revised index and release_notes per Damien recommendations.

Author: Eric Feczko

docs/index.md

@@ -1,19 +1,43 @@
+# ABCD-BIDS Community Collection (ABCC) Documentation Summary
+
+The ABCC read-the-docs page contains extensive documentation on the data, tools, and utilities that can be used to access, download, analyze, and share derived ABCD datasets. 
+
+The ABCC houses a community-shared and continually updated ABCD neuroimaging dataset available under Brain Imaging Data Structure (BIDS) standards. Source data are converted to BIDS from the [NIMH Data Archive (NDA) share of ABCD fast-track data](https://nda.nih.gov/edit_collection.html?id=2573). Only data that passed the Data Analysis Imaging Center (DAIC) quality control are included. More information on the data available, including the different processed derivatives available, can be found in the [**Release Notes**](https://collection3165.readthedocs.io/en/stable/release_notes/).
+
+In addition to the data, the ABCC read-the-docs provides helpful links to how to use, process, and analyze ABCD data. The documentation guide below will take users to different sections for more information.
+
+# How to Contribute
+
+If you would like to contribute to this effort, please visit our [Git NDA Uploads Repository](https://github.com/ABCD-STUDY/nda-abcd-collection-3165). Additionally, you may contact us by emailing [email protected]. 
+
+Latest updates are detailed below. 
+
 # Collection News
 
 ## Curator's Latest Update
 
 - 10/7/2020: An important release today to assist investigators with quality control (QC): Brain coverage quality control scores for the `derivatives.func.runs_task-(MID|nback|rest|SST)_volume` data subsets.  Remember to QC your data from the release with the [ExecutiveSummary visual report files (see Pipeline stage 7)](https://collection3165.readthedocs.io/en/stable/pipeline/#stage-7-executivesummary), available in the `derivatives.executivesummary.all` data subset.
 
-## Latest Release: Release 1.1.2
 
-Released XX/XX/2020, this is additional minimally pre-processed runs for the `task-rest` volumes and their QC scores:
 
+## Coming Soon: Release 2.0.0
+
+- Uploading 144 participants with new data due to revised fast track QC
+- Providing Connectivity matrices for those participants with discrepancies in the number of timepoints used
+- Uploading JSONs for the diffusion inputs in some participants
 - `derivatives.func.runs_task-rest_volume` data subset all runs
 - `derivatives_qc.(json|tsv)` version 1.0.1, including all `task-rest` runs
+- Updated `participants.tsv` file containing new columns indicating which participants were updated under the new `released` fast track and have `updated_dwi_input_json` files, see the [release-notes](https://collection3165.readthedocs.io/en/stable/release_notes.html#5-corrections) for more information. 
+
+- [fMRIPrep](https://fmriprep.org/)-processed derivatives for subjects in the ABCC. We are really excited to provide fMRIprep standardized outputs. Special thanks to Dylan Nielson, Oscar Esteban, and their teams!
+
+- [QSIPrep](https://qsiprep.readthedocs.io/en/stable/)-processed derivatives for subjects in the ABCC. We are really excited to provide the ABCC with the new QSIPrep standardized pipeline. Special thanks to Matt Cieslak, Sydney Covitz, Tim Hendrickson, Ted Satterthwaite, and their teams!
+
+- [ABCD-BIDS-tfmri-pipeline](https://github.com/DCAN-Labs/ABCD-BIDS-task-fmri-pipeline)-processed derivatives for subjects in the ABCC. We are really excited to provide level-2 contrast parameter estimates based off a BIDS-extension of task-derived outputs! Special thanks to Anthony Juliano and Greg Conan!
+
+- [Indiviudalized parcellated network]() derivatives for subjects in the ABCC. We are really excited to provide individualized networks derived from two different approavhes. Special thanks to Robert Hermosillo and Lucille Moore!
 
-## Coming Soon: Release 2.0.0
 
-[fMRIPrep](https://fmriprep.org/)-processed derivatives for subjects in collection 3165.  We are really looking forward to this one.  Special thanks to Dylan Nielson, Oscar Esteban, and their teams!
 
