ b/docs/recommendations.md @@ -12,7 +12,7 @@ This document highlights common recommendations for usage of the collection 3165 There are two ways to download ABCD Study data and get BIDS inputs or derivatives: -1. (*PREFERRED*) Downloading from NDA Collection 3165 will provide you an "associated files" spreadsheet with AWS S3 links and other key information. DCAN Labs has designed [a GitHub repository for selectively downloading only parts of the BIDS input and derivative data, the "nda-abcd-s3-downloader"](https://github.com/DCAN-Labs/nda-abcd-s3-downloader). +1. (*PREFERRED*) Downloading from NDA Collection 3165 will provide you an "associated files" spreadsheet with AWS S3 links and other key information. DCAN Labs has designed [a GitHub repository for selectively downloading only parts of the BIDS input and derivative data, the "nda-abcd-s3-downloader"](https://github.com/ABCD-STUDY/nda-abcd-s3-downloader). 1. [ABCD Fast Track Data on the NDA](https://nda.nih.gov/abcd/query/abcd-fast-track-data.html) can alternatively be downloaded and unpacked into BIDS with the [ABCD-STUDY abcd-dicom2bids GitHub repository](https://github.com/ABCD-STUDY/abcd-dicom2bids). ## 3. MATLAB Motion Mask Files diff --git a/docs/release_notes.md b/docs/release_notes.md index 2610275..cc9488a 100644 --- a/docs/release_notes.md +++ b/docs/release_notes.md @@ -18,10 +18,10 @@ The input DICOM data to this [BIDS version 1.2.0](https://www.nature.com/article A guiding principle for this collection is to release essential data for analysis. This collection will be updated with waves of data preparation and processing. As waves complete preparation or processing they will be uploaded and version-stamped with updated and versioned release notes. -User feedback will guide our course for future releases. Provide feedback on what you would like to see included in future releases using [GitHub issues for this repository](https://github.com/DCAN-Labs/nda-abcd-collection-3165/issues): +User feedback will guide our course for future releases. Provide feedback on what you would like to see included in future releases using [GitHub issues for this repository](https://github.com/ABCD-STUDY/nda-abcd-collection-3165/issues): -- [NDA Collection 3165 documentation repository](https://github.com/DCAN-Labs/nda-abcd-collection-3165) -- [Direct link to repository's GitHub issues for requests and feedback](https://github.com/DCAN-Labs/nda-abcd-collection-3165/issues) +- [NDA Collection 3165 documentation repository](https://github.com/ABCD-STUDY/nda-abcd-collection-3165) +- [Direct link to repository's GitHub issues for requests and feedback](https://github.com/ABCD-STUDY/nda-abcd-collection-3165/issues) The following updates to this collection are already planned. diff --git a/docs/useful.md b/docs/useful.md index 99d2bcd..fb8a982 100644 --- a/docs/useful.md +++ b/docs/useful.md @@ -8,7 +8,7 @@ Note: Clicking any link within the readthedocs site will not open a new web brow This document collects the entirety of other document's link into one. Remember, use the firt link below to report documentation issues or request more data of this collection. -- [Direct link to this repository's GitHub issues for requests and feedback](https://github.com/DCAN-Labs/nda-abcd-collection-3165/issues) +- [Direct link to this repository's GitHub issues for requests and feedback](https://github.com/ABCD-STUDY/nda-abcd-collection-3165/issues) ## 2. References @@ -20,7 +20,7 @@ This document collects the entirety of other document's link into one. Remember ## 3. Websites & Documentation -- [NDA Collection 3165 documentation repository](https://github.com/DCAN-Labs/nda-abcd-collection-3165) +- [NDA Collection 3165 documentation repository](https://github.com/ABCD-STUDY/nda-abcd-collection-3165) - [NIMH Data Archive (NDA) Collection 3165 - DCAN Labs ABCD-BIDS](https://nda.nih.gov/edit_collection.html?id=3165) - [ABCD Fast Track Data explanation on the NDA](https://nda.nih.gov/abcd/query/abcd-fast-track-data.html) - [NIMH Data Archive (NDA) collection 2573 - ABCD Fast Track Data](https://nda.nih.gov/edit_collection.html?id=2573) @@ -38,7 +38,7 @@ This document collects the entirety of other document's link into one. Remember ## 4. Software -- [DCAN Labs nda-abcd-s3-downloader GitHub repository for downloading BIDS inputs and derivatives from collection 3165 directly](https://github.com/DCAN-Labs/nda-abcd-s3-downloader) +- [DCAN Labs nda-abcd-s3-downloader GitHub repository for downloading BIDS inputs and derivatives from collection 3165 directly](https://github.com/ABCD-STUDY/nda-abcd-s3-downloader) - [ABCD repository for downloading and setting up the BIDS dataset (ABCD-STUDY/abcd-dicom2bids)](https://github.com/ABCD-STUDY/abcd-dicom2bids) - [Christophe Bedetti's Dcm2Bids GitHub repository](https://github.com/cbedetti/Dcm2Bids) - [The Chris Rorden's Lab dcm2niix](https://github.com/rordenlab/dcm2niix)