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https://github.com/enet4/dicoogle-nifti

NIfTI-1 file converter for Dicoogle
https://github.com/enet4/dicoogle-nifti

dicoogle hacktoberfest nifti-format

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NIfTI-1 file converter for Dicoogle

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README 

        
Dicoogle NIFTI converter

========================



[![Java CI with Maven](https://github.com/Enet4/dicoogle-nifti/actions/workflows/maven.yml/badge.svg)](https://github.com/Enet4/dicoogle-nifti/actions/workflows/maven.yml)



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



   file

   1.2.351.472728



```



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 .