enet4 / dicoogle-nifti

NIfTI-1 file converter for Dicoogle

Dicoogle NIFTI converter

This plugin for Dicoogle allows for the upload and automatic storage of NIFTI-1 files, a format defined by the Neuroimaging Informatics Technology Initiative (NIfTI).

Building

This is a maven project. Run mvn install to create a jar file of the plugin.

It relies on a custom version of niftijio, which is automatically fetched by Maven using JitPack.

Installing

Pass the jar file with dependencies, named with the pattern "nifti-vvvvvv-jar-with-dependencies", to the "Plugins" folder in Dicoogle's working directory.

Configuring

The plugin needs to be configured before use. The settings file can be found in the Plugin/settings folder by the name "NIFTI.xml".

• storage-scheme : The storage scheme of which to keep converted objects in. Defaults to "file".
• root-uid : Defines the base DICOM UID part to be included in all generated instance UIDs as the prefix. This is usually associated to an institution's unique identifier, although it is not required to be so. Defaults to a fixed, but valid, UID.

For instance, if your system has a simple file storage plugin with the "file" scheme and your institution is identified by the UID "1.2.351.472728", you may use the following configuration:

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<configuration>
   <storage-scheme>file</storage-scheme>
   <root-uid>1.2.351.472728</root-uid>
</configuration>

Using the Web Service API

POST /nifti/convert

Convert and store the NIFTI files contained in the HTTP request. The server expects either an entity containing the full data of the NIFTI file or a multipart/form-data entity containing one or more NIFTI-1 files, with or without GZip compression. If any of the files is compressed, the content type must mention that it is so ("application/gzip").

The name of each file, without the extension, will be used as the series' description. If the given file name is of the format «an»_«rest_of_filename» (with or without the ".nii.gz" extension), then the series' accession number «an» will be included as well.

Additional parameters can be included via query strings:

• modality : specifies the Modality attribute as well as additional attributes for compliance to that modality (currently only "CT" and "MR" are supported).
• patientName : defines the PatientName attribute, defaults to "Patient^Anonymous"
• patientID : defines the PatientID attribute, defaults to a random UUID.
• institutionName
• manufacturer
• bodyPart

The storage procedure will be delegated to the storage plugin capable of handling storage of the given scheme.

License

Copyright (C) 2017 UA.PT Bioinformatics - http://bioinformatics.ua.pt

dicoogle-nifti is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

dicoogle-nifti is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License along with this program. If not, see http://www.gnu.org/licenses/.

dicoogle-nifti's Issues

Support for storing file as a multi-frame object