Registration menu
Stereotactic frame detection
This menu is used for detecting fiducial markers of a Leksell stereotaxic frame.
A file selection dialog box appears first, and it allows you to choose a stereotactic PySisyphe volume (usually MR or CT modality).
Then, a dialog box is displayed to control the detection of the fiducial markers. This dialog box displays the volume in a Slice view widget with cross-shaped target tools located in front of each detected fiducial marker. A detection error is displayed next to each tool. If necessary, you can use the mouse to adjust the position of target tools relative to the fiducial markers.
Left-click 
in the icon bar and select a fiducial marker in the popup menu to zoom in on it. This allows for precise adjustment of the tool’s position relative to the fiducial marker.
Left-click 
in the icon bar to restore the original zoom.
Left-click Remove current slice markers button to remove all target tools from the currently displayed slice. The dialog box of error statistics is displayed after this action (see below).
Left-click Remove front plate markers button to remove all target tools from the front plate’s fiducial markers, if they exist, because they are not always installed. Their inclusion is optional in the calculation of the geometric transformation that defines the stereotactic space. The dialog box of error statistics (see below) is displayed after this action.
Left-click Calc geometric transform button to calculate the geometric transformation that defines the stereotactic space with the current position of the target tools in front of the fiducial markers. The dialog box of error statistics is displayed after this action (see below).
Left-click Error statistics button to show statistics relating to fiducial marker position errors. This information is displayed in a dialog box with a stack of tabbed widgets. The first tab Global error shows a box and whisker plot of fiducial marker position errors, and below, a table of descriptive statistics (mean, root mean square, median, standard deviation, 25th percentile, 75th percentile, minimum and maximum). The second tab Errors shows the variation curves of the error for each fiducial marker as a function of the slice level, from bottom to top, and below, a table of errors (columns = fiducial marker, rows = slice level). This makes it possible to identify the slices with the most significant errors, which can then be excluded, if necessary, to improve the results. Acceptable values are less than 1.0 mm for both the mean and RMS error.
Left-click OK button to save the stereotactic space information and close the dialog box. Two XML files are saved in the same folder and under the same name as the stereotactic volume. The first one, which has the xfid extension, saves the coordinates of the fiducial markers. The second one, with the xtrfs extension, saves the geometric transformation that defines the stereotactic space (XML node with LEKSELL ID).
Left-click Cancel button to close the dialog box without saving the stereotactic space information.
AC-PC selection
This menu is used to define anterior (AC) and posterior commissures (PC), which are anatomical landmarks used in various neurosurgical procedures.
A file selection dialog box appears first, and it allows you to choose a PySisyphe volume (.xvol).
A dialog box is then displayed to define anterior (AC) and posterior commissures (PC). This dialog displays the volume in an Orthogonal view widget widget with a cross-shaped cursor. Left-click in the view to change the cursor position.
A button bar is displayed below the view:
Left-click Lut button to popup a LUT widget.
Select AC-PC selection checkbox to activate AC-PC selection mode. In this mode, left click Set AC to define anterior commissure at the current cursor position. Left-click Get AC to move the cursor to the defined anterior commissure coordinates. Anterior commissure coordinates are displayed next to the “Get AC” button. The same buttons Set PC and Get PC are available for the posterior commissure.
Select Rotations checkbox to activate reorientation mode and set midline rotations in the axial and coronal planes. The cross-shaped cursor is centered on the center of rotation, which is placed at the mid AC-PC point. Place the mouse pointer over a cross-shaped cursor line, press the left mouse button, and drag to adjust the rotation axis in axial or coronal view (sagittal axis is locked between AC and PC). Left click Set rotations to define rotations at the current axial and coronal axis orientations. Rotations values, in degrees, are displayed next to the Set rotations button. Left-click Reset to cancel axis rotations, and the axes will return to their default vertical orientation.
The cross-shaped cursor opacity, and line width can be customized using the last two widgets.
Left-click OK button to save AC-PC coordinates and axis rotations. These information are stored as attributes in the PySisyphe volume file (.xvol).
Left-click Cancel button to the close dialog box without saving AC-PC information.
Volume reorientation
This menu is used to perform interactive manual reorientation of a volume using translations and rotations. It also allows you to modify the field of view (FOV).
A file selection dialog box appears first, and it allows you to choose a PySisyphe volume (.xvol).
A dialog box is then displayed for reorientation. It displays the volume in an Orthogonal view widget widget with a cross-shaped cursor centered in a rectangular box representing the edges of the field of view (zoom out if necessary to see the entire rectangular box). Place the mouse pointer close to the intersection of the cross-shaped cursor lines, press the left mouse button, and drag to move the FOV (i.e. translations). Place the mouse pointer over a cross-shaped cursor line away from the intersection, press the left mouse button, and drag to rotate the FOV.
A button bar is displayed below the view:
Left-click Lut button to popup a LUT widget.
