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Create Roi Mask

This plugin converts ROI masks saved in rois_series files into 3D masks in the Analyze format. It can process rois_series files from either folders on the system or directly from the Osirix database. The plugin creates a black mask volume containing the white ROIs and saves it with the same dimensions as the input DICOM series in the dir/dcm.hdr and dir/dcm.img files. The resulting masks can then be imported into Osirix for viewing.

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Kendrich
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177 views5 pages

Create Roi Mask

This plugin converts ROI masks saved in rois_series files into 3D masks in the Analyze format. It can process rois_series files from either folders on the system or directly from the Osirix database. The plugin creates a black mask volume containing the white ROIs and saves it with the same dimensions as the input DICOM series in the dir/dcm.hdr and dir/dcm.img files. The resulting masks can then be imported into Osirix for viewing.

Uploaded by

Kendrich
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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CreateROIMask: an Osirix Plugin

Introduction

This Osirix plugin “CreateROIMask” converts rois_series files into 3 dimensional mask saved 
with the Analyze format.

Installation requirements:

­MacOS X 10.5 Leopard. 
­Osirix. To download Osirix go to http://www.osirix­viewer.com/Downloads.html.
This plugin has been tested for Osirix v.3.3.2 32­bit. 

Installation

Double­click the plugin icon and OsiriX will install it for the current user.

Use

1. Organize the data

1. In the case you have folders with rois_series files and dcm files

For each mask that you want to generate, create a new directory dir containing:
⁃ the rois_series files to use to create the mask.
⁃ a sub directory  dcm  containing the dicom series used to create the masks. It can be a 
succession of sub directories: a sub directory, containing another sub directory... with 
dicom files in the last subdirectory.

Folders organization
2. In the case you have data with ROI(s) in the Osirix database

For each mask that you want to create, corresponding to one series of images:
⁃ open the series
⁃ save all the ROIs of the series in a new folder dir (Menu­>ROI­>Save all the ROIs of this 
series...)
⁃ export the series in the folder  dir  (Button “Export” or Menu­>File­>Export­>Export to 
DICOM file(s)) without adding ROIs.

Visualization of the series with ROI(s)

Save all the ROIs in a rois_series file
Export the DICOM files (without ROIs)

2. Run the plugin

⁃ Run Osirix
⁃ Click in the menu on “Plugins­>Database­>CreateROImask­>From Folders”.
⁃ A panel appears: select the directories where are located the rois_files to convert. Press 
the “Ok” button. Be careful,  the dicom directory must only contains  dicom files  (no 
hidden files), if it is not the case some errors could occur.
⁃ The process starts.
⁃ A final message will pop up to indicate if any errors occurred. 

For more details about how to run the plugin, please read the Example documentation.

If   you   want   to   see   the   Log   messages   (and   error   messages),   you   can   launch   the   Console 
application (that you can find in Applications/Utilities) while working with Osirix.

Run the plugin CreateROIMask “From Folders”
Select directories containing the rois_series and DICOM files

End of the conversion

3. Results

For   each   selected   directory,   the   process   will   create   a   3   dimensional   mask   using   the   same 
dimensions than the dicom series (volume dimensions and voxel dimensions). The created mask 
is a black volume containing white ROIs corresponding to the ROIs saved in the rois_series files. 
This mask will be saved in Analyze format in the files  dir/dcm.hdr  and  dir/dcm.img  (dir: the 
name   of   the   directory   containing   the   rois_series   files,  dcm:   the   name   of   the   sub   directory 
containing the dicom).

If the directory does not contain any rois_series files, nothing happens.
Careful: if the directory dir already contains a dcm.hdr and  dcm.img files, they will be replaced!

You can visualize the result in Osirix by importing it: click on “import”, select the .hdr: the mask 
will be added to your database.
Import the results

Select the .hdr created during the conversion

Visualize the results: on the left the created mask, on the right the dicom with the ROI

Contact

This plugin has been created by Aurelie Canale – Asclepios team – INRIA Sophia­Antipolis.
To   have   any   further   information   you   can   send   an   email   to   the   mailing   list  osirixplugin­
[email protected]. 

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