Merge pull request #25 from DouglasNeuroInformatics/fix_links

Fix broken links after refactor

docs/about_the_platform/index.md

@@ -25,7 +25,7 @@ and OpenCL acceleration suitable applications.
 The platform workstations run Ubuntu Linux variants, with full productivity
 software (LibreOffice, GIMP, Inkscape, etc), modern web browsers (Chrome, Firefox),
 and a large suite of scientific software. Scientific software is avaialble in the
-{ref}`software quarantine<doing_things/index:accessing scientific software (quarantine aka modules)>`.
+{ref}`software quarantine<using_the_system/access_to_software:accessing scientific software (quarantine aka modules)>`.
 
 ## Filesystem layout
 

docs/using_the_system/access_to_data.md

@@ -34,8 +34,8 @@ with `<PV version>` the ParaVision software version (PV5.1 or PV6.0.1) and `<use
 the login of the user performing the scans. Users are expected to access their data 
 during that time and copy it to appropriate long term storage. Recovery is available 
 with delayed access and a recovery fee associated with staff time. Data can be accessed
-by 1) accessing the {ref}`Neuroinformatics Platform<doing_things/index:accessing the system>` and then 2) 
-accessing the bruker7t computer. The {ref}`tools for data transfer<doing_things/index:transferring data>` will 
+by 1) accessing the {ref}`Neuroinformatics Platform<using_the_system/access_to_system:accessing the system>` and then 2) 
+accessing the bruker7t computer. The {ref}`tools for data transfer<using_the_system/access_to_data:transferring data>` will 
 work, provided you take into account you need to connect to an additional computer (the bruker7t).
 
 Conversion to other formats (DICOM and NIFTI) is available upon request.

docs/using_the_system/access_to_system.md

@@ -1,17 +1,17 @@
-## Accessing the System
+# Accessing the System
 
 The platform can be accessed in a number of ways:
 
 1. Physical access
 2. Remote access within the Douglas.
 3. Remote access outside the Douglas.
 
-### Physical Access
+## Physical Access
 
 Physical access to a suite of workstations is available inside the Douglas CIC,
 contact the CIC Administrative Assistant (Louis Théroux) for keycard access.
 
-### Remote Access within the Douglas
+## Remote Access within the Douglas
 
 All platform hardware is acccessible within the Douglas Research Center network
 via `ssh`. The main userserver is available at `cicus03`, the storage server
@@ -25,7 +25,7 @@ The command `who` can list currently logged-in users, while `htop` will show
 a graphical display of the current state of CPU and Memory utilization.
 ```
 
-### Remote Access outside the Douglas
+## Remote Access outside the Douglas
 
 Remote access from outside the Douglas is provided by authorization only.
-Please contact the platform to request access.
+Please contact the platform to request access.