Image size (i.e. matrix size, number of voxels in each axis) and spacing (i.e. voxel size in mm, in each axis) can be edited in spin boxes to adjust the FOV. The rectangular box representing the edges of the field of view is updated after each adjustment.
Left-click Reset FOV to undo the modifications to the size and spacing.
Left-click Reset Transform to undo FOV translations and rotations.
The cross-shaped cursor/rectangular box opacity, and line width can be customized using the last two widgets.
Left-click Resample to resample the volume with the new FOV position and orientation. A file dialog box is displayed to choose the name of the saved file. By default, it’s the same as the original prefixed with “r_”.
Left-click Exit button to close dialog box.
Manual registration
This menu is used for interactive manual coregistration of two volumes.
A file selection dialog box appears first, and it allows you to select fixed and moving PySisyphe volumes (.xvol).
A Manual registration dialog box is then displayed for co-registration. It shows the fixed volume overlaid by the moving volume in an Orthogonal view widget widget. Place the mouse pointer in the central area of each view, press the left mouse button, and drag to move the floating volume. Place the mouse pointer in the peripheral area of each view, press the left mouse button, and drag to rotate the floating volume.
A button bar is displayed below the view:
You can modify the display mode using the first combobox. In edge mode, the fixed volume is replaced by its gradient magnitude (edges). In edge and native mode, the gradient magnitude image of the fixed volume is added and overlaid in front of fixed and moving volumes.
Check Crop box to display a square box with the fixed volume inside and the moving volume outside. Place the mouse pointer inside the box, press the left mouse button, and drag to move the crop box. Place the mouse on the edge of the box, press the left mouse button, and drag to enlarge or reduce the crop box area.
Check Registration area box to display a rectangular box representing the edges of the fixed volume FOV.
Various arrow buttons are displayed at the bottom of each view to apply translations, and rotations, in the direction indicated by these arrows. Left-click on one of these buttons to trigger a translation with a step size, in mm, set in the spin box.
Moving volume opacity can be adjusted using the slider.
Left-click Fixed button to popup a LUT widget.
Left-click Moving button to popup a LUT widget.
You can select the interpolation algorithm (linear, nearest neighbor, b-spline, gaussian, hamming windowed sinc, cosine windowed sinc, welch windowed sinc, lanczos windowed sinc, blackman windowed sinc) used to resample the moving volume with the next combobox.
Left-click Auto button to initialize the alignment of volumes on the FOV centers (default) or on the centers of mass.
Left-click Reset button to undo moving volume translations and rotations.
Check Tooltip off to stop displaying tooltips in the view.
Left-click Resample to resample the moving volume. A file dialog box is displayed to choose the name of the saved file. By default, it’s the same as the original prefixed with “r_”.
Left-click Exit button to close dialog box.
Rigid registration
This menu is used for rigid coregistration, which involves three translations and three rotations, of a moving volume onto a fixed volume, using ANTs registration methods. The ANTs toolkit provides a hierarchy of transformations with adjustable levels of complexity, regularization, degrees of freedom and behavior as optimizers. ANTs provides 3 similarity metrics optimized by the rigid registration algorithm: mean squares, cross-correlation and mutual information.
Rigid transformation is an effective method for coregistering intra or inter-modality volumes of the same subject.
The Rigid registration dialog box is displayed.
Use the file selection widgets at the top to select Fixed and Moving PySisyphe volumes.
Toggle Apply transformation to checkbox to resample a list of volumes with the calculated geometric transformation. This displays a Multiple file selection. Selected volumes must have the same space/transform ID as the fixed volume (i.e. same FOV and already coregistered to the fixed volume).
Toggle Registration… button to show/hide corgistration settings:
Check Fixed volume mask to remove background voxels during coregistration processing.
Select method used to initialize translations with the Estimation combobox: FOV center alignment (default), center of mass alignment or no estimation (translations and rotations to 0.0).
Select the rigid registration algorithm using the Rigid combobox.: AntsRigid (4 multiresolution stages with last at full resolution) or AntsFastRigid (fast scheme with only 3 multiresolution stages, and no iteration at full resolution).
Select the similarity metric to optimize using the Linear metric combobox: IM (i.e. mutual information, default), CC (i.e. cross-correlation), MS (i.e. mean squares).
Select the subsampling used to calculate similarity function using the Sampling rate spinbox. The range is between 1.0 (no subsampling, all voxels are used to process similarity function) and lower values, which are greater than 0.0 and indicate the ratio of voxels used to process the similarity function under regular subsampling.
Toggle Check registration checkbox to display a dialog box, similar to Manual registration, to visually assess the quality of the coregistration.
Toggle Resample checkbox to resample (or not) the coregistered moving volume. If not, the moving volume is not resampled, but the associated XML xtrfs files are updated (geometric transformation for fixed volume coregistration will be added to the moving xtrfs, and geometric transformation for moving volume coregistration will be added to the fixed xtrfs).