 ## Documentation Guide
 

docs/release_notes.md

@@ -6,13 +6,20 @@ Note: Clicking any link within the readthedocs site will not open a new web brow
 
 ## 1. The ABCC Collection
 
-The ABCD-BIDS Community Collection (ABCC) from the Developmental Cognition and Neuroimaging (DCAN) Labs contains a regularly updated dataset of ABCD Brain Imaging Data Structure (BIDS) version 1.2.0 pipeline inputs and derivatives. Source data are currently comprised of all the ABCD Study participants baseline year 1 arm 1 DICOM imaging data that passed initial acquisition quality control from the ABCD Data Analysis and Informatics Center (DAIC) and were processed by DCAN Labs.
+The ABCC houses a community-shared and continually updated ABCD neuroimaging dataset available under Brain Imaging Data Structure (BIDS) standards. Source data are converted to BIDS from the [NIMH Data Archive (NDA) share of ABCD fast-track data](https://nda.nih.gov/edit_collection.html?id=2573). Only data that passed the Data Analysis Imaging Center (DAIC) quality control are included. 
 
-The version 1.0.0 release focuses on anatomical and resting-state fMRI derivative data.
+Currently, the ABCD-BIDS Community Collection (ABCC) from the Developmental Cognition and Neuroimaging (DCAN) Labs contains a regularly updated dataset of ABCD Brain Imaging Data Structure (BIDS) version 1.2.0 pipeline inputs and derivatives. Source data are currently comprised of all the ABCD Study participants baseline year 1 arm 1 DICOM imaging data that passed initial acquisition quality control from the ABCD Data Analysis and Informatics Center (DAIC) and were processed by DCAN Labs.
+
+The version 1.0.0 release focuses on anatomical and resting-state fMRI derivative data. Version 2.0.0 will add new derivatives including diffusion and task fMRI deriative data.
 
 ## 2. Background
 
-The input DICOM data to this [BIDS version 1.2.0](https://www.nature.com/articles/sdata201644) data collection were retrieved from the [NIMH Data Archive (NDA) share of ABCD fast-track data](https://nda.nih.gov/edit_collection.html?id=2573) and were last accessed on May 1, 2019. BIDS input data were converted from DICOMs using [Dcm2Bids](https://github.com/cbedetti/Dcm2Bids). BIDS derivatives data were derived from the [DCAN Labs ABCD-BIDS MRI processing pipeline](https://doi.org/10.5281/zenodo.2587210) which outputs [Human Connectome Project (HCP) Minimal Preprocessing Pipelines-style data](https://doi.org/10.1016/j.neuroimage.2013.04.127) in both volume and surface spaces. This collection is independent from ABCD Data Collection 2573. Users may access ABCD DICOM files via the ABCD fast-track imaging data release in Collection 2573.
+As a community share, the ABCC enables researchers to access **available derivatives** and share their **own derivatives.**. The `inputs`, `abcd-hcp-pipeline`, and `freesurfer-5.3.0-HCP` shares are continually updated as new ABCD releases become available. A list of currently available datasets are provided below:
+
+1. `inputs:` The input DICOM data to this [BIDS version 1.2.0](https://www.nature.com/articles/sdata201644) data collection were retrieved from the [NIMH Data Archive (NDA) share of ABCD fast-track data](https://nda.nih.gov/edit_collection.html?id=2573) and were last accessed on May 1, 2019. BIDS input data were converted from DICOMs using [Dcm2Bids](https://github.com/cbedetti/Dcm2Bids). 
+1. `abcd-hcp-pipeline` BIDS derivatives data were derived from the [DCAN Labs ABCD-BIDS MRI processing pipeline](https://doi.org/10.5281/zenodo.2587210) which outputs [Human Connectome Project (HCP) Minimal Preprocessing Pipelines-style data](https://doi.org/10.1016/j.neuroimage.2013.04.127) in both volume and surface spaces. This collection is independent from ABCD Data Collection 2573. Users may access ABCD DICOM files via the ABCD fast-track imaging data release in Collection 2573.
+1. `freesurfer-5.3.0-HCP` segmentation statistics and surface morphometrics from the FreeSurfer stage within the [DCAN Labs ABCD-BIDS MRI processing pipeline](https://doi.org/10.5281/zenodo.2587210) are provided here.
+
 
 ## 3. Ongoing Releases
 
@@ -47,9 +54,6 @@ This was the next big release with the addition of:
 
 This was a small version 1.0.0 release of the `derivatives_qc.(json|tsv)` with additional BIDS derivatives quality control data including a "brain coverage score" for the `derivatives.func.runs_task-(MID|nback|rest|SST)_volume` data subsets.
 
-### Release 1.1.2 (XX/XX/2020)
-
-This was a small version 1.0.1 fix release of the `derivatives_qc.(json|tsv)`, to include all `task-rest` runs.
 
 ## 5. Corrections
 

mkdocs.yml

@@ -1,4 +1,4 @@
-site_name: Collection 3165 - DCAN Labs ABCD-BIDS
+site_name: Collection 3165 - ABCD-BIDS Community Collection (ABCC)
 theme: material
 plugins:
   - search