NIMS Internal Documentation

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Contents

[edit] Roadmap

NIMS is the Neurobiological Image Management System, currently being developed at the Stanford Psychology Department. This page and its related pages provide internal documentation for system administrators and NIMS software developers. They are not intended to provide user level or tutorial documentation, but rather to link to various software engineering artifacts of use in developing and maintaining the system. The following are useful clckable links:

[edit] The NIMS architecture

  • NIMS Architectural Topics: This document covers significant architectural decisions, concerning specifically
    • A) the implementation of NRP (the NIMS Remote Processor or NIMS Request Processor), a distributable remote service facility for compute-intensive NIMS operations; and
    • B) the implementation of Association NIOs, i.e. NIOs that are derivable from image volumes via stepwise refinement filtering and processing operations.
    • C) implement NIMS DICOM_puller process that pulls DICOM images from a DICOM server. This will be the primary way of getting images into NIMS from the CNI.
    • D) Allow users to log in via Stanford's WebAuth system. The basic idea is that we can create user accounts in NIMS that are flagged as SUNet id accounts. The username that NIMS stores will exactly match the user's SUNet id and NIMS will not store a password for that user. We need to figure out the best way to present this to the user. One option is that we request the username first (no password) and then decide what to do. We check the NIMS User list and either: 1. reject the user as non-existent (log the attempt and impose a retry delay penalty), 2. send the username to the WebAuth authorization page where the user will enter their password and be authenticated by WebAuth, or 3. send the username to the NIMS login form for a standard NIMS authentication. We can install webauth with 'sudo aptitude install libapache2-webauth', then follow these instructions: install webauth.

[edit] NIMS bugs, issues, suggestions

  • NIMS Issues and Bugs: This document is used to track known issues and bugs reported during testing, as well as issues that have been resolved or that are non-issues as they arise from architectural and/or design decisions. If you are testing NIMS use the corresponding section to flag issues or problems.

[edit] New tasks

  1. Update to latest version of pyro (Gunnar will try installing the old version for now)
  2. Replace pynifti with the pure python nifti reader/writer in nipy
  3. Replace dinifti with pure python. We read the dicoms to get headers with pydicom anyway, so just also write the nifti out directly from there. Nipy might have example code for doing this.
  4. Gunnar start looking at webauth and coordinate with Jorge for integrating changes into NIMS
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