Merge pull request #22 from v-kyriakopoulou/master

Updated biomedia following discussion with Jo

_layouts/default.html

@@ -22,11 +22,9 @@ <h2 class="project-tagline">{{ site.description }}</h2>
 
       <a href="{{ site.baseurl }}/index.html" class="btn">Overview</a>
       <a href="{{ site.baseurl }}/download.html" class="btn">Download</a>
-      <a href="{{ site.baseurl }}/organisation.html" class="btn">Data Organisation</a>
       <a href="{{ site.baseurl }}/cite.html" class="btn">Cite</a>
-      <a href="https://github.com/BioMedIA/dHCP-release-notes/tree/master/supplementary_files" class="btn">Supplementary Files</a>
       <a href="{{ site.baseurl }}/open-resources.html" class="btn">Open Resources</a>
-      <a href="https://neurostars.org/tags/developing-hcp" class="btn">Issues</a>
+      <a href="{{ site.baseurl }}/issues.html" class="btn">issues</a>
 
     </section>
 
@@ -35,7 +33,6 @@ <h2 class="project-tagline">{{ site.description }}</h2>
 
       <footer class="site-footer">
         <span class="site-footer-credits">
-          <a href="{{ site.github.repository_url }}">View on GitHub</a>
         </span>
         <a style='float: right;' href="{{ site.baseurl }}/feed.xml"><img src="{{ site.baseurl }}/assets/images/rss.png" alt="subscribe via rss"/></a>
       </footer>

download.md

@@ -1,94 +1 @@
----
----
-
-## Download
-
-In order to be able to browse/download data,
-you will need to register by following [this
-link](https://data.developingconnectome.org/app/template/Login.vm). On
-the dHCP data login page, select 'Register' and fill out the mandatory
-fields including **Lab/Department, Institute Full Name, Country and your
-institutional email address**. You will receive a verification email. After
-you verify your email address, you will be able to login to sign an agreement
-and access the public face of the dHCP database (db). This includes browsing
-(although not downloading) available Projects (data sets).
-
-If you experience any technical issues, please [submit your query
-here](https://neurostars.org/t/dhcp-infant-data-downloading-issue/2500).
-
-<div id="toc"></div>
-
-## Data review and download
-
-In order to unlock download options for available Projects (data sets),
-you will have to sign user terms. Open any Project and hit 'Sign user
-terms'. Once confirmed you will be able to view a list of subjects,
-preview the available data as acquired (without any pre-processing) and
-will be provided two download options.
-
-### Academic Torrent download (recommended)
-
-Since data sets are fairly large (expect > 700GB) this is
-a fail-safe way to get hold of desired releases. A [separate
-document](https://drive.google.com/file/d/1llcifaLWicGZ-DxVWCpyhBqJfEwToWb_/view)
-provides more detailed instructions. Be sure to have a Torrent client
-such as [BitTorrent](https://www.bittorrent.com/) installed on your
-computer. Clicking on the 'Download Data Set (Torrent)' button will provide
-you with a `.torrent` file a few kB in size. Opening this `.torrent` file in
-your Torrent client will give you the option to select among subsets of the
-selected release. Once confirmed, your torrent client will automatically
-start the download from multiple peers. You can pause/stop the download
-at any time. By downloading parts of the bundle you automatically become
-a peer for the selected `.torrent` file, which increases bandwidth for
-other peers. You are encouraged to at least upload the same amount of data
-that you downloaded (a download/upload ratio of 1.0 in the Torrent client),
-however this is not a must. Caveat: Your system administrator / institution
-might block (or be unhappy with) peer-to-peer traffic for various reasons.
-
-Once you start downloading the dataset, you will notice that your torrent
-client mentions a sharing / seeding ratio. It means that as soon as you
-start downloading the dataset, you become part of our community of sharers
-and contribute to making the dataset available to other researchers all
-around the world!
-
-There is no reason to be scared! It's perfectly legal as long as you are
-allowed to have a copy of the dataset (that is the information you need to
-forward to your lab's IT team if they are blocking your ports). You are
-actually providing a tremendous contribution to dHCP by spreading the data,
-so thank you again for that. With your help, we can make sure this data
-remains available and can be downloaded relatively fast in the future.
-
-Over time, the dataset will grow and your contribution will be more and
-more important so that each and everyone of you can still obtain the data
-in the smoothest possible way.
-
-#### NOTE: 
-- (26/07/2021) Due to an oversight, the original preprocessed-fMRI torrent (`dhcp_3rd_fmri_pipeline.torrent`) was missing some files. These files have been been included in an additional patch torrent (`dhcp_3rd_fmri_pipeline_patch1.torrent`). To obtain the complete dataset of preprocessed fMRI, you will need to download both the original fMRI torrent AND the fMRI patch torrent.
-
-##  Downloading non-imaging data
-
-### List of Subjects, Gender, GA
-
-The data release contains some non-imaging data, which can be directly
-downloaded as an Excel spreadsheet by selecting 'Spreadsheet' from the
-'Options' drop down menu from the table view page.  The data release
-supplementary documentation can be directly downloaded by clicking on the
-link 'documentation: Data Release' on the main table view page.
-
-### Metadata 
-
-Metadata file includes the following information.
-
-Column | Notes
-:---------- | :----
-`birth_age` | Gestational age at birth in weeks
-`birth_weight` | Birthweight (kg)
-`singleton` | Singleton / multiple status of the pregnancy
-`scan_age` |  Gestational age at scan in weeks
-`scan_head_circumference` |  Head circumference (cm)
-`scan_number` | 1 for the first scan, 2 for the second
-`radiology_score` |  The MRI scans were reviewed by a specialist perinatal neuroradiologist who scored each subject using the following scale:<br /> 1=Normal appearance for age<br/> 2=Incidental findings with unlikely significance for clinical outcome or analysis (e.g. subdural haemorrhage. Isolated subependymal cysts. Mild inferior vermis rotation)<br/> 3=Incidental findings with unlikely clinical significance but possible analysis significance (e.g. several punctate lesions or other focal white matter / cortical lesions not thought to be of clinical significance)<br/> 4=Incidental findings with possible clinical significance. Unlikely analysis significance (e.g. Isolated non brain anomaly for example in pituitary / on tongue) 5=Incidental finding with possible / likely significance for both clinical and imaging analysis (e.g. Major lesions within white matter cortex, cerebellum and or basal ganglia; small head / brain < 1 st centile) <br/> Q=Poor quality anatomical data 
-`sedation` |  1 if the subject was sedated during the scan, 0 otherwise
-
-The file can be downloaded from
-[combined.tsv](supplementary_files/combined.tsv).
+link to go straight to supplementary files

