01 The User Interface - LICE-dev/swane GitHub Wiki
SWANe includes an easy-to-use interface for managing subject records, importing DICOM images, generating and executing workflow, and exporting results.
The HOME tab of SWANe user interface shows the results of dependency presence and version check processes.
If a dependency is missing or obsolete, an error message and a link to the dependency installation guide are displayed.
If a license or an optional dependency is missing, a warning message and a link to the referred instructions are displayed.
For a complete installation guide, see the Getting Started section of this wiki.
Note
When SWANe starts for the first time, the user needs to choose a main working directory to store the subject subfolders.
The user can change the main working directory in the application preferences.
The user can create or load a subject using the File option on the application menu bar.
Note
The Create new subject option will create a new subject subfolder inside the SWANe main working directory. This subfolder will contain all the results, logs and info related to this subject and the workflows launched on its series (see the Advanced Info section for further details).
After the creation of a subject subfolder, the user can access and modify it using the Load existing subject option and selecting the desired subject subfolder from inside the SWANe main working directory.
A subject tab consists of three subtabs: Data Load , Workflow Execution , and Result export.
In the Data Load subtab, the user can select a local folder or an archive (hard-disk, CD, DVD, pen drive, etc.) to scan for looking for DICOM files.
The found series are listed in the right section of the subtab.
Important
The DICOM files must have the same Subject ID, otherwise SWANe will return an error.
The Subject ID check has been implemented to avoid the erroneous loading of DICOM files referred to different subjects in the same subject folder.
If DICOM files with different Subject IDs refer to the same subject, the workflows can still be executed by placing the files in different folders based on their Subject IDs.
Tip
Some data slots have tooltips to help the User to correctly use them.
Move your mouse cursor on 
symbol, if any, to show the tooltip.
The user can select and copy a series to the subject's chart using one of the Import buttons in the left section.
It is also possible to delete a series from the subject's chart using the Clear button.
Important
The 3D T1w series is mandatory for the start of the workflow.
The Workflow Execution subtab will be accessible after the load of at least the 3D T1w Series in the Data Load subtab.
In the Workflow execution subtab, the user can manage the preferences and execution of workflow types.
It is possible to choose between two sets of preset analyses preferences, labelled as structural and morpho-functional.
Note
At its creation, a subject inherits its Workflow Preferences from the application Default Workflow Preferences the user can set up via the homonym option under the Tools option on the application menu bar.
The user can set up the subject-specific workflow preferences by clicking the Workflow preferences button.
Important
The Subject Workflow Preference Window will show only the tabs relative to a loaded series.
The tabs relative to missing series will be automatically hide.
Important
If an external dependency (e.g.: FreeSurfer for recon-all) or series (e.g.: DTI for tractography) is missing, relative analysis preferences will be disabled.
After setting preferences and clicking the Generate SWANe workflow button, SWANe will show the list of the chosen analyses on the left section of the tab.
The user can select one of the analyses on the left section to expand it, show its step list and display the workflow chart in the right section of the tab.
The user can start the workflow by clicking on the Execute SWANe Workflow button.
SWANe will display a status icon next to the steps of each analysis.
Important
In case of error during the execution of one of the scheduled steps, SWANe will continue with the other analyses, if possible.
The Results export subtab will be accessible after the first successful workflow execution of the subject.
In the Results export subtab, the user can view the results of the tests performed on the subject during the current or previous sessions.
Warning
If the results folder is missing inside the subject folder, this subtab will be disabled until a new workflow execution is completed successfully for the subject.
If the optional external dependency 3D Slicer is installed in the system, the user can export the analyses results to a 3D Slicer scene using the Export results into Slicer scene button.
SWANe will generate a 3D model of the tractography results and display functional maps on cortical surfaces, if available.
The user can customize the application settings using the Tools --> Application Settings window on the application menu bar.
The application settings consist in three subsections:
The base settings of the application.
The options that affect the performance of the analyses.
- Subject tab limit is the maximum number of subjects the user can open at the same time.
- CPU core limit per subject is the maximum analysis steps each subject workflow can execute at the same time.
- CPU management for multicore steps is the performance policy for the parallel capable tools (e.g.: FSL bedpostx).
- Enable CUDA for GPUable commands enables the use of the GPU computing if an NVIDIA GPU is available on the machine.
- GPU process limit per subject is the maximum analysis steps each subject workflow can execute at the same time using the GPU (it should not exceed the number of physical GPU on the machine).
Activates the workflow optional series for:
- 2D Flair
- 2D Coronal
The mail manager configuration window. It can be configured like any other mail client.
- Enabled toggles on/off the mail report sending service. If enabled, a mail report will be sent to the chosen email at each workflow completion.
- Address is the POP3/IMAP address of the mail host.
- Port is the port indicated in the mail host documentation.
- Username is the username used to log into the email. Usually it's the email address (e.g.: [email protected]).
- Password is password used to log into the email. SWANe will encrypt this data to protect it.
- Use SSL allows the activation of SSL security protocol, if required by the mail host.
- Use TLS allows the activation of TLS security protocol, if required by the mail host. Not used if Use SSL is active.
The user can customize the default workflow preferences using the Tools --> Default Workflow Preferences window on the application menu bar.
The default workflow preferences window contains a subsection for each of the analyses that can be managed with SWANe.
At the creation of a subject, the default workflow preferences will be inherited by the specific subject workflow preferences.
The user can customize the subject workflow preferences as explained in the Workflow subtab section.