SWANe main config file

All SWANe application preferences are stored in a .SWANe hidden text file contained in the $HOME directory.

If a conflict occurs during the SWANe execution, the User can refresh the application to the default status by deleting this file. SWANe will create a new .SWANe text file with the default preferences at the next start.

Moreover, you can manually change each preference (at your own risk).

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The subject folder tree

At the creation of a new subject, SWANe sets up its folder tree inside the software main working directory.

The subject folder tree contains the results of the analyses launched on the subject DICOM files and a wide variety of information that can be useful for whom wants to better understand the SWANe functionalities.

Each subject folder contains a hidden .config text file. This file stores all the analyses options set via the Workflow Preferences window.

Deleting this file will reset all the subject options to default.

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The DICOM folder

The DICOM folder is the storage of the DICOM files added to the subject in the Data Load subtab.

This folder contains a subfolder for each type of analysis that can be done with SWANe.

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The Graph folder

The Graph folder contains the images of the analysis algorithms launched on the subject.

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The Log folder

The Log folder contains the log of the analysis done on the subject and their crash reports.

[!TIP] It is good practice to attach the log file and the crash reports to any bug reports to allow SWANe developers to understand the issue you are encountering.

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The Nipype folder

The Nipype folder is the storage of the commands and the algorithm operations of each analysis.

[!TIP] For those interested in more details about the operations of SWANe and the external libraries used (FSL, FreeSurfer, etc.), it is possible to read the full command launched by SWANe reading the file command.txt

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The Results folder

The Results folder contains the outputs of all the completed SWANe analyses for the subject.

This folder also stores the 3D Slicer scene file, if exported.

Deleting this folder will disable the Results subtab for the referred subject.