PySiSyphe file extensions

All PySiSyphe files are saved in XML text format.

.xbval

It records a list of diffusion gradient B-values. This file is created automatically during the DICOM conversion of diffusion-weighted series. It can also be created from the Gradients menu.

.xbvec

It records a list of diffusion gradient B-vectors. This file is created automatically during the DICOM conversion of diffusion-weighted series. It can also be created from the Gradients menu.

.xdcm

This file is associated with a PySisyphe volume (.xvol) when converted from DICOM series (Dicom import). It contains all non-private DICOM fields. It can be viewed using the XML Dicom attributes menu.

.xdmodel

This file stores a diffusion model that is processed from the Diffusion model menu.

.xfid

This file is associated with a PySisyphe volume (.xvol) after a stereotactic frame is detected using the Stereotactic frame detection menu. It records the position of each detected fiducial marker in the world coordinate system (in mm, according to the LPS+ convention).

.xlabels

This file is associated with a PySisyphe volume (.xvol) with the LB modality, i.e., label image. It stores a dictionary that lists the label names associated with each numeric label index value.

.xline

This is a trajectory tool associated with a PySisyphe volume (.xvol). It can be displayed in the Orthogonal view of the central area. It is loaded from the Target/Trajectory tab of the dock.

.xlut

This is the native format for storing PySisyphe LUT colormaps; it records a list of 256 RGB colors. You can create or edit a LUT from the Edit LUT menu.

.xmodel

This file records a voxel-by-voxel statistical GLM model. It is created from the fMRI model definition or General linear model definition menu.

.xpoint

This file stores a target tool associated with a specific PySisyphe volume (.xvol). It can be displayed in the Orthogonal view of the central area. It is loaded from the Target/Trajectory tab of the dock.

.xmesh

This is the native format for storing PySisyphe mesh. Meshes are displayed in the Orthogonal view of the central area. They are loaded from the Mesh tab of the dock.

.xroi

This is the native format for storing the region of interest (ROI) associated with a particular PySisyhe volume (.xvol). ROIs are displayed in the Slice view and/or Synchronized view of the central area. They are loaded from the ROI tab of the dock.

.xsheet

This is the native format for storing an array of numeric values.

.xstruct

This file stores the parameters for segmenting a specific anatomical structure from the Registration based segmentation menu. It is saved in the ~/.PySisyphe/segmentation folder by default.

.xtools

It records a list of target and/or trajectory tools. These tools can be displayed in the Orthogonal view of the central area. They are loaded from the Target/Trajectory tab of the dock.

.xtract

This is the native format for storing a list of streamlines, i.e., a tractogram. This file is created from the tractogram generation menu. Streamlines are displayed in the Orthogonal view of the central area. They are loaded from the Tracking tab of the dock.

.xtrf

This file records a geometric transformation between a fixed reference volume and a moving volume.

.xtrfs

This file is associated with a PySisyphe volume (.xvol) and records a list of geometric transformations between this volume and all volumes with which it has been co-registered.

.xvol

This is the native format for storing a PySisyphe volume.

.xwflow

This file records a list of PySisyphe processing to run in batch mode. This file is created from the Workflows menu. It is saved in the ~/.PySisyphe/workflows folder by default.

PySiSyphe files

.PySisyphe folder

It is located in the user folder (C:UsersYourUsername in windows platform, /Users/YourUsername in mac os platform and /home/YourUsername in linux platform). It can be quickly opened in the OS platform’s file manager by selecting the menu Open user folder. It contains configuration files (functions.xml, settings.xml), a log file (PySisyphe.log), and a file listing the most recently opened volumes (recent.xml).

Eight default subdirectories are provided for storing user data:

/controls: control populations for 3D T1 MR, FDG PET, and HMPAO SPECT can be downloaded from the Download manager menu. These files are saved to this folder by default.
/database: PySisyphe provides a patient database manager (Download manager). It is stored in this directory by default.
/dicom: this directory is intended for storing PySisyphe volumes generated from the conversion of DICOM series (Dicom import).
/models: this is the default directory used to save user-defined voxel-by-voxel statistical models (fMRI model definition or General linear model definition). There is a shortcut Models menu for quickly opening these models in PySisyphe.
/prompts: this directory is intended for storing gemini prompts that are generated from PySisyphe (Gemini prompt).
/samples: various sample volumes can be downloaded from the Download manager menu for testing PySisyphe.
/segmentation: this is the default directory where user-defined settings for segmenting (Registration based segmentation) a specific anatomical structure are saved. There is a shortcut Structs menu for quickly opening the anatomical structure parameters in the Registration based segmentation interface.
/workflows: this is the default directory where batch processing files (.xwflow files) generated from the Workflow processing menu are stored. There is a shortcut Models menu for quickly opening these workflows in the Workflow processing interface.

PySisyphe.log

This file is located in the ~/.PySisyphe folder. It stores user actions and the traceback details when an unhandled exception occurs. Please send this file to the contact email address pysisyphe@gmail.com when you wish to report a bug.

functions.xml

This file is located in the ~/.PySisyphe folder. It stores the default settings for most PySisyphe functions. These settings can be edited from the Preferences menu. It is not recommended to edit this file directly because the software will no longer work if the file becomes corrupted. In that case, delete this file, and a new default file will be created the next time the application is launched.

recent.xml

This file is located in the ~/.PySisyphe folder. It lists the most recently edited volumes. There is a shortcut Open recent menu for quickly opening these volumes in PySisyphe.

settings.xml

This file is located in the ~/.PySisyphe folder. It stores the default settings for the PySisyphe graphic user interface. These settings can be edited from the Preferences menu. It is not recommended to edit this file directly because the software will no longer work if the file becomes corrupted. In that case, delete this file, and a new default file will be created the next time the application is launched.