Toggle Resample… button to show/hide resampling settings: - Select the interpolation algorithm (linear, nearest neighbor, b-spline, gaussian, hamming windowed sinc, cosine windowed sinc, welch windowed sinc, lanczos windowed sinc, blackman windowed sinc) used to resample the moving volume. - Resampled moving volume is saved with its original file name, which is prefixed and/or suffixed by the strings edited in the prefix and suffix parameters.
Left-click Execute button to perform coregistration. The moving volume is resampled if the Resample checkbox is checked. PySisype XML xtrfs files associated with fixed and moving volumes are updated to store geometric transformations (geometric transformation for fixed volume coregistration will be added to the moving xtrfs, and geometric transformation for moving volume coregistration will be added to the fixed xtrfs).
Left-click Cancel button to close dialog box without coregistration.
Affine registration
This menu is used for affine coregistration of a moving volume onto a fixed volume using ANTs registration methods. This process involves twelve parameters: three translations and nine linear matrix parameters for rotation, scaling, and shearing. The ANTs toolkit provides a hierarchy of transformations with adjustable levels of complexity, regularization, degrees of freedom and behavior as optimizers. ANTs provides 3 similarity metrics optimized by the affine registration algorithm: mean squares, cross-correlation and mutual information.
Affine transformation is an effective method for coregistering inter-modality volumes of the same subject, to compensate for the overall distortions caused by certain acquisition modalities (SPECT/PET versus MR, MR versus CT) or sequences (EPI/Diffusion MR versus 3D T1 MR). It can be also used for intra-modality/inter-subject coregistration of low-resolution modalities (SPECT).
The Affine registration dialog box is displayed.
Use the file selection widgets at the top to select Fixed and Moving PySisyphe volumes.
Toggle Apply transformation to checkbox to resample a list of volumes with the calculated geometric transformation. This displays a Multiple file selection. Selected volumes must have the same space ID as the fixed volume (i.e. same FOV and already coregistered to the fixed volume).
Toggle Registration… button to show/hide coregistration settings:
Check Fixed volume mask to remove background voxels during registration processing.
Select method used to initialize translations with the Estimation combobox: FOV center alignment (default), center of mass alignment or no estimation (translations and rotations to 0.0).
Select the affine registration algorithm using the Affine combobox.: AntsAffine (4 multiresolution stages with last at full resolution) or AntsFastAffine (fast scheme with only 3 multiresolution stages, and no iteration at full resolution).
Select the similarity metric to optimize using the Linear metric combobox: IM (i.e. mutual information, default), CC (i.e. cross-correlation), MS (i.e. mean squares).
Select the subsampling used to calculate similarity function using the Sampling rate spinbox. The range is between 1.0 (no subsampling, all voxels are used to process similarity function) and lower values, which are greater than 0.0 and indicate the ratio of voxels used to process the similarity function under regular subsampling.
Toggle Check registration checkbox to display a dialog box, similar to Manual registration, to visually assess the quality of the coregistration.
Toggle Resample checkbox to resample (or not) the coregistered moving volume. If not, the moving volume is not resampled, but the associated XML xtrfs files are updated (geometric transformation for fixed volume coregistration will be added to the moving xtrfs, and geometric transformation for moving volume coregistration will be added to the fixed xtrfs).
Toggle Resample… button to show/hide resampling settings:
Select the interpolation algorithm (linear, nearest neighbor, b-spline, gaussian, hamming windowed sinc, cosine windowed sinc, welch windowed sinc, lanczos windowed sinc, blackman windowed sinc) used to resample the moving volume.
Resampled moving volume is saved with its original file name, which is prefixed and/or suffixed by the strings edited in the prefix and suffix parameters.
Left-click Execute button to perform coregistration. The moving volume is resampled if the Resample checkbox is checked. PySisyphe XML xtrfs files associated with fixed and moving volumes are updated to store geometric transformations (geometric transformation for fixed volume coregistration will be added to the moving xtrfs, and geometric transformation for moving volume coregistration will be added to the fixed xtrfs).
Left-click Cancel button to close dialog box without coregistration.
Displacement field registration
This menu is used for displacement field coregistration of a moving volume onto a fixed volume using ANTs registration methods. This non linear method provides local/dense/high-dimensionaltiy transformation via a a displacement field. The displacement field stores 3D vectors of displacements. Transformation is performed at a given point by adding the displacement at that point to the input point. The ANTs toolkit provides a hierarchy of transformations with adjustable levels of complexity, regularization, degrees of freedom and behavior as optimizers. ANTs provides 4 similarity metrics optimized by the displacement field coregistration algorithm: mean squares, cross-correlation, mutual information and and demons.
Reference
Article: Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain. BB Avants, CL Epstein, M Grossman, JC Gee. Med Imag Anal. 2008 Feb, 12(1):26-41.
Displacement field transformation is an effective method for inter-subject coregistration of high-resolution modalities (MR).
The Displacement field registration dialog box is displayed.
