This project is a tool to be used to manage the MR scanner data, and package it for distribution to users. Specific features include:

• Pulls down all images available from the DICOM server on the scanner
• Pulls down related pfiles
• Renames files and folders to follow a naming convention
• Stages all files for a scan in a working directory for admin inspection

Installation

Dependencies:

• Python 2.x
• [dcmtk](http://dcmtk.org)

I recommend using a conda environment to get set up:

$ conda create -n mritool python
$ source activate mritool

Then clone this repo and setup:

$ git clone git@github.com:TIGRLab/mritool.git
$ cd mritool
$ python setup.py install

The install command will install some python dependencies.

Basic usage

The command line tool is mritool. Check the usage help via:

$ mritool --help

Finds and copies exam data into a well-organized folder structure.

Usage:
    mritool [options] pull <exam> [<series>] [-o <outputdir>] [--bare]
    mritool [options] check <exam>
    mritool [options] complete <exam>
    mritool [options] list-exams [-b <booking_code>] [-e <exam>] [-d <date>]
    mritool [options] list-series <exam>
    mritool [options] list-inprocess
    mritool [options] sync-exams
    mritool pfile-headers <pfile>

Commands:
    pull                      Get an exam from the scanner
    check                     Check that an exam being processed has all of its files
    complete                  Mark an exam as complete by moving it to the processed folder
    list-exams                List all exams on the scanner
    list-series               List all series for the exam on the scanner
    list-inprocess            List the exams in the inprocess area
    sync-exams                Pulls all unpulled exams into the processing folder
    pfile-headers             Show the headers of a pfile

Command options:
    -b <bookingcode>          Booking code (StudyDescription)
    -d <date>                 Date (StudyDate)
    -e <exam>                 Exam number (StudyID)
    -o <outputdir>            Output directory (overrides --inprocess-dir)
    --bare                    Only pull dicom files

Global options:
    --inprocess-dir=<dir>     In-process exams directory [default: /data/mritooltest/InProcess]
    --processed-dir=<dir>     Processed exams directory [default: /data/mritooltest/Processed]
    --log-dir=<dir>           Logging directory [default: /data/mritooltest/logs]
    --host=<str>              Scanner hostname [default: CAMHMR]
    --port=<num>              Scanner port [default: 4006]
    --aet=<str>               Scanner AET [default: mr-srv1]
    --aec=<str>               Calling machine AEC [default: CAMHMR]
    -f, --force               Force a command, even if there are warnings.
    -v, --verbose             Verbose messaging.

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Known Issues

• mritool sync-exams doesn't re-pull exams when they have been updated. See https://github.com/TIGRLab/mritool/issues/34. If sync has pulled an exam, and the exam is later updated, sync won't notice. You'll need to handle this situation by hand.

Scanner data

The GE scanner serves most data via a DICOM server which is accessible using the gcmtk toolkit. pfiles (research scan data) are not accessible over DICOM transfer.

The GE scanner drops pfiles into the folder /export/home/signa/research/mrraw. It keeps no record of them through the DICOM interface, so the files must be scavanged from this folder. pfiles are named <id>.7, where <id> is reused after a scanner restart (which happens daily). The upshot of this is that pfiles must be pulled from the 'mrraw' folder at least daily, or else the may be overwritten.