index.md

@@ -2,6 +2,7 @@
 ---
 ## Fourth data release (Feb 2024)
 ## Consolidated release, now including data from both fetuses and neonates
+Details to be found in https://pubmed.ncbi.nlm.nih.gov/35677357/.
 
 ## 1.	Cohort 
 •	Neonatal participants: 783 subjects (886 datasets).  

issues

@@ -0,0 +1,4 @@
+
+
+The dhcp project is now complete. 
+For access to resources please see the [NDA website](https://nda.nih.gov/experiment.html?id=2018&collectionId=3955). The data is now being hosted by the NDA, please contact them for any access related issues at NDAHelp@mail.nih.gov and quote collection 3955. The [Neurostars](https://neurostars.org/tag/developing-hcp) is no longer being monitored systematically. 

open-resources.md

@@ -1,14 +1,7 @@
 # Open Science Resources
 
 ## Data
-1. First Release (2017)
-    - 40 representative neonatal subjects
-    - Structural, Diffusion, Functional, and derivatives
-    - [http://www.developingconnectome.org/project/data-release-user-guide/](http://www.developingconnectome.org/project/data-release-user-guide/)
-2. Second Release (2019)
-    - 569 sessions from 511 neonatal subjects
-    - Structural, Diffusion, Functional, and derivatives
-    - [http://www.developingconnectome.org/information-registration-and-download/](http://www.developingconnectome.org/information-registration-and-download/)
+Data are available from the [NDA website](https://nda.nih.gov/experiment.html?id=2018&collectionId=3955).
 
 ## Developmental Atlases
 1. Volumetric neonatal atlas
@@ -20,12 +13,15 @@
     - [https://brain-development.org/brain-atlases/atlases-from-the-dhcp-project/cortical-surface-template/](https://brain-development.org/brain-atlases/atlases-from-the-dhcp-project/cortical-surface-template/)
 
 ## Pipelines
-1. Structural Pipeline
-    - [https://github.com/BioMedIA/dhcp-structural-pipeline](https://github.com/BioMedIA/dhcp-structural-pipeline)
-2. Diffusion Pipeline
-    - [https://git.fmrib.ox.ac.uk/matteob/dHCP_neo_dMRI_pipeline_release](https://git.fmrib.ox.ac.uk/matteob/dHCP_neo_dMRI_pipeline_release)
-3. Functional Pipeline
-    - [https://git.fmrib.ox.ac.uk/seanf/dhcp-neonatal-fmri-pipeline](https://git.fmrib.ox.ac.uk/seanf/dhcp-neonatal-fmri-pipeline)
+See modality specific [papers](https://biomedia.github.io/dHCP-release-notes/cite.html).
+## Neonatal
+1. Anatomical
+2. Functional
+3. Diffusion
+## Fetal
+1. Anatomical
+2. Functional
+3. Diffusion
 
 ## Other
 1. Scripts to align dHCP native surfaces to the dHCP surface template/atlas