Use the file selection widgets at the top to select Fixed and Moving PySisyphe volumes.
Toggle Apply transformation to checkbox to resample a list of volumes with the calculated geometric transformation. This displays a Multiple file selection. Selected volumes must have the same space/transform ID as the fixed volume (i.e. same FOV and already coregistered to the fixed volume).
Toggle Registration… button to show/hide coregistration settings:
Check Fixed volume mask to remove background voxels during registration processing.
Select method used to initialize translations with the Estimation combobox: FOV center alignment (default), center of mass alignment or no estimation (translations and rotations to 0.0).
Select the displacement field registration algorithm using the Displacement field combobox:
AntsSplineDiffeomorphic: affine step followed by diffeomorphic step, displacement field modelled using B-spline basis functions, 4 multiresolution stages with last at full resolution.
AntsDiffeomorphic: affine step followed by diffeomorphic step, displacement field optimized at voxel level, 4 multiresolution stages with last at full resolution.
AntsFastSplineDiffeomorphic: affine step followed by diffeomorphic step, displacement field modelled using B-spline basis functions, fast scheme with only 3 multiresolution stages, and no iteration at full resolution.
AntsFastDiffeomorphic: affine step followed by diffeomorphic step, displacement field optimized at voxel level, fast scheme with only 3 multiresolution stages, and no iteration at full resolution.
AntsRigidSplineDiffeomorphic: rigid step (no affine step) followed by diffeomorphic step, displacement field modelled using B-spline basis functions, 4 multiresolution stages with last at full resolution.
AntsRigidDiffeomorphic: rigid step (no affine step) followed by diffeomorphic step, displacement field optimized at voxel level, 4 multiresolution stages with last at full resolution.
AntsFastRigidSplineDiffeomorphic: rigid step (no affine step) followed by diffeomorphic step, displacement field modelled using B-spline basis functions, fast scheme with only 3 multiresolution stages, and no iteration at full resolution.
AntsFastRigidDiffeomorphic: rigid step (no affine step) followed by diffeomorphic step, displacement field optimized at voxel level, fast scheme with only 3 multiresolution stages, and no iteration at full resolution.
AntsSplineDiffeomorphicOnly: single step of diffeomorphic coregistration without previous rigid of affine step, displacement field modelled using B-spline basis functions, 4 multiresolution stages with last at full resolution.
AntsDiffeomorphicOnly: single step of diffeomorphic coregistration without previous rigid of affine step, displacement field optimized at voxel level, 4 multiresolution stages with last at full resolution.
Select the similarity metric to optimize linear stage (rigid/affine) using the Linear metric combobox: IM (i.e. mutual information, default), CC (i.e. cross-correlation), MS (i.e. mean squares).
Select the similarity metric to optimize non-linear stage (displacement field) using the Non linear metric combobox: IM (i.e. mutual information, default), CC (i.e. cross-correlation), MS (i.e. mean squares), DEMONS.
Select the subsampling used to calculate similarity function using the Sampling rate spinbox. The range is between 1.0 (no subsampling, all voxels are used to process similarity function) and lower values, which are greater than 0.0 and indicate the ratio of voxels used to process the similarity function under regular subsampling.
Toggle Save inverse displacement field checkbox to save the inverse displacement field that coregisters the fixed volume to the moving volume.
Toggle Check registration checkbox to display a dialog box, similar to Manual registration, to visually assess the quality of the coregistration.
Toggle Resample checkbox to resample (or not) the coregistered moving volume. If not, the moving volume is not resampled, but the associated XML xtrfs files are updated (geometric transformation for fixed volume coregistration will be added to the moving xtrfs, and geometric transformation for moving volume coregistration will be added to the fixed xtrfs) and the displacement field is saved as a PySisyphe volume file (.xvol).
Toggle Resample… button to show/hide resampling settings:
Select the interpolation algorithm (linear, nearest neighbor, b-spline, gaussian, hamming windowed sinc, cosine windowed sinc, welch windowed sinc, lanczos windowed sinc, blackman windowed sinc) used to resample the moving volume.
Resampled moving volume is saved with its original file name, which is prefixed and/or suffixed by the strings edited in the prefix and suffix parameters.
Left-click Execute button to perform coregistration. The moving volume is resampled if the Resample checkbox is checked. PySisyphe XML xtrfs files associated with fixed and moving volumes are updated to store geometric transformations (geometric transformation for fixed volume coregistration will be added to the moving xtrfs, and geometric transformation for moving volume coregistration will be added to the fixed xtrfs) and the displacement field is saved as a PySisyphe volume file (.xvol).
Left-click Cancel button to close dialog box without coregistration.
ICBM spatial normalization
This menu is used for spatial normalization in the MNI-ICBM152 atlas space (see ICBM152 page) of a moving volume using ANTs registration methods. Symmetric and asymmetric versions of MNI-ICBM152 templates are provided for various modalities (MR, CT, SPECT, and PET) and sequences (T1, T2, PD, FLAIR, TOF, GM, WM, and CSF). These templates are used as fixed volumes in coregistration processing.
The ICBM normalization dialog box is displayed.
Use the file selection widgets at the top to select Moving and Template PySisyphe volumes (.xvol). If an MNI-ICBM152 template is defined for this fixed-volume modality/sequence in the PySisyphe settings (see Preferences), it is automatically added to the template selection widget.
Toggle Apply transformation to checkbox to resample a list of volumes with the calculated geometric transformation. This displays a Multiple file selection. Selected volumes must have the same space/transform ID as the fixed volume (i.e. same FOV and already coregistered to the fixed volume).
Toggle Registration… button to show/hide coregistration settings:
Check Fixed volume mask to remove background voxels during registration processing.
Select method used to initialize translations with the Estimation combobox: FOV center alignment (default), center of mass alignment or no estimation (translations and rotations to 0.0).
Select the registration algorithm using the Transform combobox:
AntsAffine: single step of affine coregistration (no diffeomorphic step), 4 multiresolution stages with last at full resolution.
AntsFastAffine: single step of affine coregistration (no diffeomorphic step), fast scheme with only 3 multiresolution stages, and no iteration at full resolution.
AntsSplineDiffeomorphic: affine step followed by diffeomorphic step, displacement field modelled using B-spline basis functions, 4 multiresolution stages with last at full resolution.
AntsDiffeomorphic: affine step followed by diffeomorphic step, displacement field optimized at voxel level, 4 multiresolution stages with last at full resolution.
AntsFastSplineDiffeomorphic: affine step followed by diffeomorphic step, displacement field modelled using B-spline basis functions, fast scheme with only 3 multiresolution stages, and no iteration at full resolution.
AntsFastDiffeomorphic: affine step followed by diffeomorphic step, displacement field optimized at voxel level, fast scheme with only 3 multiresolution stages, and no iteration at full resolution.
Select the similarity metric to optimize linear stage (rigid/affine) using the Linear metric combobox: IM (i.e. mutual information, default), CC (i.e. cross-correlation), MS (i.e. mean squares).
Select the similarity metric to optimize non-linear stage (displacement field) using the Non linear metric combobox: IM (i.e. mutual information, default), CC (i.e. cross-correlation), MS (i.e. mean squares), DEMONS.
Select the subsampling used to calculate similarity function using the Sampling rate spinbox. The range is between 1.0 (no subsampling, all voxels are used to process similarity function) and lower values, which are greater than 0.0 and indicate the ratio of voxels used to process the similarity function under regular subsampling.
Toggle Save inverse displacement field checkbox to save the inverse displacement field that coregisters the template volume to the moving volume.
Toggle Check registration checkbox to display a dialog box, similar to Manual registration, to visually assess the quality of the coregistration.
Toggle Resample checkbox to resample (or not) the coregistered moving volume. If not, the moving volume is not resampled, but the associated XML xtrfs file is updated (geometric transformation for fixed volume coregistration will be added to the moving xtrfs) and the displacement field is saved as a PySisyphe volume file (.xvol).
Toggle Resample… button to show/hide resampling settings:
Select the interpolation algorithm (linear, nearest neighbor, b-spline, gaussian, hamming windowed sinc, cosine windowed sinc, welch windowed sinc, lanczos windowed sinc, blackman windowed sinc) used to resample the moving volume.
Resampled moving volume is saved with its original file name, which is prefixed and/or suffixed by the strings edited in the prefix and suffix parameters.
Left-click Execute button to perform spatial normalization. The moving volume is resampled if the Resample checkbox is checked. PySisyphe XML xtrfs files associated with moving volume is updated to store geometric transformation (geometric transformation for template volume coregistration will be added to the moving xtrfs) and the displacement field is saved as a PySisyphe volume file (.xvol).
Left-click Cancel button to close dialog box without coregistration.
Batch registration
The batch processing of this menu involves the coregistration of multiple volumes to a single fixed volume.
The Batch registration dialog box is displayed.
Use the Single file selection widget at the top to select Fixed PySisyphe volume. Use the Multiple file selection widget to select Moving volumes.
Toggle Registration… button to show/hide coregistration settings:
Check Fixed volume mask to remove background voxels during registration processing.
Select method used to initialize translations with the Estimation combobox: FOV center alignment (default), center of mass alignment or no estimation (translations and rotations to 0.0).
Use the Batch combobox to select the type of coregistration: rigid, affine, or displacement field.
Select the coregistration algorithm using the Rigid/Affine/Displacement field combobox:
AntsRigid: single step of rigid coregistration (no diffeomorphic step), 4 multiresolution stages with last at full resolution.
AntsFastRigid: single step of rigid coregistration (no diffeomorphic step), fast scheme with only 3 multiresolution stages, and no iteration at full resolution.
AntsAffine: single step of affine coregistration (no diffeomorphic step), 4 multiresolution stages with last at full resolution.
