Caret6:Documentation/UserInterface/BorderOperationsWindow

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Contents

Border Operations

Toolbar

  • RN - Rename borders that are clicked with the mouse. When a border is selected, a dialog pops up containing the current name of the border. Change the name of the border and press the OK button. If there is not an appropriate color, use the Edit Border Colors page to create a new color.
  • RS - Resample borders.
  • DA - Delete all borders.
  • DN - Delete non-displayed borders.
  • DB - Delete borders that are clicked with the mouse.

Page Selection - Use the page selection controls to choose pages for other border operations.

Draw New Borders Page

Use this page to draw borders. After all of the proper data is entered, press the Apply button. If there is not a color that matches the border name, you will be prompted to choose a color. Next, move the mouse to the start of the border. While holding down the left mouse button, drag the mouse to create the border. When you have reached the end of the border, release the mouse button, hold down the shift key, and click the mouse.

Attributes

  • Name - Name for the border that will be drawn.
  • Sampling - Desired distance between points of the border.

Type

  • Closed (Areal) - Select to draw a border that enclosed a region. When the border is finished, an additional segment is added that connects the last point in the border to the first point in the border.
  • Open (Linear) - Select to draw a border that is a connect set of line segments.

Miscellaneous

Reset Drawing - If you start to draw a border but something goes wrong, click this button. Any partially drawn border is eliminated so that you can start over.

Project Borders Page

Projection Surfaces

Use to select the surfaces for projection of borders.

Projection Parameters

  • Surface Offset - Enables the border to be placed above the surface (positive value) or on the surface (zero value).

Draw Updates to Existing Borders Page

Use this page to modify existing borders.

Update Mode

  • Erase Segment - Use this to remove part of a border. Place the mouse over the starting location of the border that you want to remove. Hold down the left mouse button and drag the mouse along the border to the ending location in the border. Release the left mouse button, hold down the shift key, and click the left mouse button.
  • Extend From Either End - Use this to extend a border. Place the mouse over the end of the border that you want to extend. Hold down the left mouse button and drag the mouse along the border to the new ending point of the border. Release the left mouse button, hold down the shift key, and click the left mouse button.
  • Replace Segment - Use this to replace a segment within a border. Place the mouse over the first location of the border that you want to modify. Hold down the left mouse button and drag the mouse to draw the new segment and continue until the mouse is over a point in the border. Release the left mouse button, hold down the shift key, and click the left mouse button.

Attributes

  • Sampling - Desired distance between points of the border.

Miscellaneous

Reset Drawing - If you start to draw a border but something goes wrong, click this button. Any partial border update is eliminated so that you can start over.

Edit Border Colors Page

Use this page to edit the border colors.

Color Names

This section contains a list of the current border colors. To edit a border color, simply click the name of the border color and modify the color's components in the Color Component Editing section.

  • New Color Button - Press this to enter a new color name.
  • Change Name - Changes the name of the currently selected color.
  • Delete Selected Color - Press this button to delete the selected color.

Color Component Editing

A the top of this section is an alternating black and white pattern. For opaque colors (Alpha = 255) this pattern is not seen. As the Alpha value is reduced, this black and white pattern appears. Its purpose is to provide feedback for transparent colors (those with Alpha less than 255).

  • Name - Name of the currently edit color.
  • Red - The red color component.
  • Green - The green color component.
  • Blue - The blue color component.
  • Alpha - The alpha (transparency) color component.

Advanced - Pressing this button provides other user-interface components for setting a color's components.


Miscellaneous

Delete Unused Colors - Removes any colors that are not assigned to a border.

Create Landmark Borders

User-Interface

  • Space The stereotaxic space of the individual. A limited number of stereotaxic spaces are supported.
  • Structure Structure of the individual.
  • Anatomical Volume The individual's anatomical volume. This may also contain just the corpus callosum in which case the name of the volume file must contain the two words corpus and callosum.
  • Anatomical Surface The individual's anatomical surface.
  • Inflated Surface The individual's inflated surface.
  • Very Inflated Surface The individual's very inflated surface.
  • Sphere/Ellipsoid Surface The individual's ellipsoid or spherical surface.
  • Label Geography The label column containing geography information (sulci/gyri) in the Label file.
  • Shape Depth The depth column containing depth information in the Shape file.

If needed inflated, very inflated, and ellipsoid surfaces may be created using the Surface Geometry Operations Dialog.

Landmark Border Information

An algorithm that draws the Core 6 landmarks is available in Caret. