MRI File Manager (IRMaGe)

Installation - Launching of the software - ImageJ plugins

Installation

This section explains how to install MRI File Manager

Firstly, make sure to have Java 8 (or more) installed on your machine (help here)
Download MRI File Manager here
Unzip the archive in the folder of your choice.

Launching of the software

This section explains how to launch MRI File Manager:
    - in standalone mode (with GUI)
    - by script (with GUI)
    - by script in windowless mode (without GUI).

In standalone mode:

You can double-click directly on the MRIManager.jar file.

But it's better to use batch file ( MRIManager.bat for Windows) or shell (MRIManager.sh for Linux and MacOS), the reasons are :
    - to show error messages in the terminal
    - you can force to exit software when crashed (by closing terminal)
    - you can allocate memory for classes of Java

Edit the MRIManager.bat or MRIManager.sh file according to your operating system (with a simple text editor):
```
java -Xms512m -Xmx4096m -jar MRIManager.jar
```
- Xms specifies the initial memory allocation pool for a Java virtual machine (JVM) (keep the default value 512m)
- Xmx specifies the maximum memory allocation pool, set the value 1/2 of the total RAM memory of your machine (for example 4096m for 8Go of RAM)

Launch the batch or shell file in a terminal:
```
C:\Program Files\MFM_Irmage\MRIFileManager> MRIManager.bat 		(Windows)
```
```
wiki@ubuntu:~/MRIFileManager$ ./MRIManager.sh 		(Linux, Mac)
```

By script (with GUI):

You can launch MRI File Manager through another application by script with some options. In this instance, some functions are deactivated.

usage :

 java -Xms512m -Xmx4096m -jar MRIManager.jar [options]

options :

'[ExportNifti] <repertory>'	(1)
'[ExportToMP3] <string>'	(2)
'CloseAfterExport'	(3)
'NoLogExport'	(4)
'[LookAndFeel] <string>'	(5)
'NoExitSystem'	(6)
'[ExportOptions] <integer>'	(7)
'[ProjectsDir] <string>'	(8)

(1)	java -Xms512m -Xmx4096m -jar MRIManager.jar '[ExportNifti] C:\\Users\\Documents\\DataIRM\\NifTI'
(2)	java -Xms512m -Xmx4096m -jar MRIManager.jar '[ExportToMP3] PatientName-StudyName-CreationDate- SeqNumber-Protocol-SequenceName-AcquisitionTime'
(3)	java -Xms512m -Xmx4096m -jar MRIManager.jar 'CloseAfterExport'
(4)	java -Xms512m -Xmx4096m -jar MRIManager.jar 'NoLogExport'
(5)	java -Xms512m -Xmx4096m -jar MRIManager.jar '[LookAndFeel] com.sun.java.swing.plaf.windows.WindowsLookAndFeel'
(6)	java -Xms512m -Xmx4096m -jar MRIManager.jar 'NoExitSystem'
(7)	java -Xms512m -Xmx4096m -jar MRIManager.jar '[ExportOptions] 00000'
(8)	java -Xms512m -Xmx4096m -jar MRIManager.jar '[ProjectsDir] //home//user//Documents'

examples :

Python

 import subprocess
 subprocess.call(['java','-Xms512M','-Xmx4096M','-jar','MRIManager.jar',options])

By script in windowless mode (without GUI):

You can launch MRI File Manager by script without opening its GUI. In the command line, arguments are the list of files to convert, the conversion directory and the naming. An export option must also be added.

usage : (The current version of the software allows for the moment only the conversion Bruker and Philips files in windowless mode)

 java -classpath MRIManager.jar BrukerToNifti "file1;file2;..." "export directory" "nifti files naming" [options]

 java -classpath MRIManager.jar PhilipsToNifti "file1;file2;..." "export directory" "nifti files naming" [options]

list of files to convert : list of files or directories separated by the character ';'.
Bruker : 2dseq files (file by file) or subject files (all sequences).
Philips : *.REC files (file by file) or directory containing all the PAR/REC or XML/REC files.

export directory : directory where the exported files should be saved

nifti files naming : only the following terms can be used : 'PatientName', 'StudyName', 'CreationDate', 'SeqNumber', 'Protocol', 'SequenceName', 'AcquisitionTime'. Use slash (/) to indicate the directory and a separating charactere in the name of file ('-' or '_' character advised)

[options] : [ExportOptions] 00000 (put 00013 if you want generate bvecs/bvals files for diffusion sequences)

Examples (Click on the image to enlarge)
Bruker		Philips
with subject files with 2dseq files		with directory containing all the PAR/REC or XML/REC files with *.REC files

ImageJ plugins

For ImageJ users, it's possible to install his plugins in the 'dist' folder of MRI File Manager

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