AntsFastAffine: single step of affine coregistration (no diffeomorphic step), fast scheme with only 3 multiresolution stages, and no iteration at full resolution.
AntsSplineDiffeomorphic: affine step followed by diffeomorphic step, displacement field modelled using B-spline basis functions, 4 multiresolution stages with last at full resolution.
AntsDiffeomorphic: affine step followed by diffeomorphic step, displacement field optimized at voxel level, 4 multiresolution stages with last at full resolution.
AntsFastSplineDiffeomorphic: affine step followed by diffeomorphic step, displacement field modelled using B-spline basis functions, fast scheme with only 3 multiresolution stages, and no iteration at full resolution.
AntsFastDiffeomorphic: affine step followed by diffeomorphic step, displacement field optimized at voxel level, fast scheme with only 3 multiresolution stages, and no iteration at full resolution.
AntsRigidSplineDiffeomorphic: rigid step (no affine step) followed by diffeomorphic step, displacement field modelled using B-spline basis functions, 4 multiresolution stages with last at full resolution.
AntsRigidDiffeomorphic: rigid step (no affine step) followed by diffeomorphic step, displacement field optimized at voxel level, 4 multiresolution stages with last at full resolution.
AntsFastRigidSplineDiffeomorphic: rigid step (no affine step) followed by diffeomorphic step, displacement field modelled using B-spline basis functions, fast scheme with only 3 multiresolution stages, and no iteration at full resolution.
AntsFastRigidDiffeomorphic: rigid step (no affine step) followed by diffeomorphic step, displacement field optimized at voxel level, fast scheme with only 3 multiresolution stages, and no iteration at full resolution.
AntsSplineDiffeomorphicOnly: single step of diffeomorphic coregistration without previous rigid of affine step, displacement field modelled using B-spline basis functions, 4 multiresolution stages with last at full resolution.
AntsDiffeomorphicOnly: single step of diffeomorphic coregistration without previous rigid of affine step, displacement field optimized at voxel level, 4 multiresolution stages with last at full resolution.
Select the similarity metric to optimize linear stage (rigid/affine) using the Linear metric combobox: IM (i.e. mutual information, default), CC (i.e. cross-correlation), MS (i.e. mean squares).
Select the similarity metric to optimize non-linear stage (displacement field) using the Non linear metric combobox: IM (i.e. mutual information, default), CC (i.e. cross-correlation), MS (i.e. mean squares), DEMONS.
Use the Sampling rate spinbox to select the subsampling method used to calculate the similarity function. The range is between 1.0, which indicates that all voxels are used to process the similarity function with no subsampling, and lower values, which are greater than 0.0 and indicate the ratio of voxels used to process the similarity function with regular subsampling.
Toggle Resample checkbox to resample (or not) the coregistered moving volume. If not, the moving volume is not resampled, but the associated XML xtrfs file is updated (geometric transformation for fixed volume coregistration will be added to the moving xtrfs) and the displacement field is saved as a PySisyphe volume file (.xvol).
Toggle Resample… button to show/hide resampling settings:
Select the interpolation algorithm (linear, nearest neighbor, b-spline, gaussian, hamming windowed sinc, cosine windowed sinc, welch windowed sinc, lanczos windowed sinc, blackman windowed sinc) used to resample the moving volume.
Resampled moving volume is saved with its original file name, which is prefixed and/or suffixed by the strings edited in the prefix and suffix parameters.
Left-click Execute button to run batch coregistration.
Left-click Cancel button to close dialog box without coregistration.
Time series realignment
The purpose of this menu is to realign time series images as fMRI series, resting state series, or dynamic susceptibility contrast MR perfusion series.
The Time series realignment dialog box is displayed.
To select PySisyphe time series volumes, use the Multiple file selection widget at the top.
Toggle Settings… button to show/hide realignment parameters:
Use the Reference combobox to choose the volume that will be used as a reference to realign all volumes in the time series. This could be the first, middle, or time series mean or median volume.
Select the similarity metric using the Metric combobox: IM (i.e. mutual information), CC (i.e. cross-correlation), MS (i.e. mean squares, default).
Use the Sampling rate spinbox to select the subsampling method used to calculate the similarity function. The range is between 1.0, which indicates that all voxels are used to process the similarity function with no subsampling, and lower values, which are greater than 0.0 and indicate the ratio of voxels used to process the similarity function with regular subsampling.
Check Compute mean volume to save the time series mean volume.
Toggle Resample… button to show/hide resampling parameters:
Select the interpolation algorithm (linear, nearest neighbor, b-spline, gaussian, hamming windowed sinc, cosine windowed sinc, welch windowed sinc, lanczos windowed sinc, blackman windowed sinc) used to resample the moving volume.
Resampled volumes are saved with their original names, which are prefixed and/or suffixed by the strings edited in the “prefix” and “suffix” parameters. Each resampled volume is associated with an XML xtrfs file (geometric transformation).
