Add mermaid diagram from Jamie and fix descriptions for transfer

Author: yarikoptic

mkdocs.yml

@@ -12,6 +12,11 @@ extra_javascript:
 markdown_extensions:
     - toc:
         anchorlink: true
+    - pymdownx.superfences:
+        custom_fences:
+          - name: mermaid
+            class: mermaid
+            format: !!python/name:pymdownx.superfences.fence_code_format
 plugins:
     - search
 docs_dir: 'src'

src/mri/dataaccess.md

@@ -2,7 +2,45 @@
 
 All data is collected and provided for access and conversion into BIDS on rolando.cns.dartmouth.edu.
 
-You need to request access permissions from [Andrew Connolly](mailto:[email protected]).
+You need to request access permissions from [Research Computing](mailto:[email protected]).
+
+
+```mermaid
+---
+config:
+      theme: redux
+---
+flowchart TD
+
+subgraph subGraph1["Source Data from Scanner"]
+       inbox-dicom(("/inbox/DICOM"))
+       details1("Accessions stored by date<br>/YYYY/MM/DD/A#")
+ end
+subgraph subGraph2["Converted Data"]
+       inbox-bids(("/inbox/BIDS"))
+       details2("Stored as /PI/Lead/Study<br/><a href='https://github.com/bids-standard/bids-specification/pull/1861#issuecomment-2183701293'>BIDS Project</a><br/>under 'sourcedata/raw/'")
+ end
+   local-storage("local storage")
+   inbox-dicom -- "<a href='https://dbic-handbook.readthedocs.io/en/latest/mri/dataaccess.html#dicoms'>scp/rsync</a>" --> local-storage
+   inbox-bids -- "<a href='https://dbic-handbook.readthedocs.io/en/latest/mri/dataaccess.html#bids'>scp/rsync/DataLad</a>" --> local-storage
+   inbox-dicom --> request("PI requests<br/>dataset conversion")
+   request --> conversion{"<a href='https://github.com/repronim/reproin'>Reproin<br/>conversion</a>"}
+   conversion --> inbox-bids
+
+
+   style subGraph1 fill:#FFFFFF,stroke:#000000
+   style subGraph2 fill:#FFFFFF,stroke:#000000
+   style inbox-dicom fill:#C8E6C9,stroke-width:4px,stroke-dasharray: 0,stroke:#00C853
+   style details1 stroke:#000000
+   style inbox-bids fill:#C8E6C9,stroke-width:4px,stroke-dasharray: 0,stroke:#00C853
+   style details2 stroke:#000000
+   style request stroke-width:4px,stroke-dasharray: 0,fill:#FFE0B2,stroke:#00C853
+   style local-storage fill:#C8E6C9,stroke-width:4px,stroke-dasharray: 0,stroke:#00C853
+   style conversion stroke:#00C853,stroke-width:4px,stroke-dasharray: 0
+```
+
+N.B. Storing under `sourcedata/raw/` is a planned solution.
+At the moment it would be just in the root of the dataset.
 
 ## DICOMs
 
@@ -11,31 +49,25 @@ You can `scp` or `rsync` them to your local storage.
 
 ## BIDS
 
-At the moment, upon request from a lab member to [Yaroslav Halchenko](mailto:[email protected]), data is converted from DICOMs into BIDS within the directories hierarchy under `/inbox/BIDS`, following convention described in ReproIn section (TODO: make into a reference).
+At the moment, upon request from a lab member to [Yaroslav Halchenko](mailto:[email protected]), data is converted from DICOMs into BIDS within the directories hierarchy under `/inbox/BIDS`, following convention described in the [ReproIn section](./reproin.md).
+If any metadata (`subject_id` or `session_id`) need to be corrected, inform ahead of time.
 
 These directories are also DataLad datasets, so you have two options on how to transfer them:
 
-##### Reckless clone still wants to access rolando
+### DataLad
 
-TODO: Yarik figureout
+Before you proceed, please refer to the [DataLad section](../basics/datalad.md) of the handbook.
+When you are all set, you can do simply something like
 
+```commandline
+datalad clone [email protected]:/inbox/BIDS/dbic/dbic-animals dbic-animals
 ```
-(conda-20200210-datalad) [d31548v@discovery7 tmp]$ datalad install -s 1021_actions --reckless auto 1021_actions_reckless
-[INFO   ] Fetching updates for <Dataset path=/dartfs/rc/lab/D/DBIC/DBIC/tmp/1021_actions_reckless>
-
-
-    Dartmouth College, Department of Psychological and Brain Sciences
-                      Authorized access only
 
-
-
-
-[email protected]'s password:
-```
+This will create a local clone of the dataset, and you can use `datalad get` to get the data you need.
 
 ### Old fashion way
 
-`scp` or `rsync`. But you would need to take care about dereferencing symlinks.
+`scp` or `rsync`. But you would need to take care about de-referencing symlinks.
 
     rsync --exclude=.git --copy-links -r \
         rolando.cns.dartmouth.edu:/inbox/BIDS/dbic/dbic-animals dbic-animals