remove dwiqc leftovers in user_docs

LICENSE

@@ -1,4 +1,4 @@
-Copyright 2024 The President and Fellows of Harvard College. All rights reserved.
+Copyright 2025 The President and Fellows of Harvard College. All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification, 
 are permitted provided that the following conditions are met:

docs/source/index.rst

@@ -1,26 +1,19 @@
-.. AnatQC documentation master file, created by
-   sphinx-quickstart on Tue Jun 20 12:46:20 2023.
+.. Scanbuddy documentation master file, created by
+   sphinx-quickstart on Tue Jan 7 12:46:20 2025.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to DWIQC's documentation!
+Welcome to Scanbuddy's documentation!
 ==================================
-.. _Prequal: https://doi.org/10.1002/mrm.28678 
-.. _QSIPREP: https://doi.org/10.1038/s41592-021-01185-5 
-.. _XNAT: https://doi.org/10.1385/NI:5:1:11
 
-DWIQC is a diffusion MRI preprocessing and quality control pipeline built on the `Prequal`_ and `QSIPREP`_ software packages. Working closely with neuroimaging experts, we designed an ergonomic user interface for the `XNAT`_ informatics and data management platform that allows users to quickly assess image quality and use those insights to get ahead of issues within the data acquisition workflow. Non-XNAT users can also benefit from DWIQC as a one-stop shop for running two state of the art diffusion pipelines simultaneously and receiving their associated outputs. See `Prequal`_ and `QSIPREP`_ documentation for further details.
-
-
-.. image:: images/logo.png
+Scanbuddy is an fMRI motion plotting software that allows users to see motion estimates at the time of scan acquisition. Scanbuddy also computes an SNR estimate for the scan. Scanbuddy is written in python and has been containerized to work across platforms, though it was developed for Linux.
 
 .. toctree::
    :maxdepth: 3
    :caption: Contents:
 
-   xnat
+   users
    developers
-   xnattagger
 
 Indices and tables
 ==================

docs/source/user_docs.rst

@@ -0,0 +1,91 @@
+User Documentation
+==================
+
+
+.. note::
+    This documentation assumes a basic understanding of the command line, the Linux operating system and Siemens MRI scanner host PCs. Here's a quick (and free!) crash `course <https://www.codecademy.com/learn/learn-the-command-line>`_ on the command line if needed. Instructions on streaming data to the Scanbuddy machine from a scanner are shown on a Siemens XA-30 system.
+
+
+Overview
+^^^^^^^^
+Let's start with what Scanbuddy is all about. fMRI is a powerful research and clinical tool that allows us to peer into the brain function of living humans. One of the biggest challenges facing fMRI data quality is subject movement during data acquisition. Even subtle actions, such as swallowing or yawning, can have large impacts on data quality. 
+
+To combat subject motion and optimize data quality, motion-correcting software algorithms can be employed at the post-processing stage, as well as data deletion and imputation methods. However, there are instances of subject motion being severe enough to make the dataset unusable. This is where Scanbuddy comes in! Scanbuddy produces motion plots to be viewed by researchers at the time of data acquisition, appearing on screen at the conclusion of fMRI scans. Individual researchers will determine acceptable motion standards. Seeing motion plots at acquisition can help researchers decide if a scan should be re-acquired. You no longer have to wait until data processing to get an idea of how much your subject has or has not moved.
+
+Scanbuddy also provides an estimate of the Signal-to-Noise Ratio (SNR) with the motion plots to give researchers an idea of overall data quality. Scanbuddy does not save motion plots by default and does not store data on its host machine. Scanbuddy will create a new motion plot and compute a new SNR metric for every fMRI scan acquired. Scanbuddy currently does not support Multi-Echo BOLD imaging, though work is being done to make this feature available soon. Scanbuddy is containerized with docker and is available on Github Container Repository.
+
+
+What You Will Need
+^^^^^^^^^^^^^^^^^^
+Scanbuddy should be run on a standalone machine (separate from the scanner host PC) that runs Linux and you have sudo privileges. We've used several distibutions of Linux in development (ubuntu, debian, asahi) and all have run Scanbuddy successfully. Scanbuddy may work on MacOS and/or Windows, though it has not been tested by the developers. The Scanbuddy machine should have 16 GB of RAM if possible. It may still work with less memory depending on the size of the data being acquired. The machine should be capable of running a web broswer and Docker. You will also need a monitor to connect to the machine to display the motion plots.
+
+.. note::
+     Take a look at installing Docker on Linux `here <https://docs.docker.com/engine/install/>`_.
+
+Samba Share
+^^^^^^^^^^^
+Data streaming from the scanner to the Scanbuddy machine should be setup via a Samba share mount. Samba enables the scanner to stream dicom data directly to the Scanbuddy machine so that Scanbuddy can build the motion plots and display them when the scan ends.
+
+Let's get Samba up and running! First thing to do, install Samba:
+
+.. code-block:: shell
+    
+     sudo apt install samba
+
+Create the directory you want to share over Samba and set ownership to a system account:
+
+.. code-block:: shell
+
+     sudo mkdir -p /data/folder
+     sudo chown username:group /data/folder
+
+If you are using SE Linux, you will need to make sure this directory is accessible to Samba:
+
+.. code-block:: shell
+    
+     sudo semanage fcontext -a -t samba_share_t "/data/folder"
+     sudo restorecon -R -v /data/folder
+
+Check ``/var/log/audit/audit.log`` for Samba denial messages. You may not see any messages until the scanner attempts to mount the drive.
+
+You will also need to create a Samba password. Samba uses its own password database for authentication. The password you choose for Samba may be different from the user's system password. Adding a new Samba user should automatically enable the user, but it's still a good idea to make sure the user is enabled with ``smbpasswd -e username``
+
+.. code-block:: shell
+
+      sudo smbpasswd -a username
+
+Configure Samba
+"""""""""""""""
+Add the following to the end of ``/etc/samba/smb.conf``
+
+.. code-block:: yaml
+
+  [sharedfolder]
+      comment = My Shared Folder
+      path = /data/folder
+      read only = no
+      writable = yes
+      browsable = yes
+      create mode = 0660
+      directory mode = 0770
+
+Save the above file and restart Samba:
+
+.. code-block:: yaml
+
+     sudo service smbd restart
+
+Your Samba share should be up and running now!
+
+Configuring the Plugin
+^^^^^^^^^^^^^^^^^^^^^^
+We have to tell the scanner which scans should be exported to the Scanbuddy machine and where the scanbuddy machine is.
+
+Building the Container
+^^^^^^^^^^^^^^^^^^^^^^
+Scanbuddy is packaged up in a Docker container to abstract away the hassle of installing the specific software it needs. Hurray for Docker!
+
+Running Scanbuddy
+^^^^^^^^^^^^^^^^^
+With the plugin and Samba configured and the container built, we're ready to run Scanbuddy! 
+