Left-click Execute button to run realignment. After processing is complete, a realignment dialog box will appear displaying the values of the translations and rotations applied to the time series volumes. The chart displays the translation (mm) and rotation (degrees) curves, and the table below presents the values. Left-click the Save map button to save the chart as a bitmap file (.bmp, .jpg, .png, .tiff or .svg). Left-click the Copy to clipboard button to copy the chart to the clipboard as a bitmap. Left-click the Save dataset button to save the table (.csv, .json, .latex, .text, .xlsx, .PySisyphe xsheet). Left-Click Close button to exit.
Left-click Cancel button to close dialog box without realignment.
Eddy current correction
Image distortion due to field gradient eddy currents can create image artifacts in diffusion-weighted MR images. This menu allows you to correct image distortion using affine or non-linear coregistration of diffusion-weighted images with B0 used as the fixed image (image without gradient diffusion).
The Eddy current correction dialog box is displayed.
Use the Single file selection widget at the top to select B0 volume. Use the Multiple file selection widget to select Diffusion-weighted volumes.
Toggle Registration… button to show/hide parameters:
Select the the coregistration algorithm using the Transform combobox:
AntsAffine (default): single step of affine coregistration, 4 multiresolution stages with last at full resolution.
AntsSplineDiffeomorphicOnly: single step of diffeomorphic coregistration without previous affine step, displacement field modelled using B-spline basis functions, 4 multiresolution stages with last at full resolution.
AntsDiffeomorphicOnly: single step of diffeomorphic coregistration without previous affine step, displacement field optimized at voxel level, 4 multiresolution stages with last at full resolution.
AntsFastSplineDiffeomorphicOnly: single step of diffeomorphic coregistration without previous affine step, displacement field modelled using B-spline basis functions, fast scheme with only 3 multiresolution stages, and no iteration at full resolution.
AntsFastDiffeomorphicOnly: single step of diffeomorphic coregistration without previous affine step, displacement field optimized at voxel level, fast scheme with only 3 multiresolution stages, and no iteration at full resolution.
Select the similarity metric to optimize linear stage (rigid/affine) using the Linear metric combobox: IM (i.e. mutual information, default), CC (i.e. cross-correlation), MS (i.e. mean squares).
Select the similarity metric to optimize non-linear stage (displacement field) using the Non linear metric combobox: IM (i.e. mutual information, default), CC (i.e. cross-correlation), MS (i.e. mean squares), DEMONS.
Use the Sampling rate spinbox to select the subsampling method used to calculate the similarity function. The range is between 1.0, which indicates that all voxels are used to process the similarity function with no subsampling, and lower values, which are greater than 0.0 and indicate the ratio of voxels used to process the similarity function with regular subsampling.
Toggle Resample… button to show/hide resampling parameters:
Select the interpolation algorithm (linear, nearest neighbor, b-spline, gaussian, hamming windowed sinc, cosine windowed sinc, welch windowed sinc, lanczos windowed sinc, blackman windowed sinc) used to resample the moving volume.
Resampled volumes are saved with their original names, which are prefixed and/or suffixed by the strings edited in the “prefix” and “suffix” parameters.
Left-click Execute button to run eddy current correction.
Left-click Cancel button to close dialog box without processing.
Resample
This menu lets you resample a volume after applying a geometric transformation.
The Resample dialog box is displayed.
Select the PySisyphe moving volume with the Single file selection widget at the top.
If you want to select a geometric transformation from the XML xtrfs file associated with the moving volume, check the Self geometric transform option. The XML xtrfs file stores all geometric transformations calculated from previous coregistration of its associated volume with other volumes used as reference (i.e. target of the coregistration), which are identified by their space/transform ID number. These ID numbers are added to the Transformations combbox. The Transformations combbox remains empty if the moving volume does not have an associated XML xtrfs file. Information regarding the geometric transformation currently selected in the combobox is displayed in a box below: reference volume of the coregistration (space/transform ID, name, size, spacing, center) and parameters (translations, rotations, zooms, shears, matrix for linear transformation; displacement field file for non-linear transformation).
Left-click Get Fixed Volume button to select a volume, search for its space/transformation ID, and select it from the Transformations combobox.
If you want to create a geometric transformation, check Free geometric transform. You can then edit the resampling space directly (size, spacing), the rigid geometric transformation parameters (translations in mm and rotations in degrees), or provide a displacement field file for a non-linear transformation. You can also set the resampling space from a volume selected using the From volume button.
Left-click Load transforms button to open an XML xtrfs file. You can also select a PySisyphe volume to open its associated XML xtrfs file.
Left-click Save button to save the current geometric transformation in various formats (PySisyhe .xtrf, ANTs .mat, ITK .tfm, MINC .xfm, Matlab .mat, text .txt).
Left-click Affine to displacement field button to convert an affine geometric transformation to a displacement field.
Toggle Resample… button to show/hide resampling parameters:
Select the interpolation algorithm (linear, nearest neighbor, b-spline, gaussian, hamming windowed sinc, cosine windowed sinc, welch windowed sinc, lanczos windowed sinc, blackman windowed sinc) used to resample the moving volume.
Resampled volumes are saved with their original names, which are prefixed and/or suffixed by the strings edited in the “prefix” and “suffix” parameters.
Left-click Execute button to resample moving volume with the current geometric transformation.
Left-click Cancel button to close dialog box without resampling.
Asymmetry displacement field
The purpose of this menu is to perform the asymmetry analysis of a volume. This is achieved by performing a nonlinear coregistration of a volume with its symmetrical counterpart in the x-axis. The result is the Jacobian determinant image of the displacement field calculated from the coregistration. The scalar values in this image represent volume ratios. A value less than 1.0 indicates local deflation at the current voxel coordinate relative to the contralateral hemisphere. Conversely, a value greater than 1.0 indicates local inflation at the current voxel coordinate.
The Asymmetry analysis dialog box is displayed.
Select the volumes to be analyzed with the Multiple file selection widget at the top.
Toggle Registration… button to show/hide parameters:
Check Fixed volume mask to remove background voxels during registration processing.
Select method used to initialize translations with the Estimation combobox: FOV center alignment (default), center of mass alignment or no estimation (translations and rotations to 0.0).
Select the displacement field registration algorithm using the Displacement field combobox:
AntsSplineDiffeomorphic: affine step followed by diffeomorphic step, displacement field modelled using B-spline basis functions, 4 multiresolution stages with last at full resolution.
AntsDiffeomorphic: affine step followed by diffeomorphic step, displacement field optimized at voxel level, 4 multiresolution stages with last at full resolution.
AntsFastSplineDiffeomorphic: affine step followed by diffeomorphic step, displacement field modelled using B-spline basis functions, fast scheme with only 3 multiresolution stages, and no iteration at full resolution.
AntsFastDiffeomorphic: affine step followed by diffeomorphic step, displacement field optimized at voxel level, fast scheme with only 3 multiresolution stages, and no iteration at full resolution.
AntsRigidSplineDiffeomorphic: rigid step (no affine step) followed by diffeomorphic step, displacement field modelled using B-spline basis functions, 4 multiresolution stages with last at full resolution.
AntsRigidDiffeomorphic: rigid step (no affine step) followed by diffeomorphic step, displacement field optimized at voxel level, 4 multiresolution stages with last at full resolution.
AntsFastRigidSplineDiffeomorphic: rigid step (no affine step) followed by diffeomorphic step, displacement field modelled using B-spline basis functions, fast scheme with only 3 multiresolution stages, and no iteration at full resolution.
AntsFastRigidDiffeomorphic: rigid step (no affine step) followed by diffeomorphic step, displacement field optimized at voxel level, fast scheme with only 3 multiresolution stages, and no iteration at full resolution.
AntsSplineDiffeomorphicOnly: single step of diffeomorphic coregistration without previous rigid of affine step, displacement field modelled using B-spline basis functions, 4 multiresolution stages with last at full resolution.
AntsDiffeomorphicOnly: single step of diffeomorphic coregistration without previous rigid of affine step, displacement field optimized at voxel level, 4 multiresolution stages with last at full resolution.
Select the similarity metric to optimize linear stage (rigid/affine) using the Linear metric combobox: IM (i.e. mutual information, default), CC (i.e. cross-correlation), MS (i.e. mean squares).
Select the similarity metric to optimize non-linear stage (displacement field) using the Non linear metric combobox: IM (i.e. mutual information, default), CC (i.e. cross-correlation), MS (i.e. mean squares), DEMONS.
Select the subsampling used to calculate similarity function using the Sampling rate spinbox. The range is between 1.0 (no subsampling, all voxels are used to process similarity function) and lower values, which are greater than 0.0 and indicate the ratio of voxels used to process the similarity function under regular subsampling.
Toggle Displacement field jacobian determinant button to show/hide parameters: - Jacobian determinant volume is saved with the original file name, which is prefixed and/or suffixed by the strings edited in the prefix and suffix parameters.
Left-click Execute button to run asymmetry analysis.
Left-click Cancel button to close dialog box without processing.
Displacement field jacobian determinant
The purpose of this menu is to calculate Jacobian determinant volume from a displacement field. The scalar values in this image represent volume ratios. A value less than 1.0 indicates local deflation at the current voxel coordinate. Conversely, a value greater than 1.0 indicates local inflation at the current voxel coordinate.
The Jacobian determinant of displacement field dialog box is displayed.
Select the displacement field volumes with the Multiple file selection widget at the top.
Toggle Displacement field jacobian determinant button to show/hide parameter:
Jacobian determinant volume is saved with the original file name, which is prefixed and/or suffixed by the strings edited in the prefix and suffix parameters.
Left-click Execute button to calculate Jacobian determinant volumes.
Left-click Cancel button to close dialog box without processing.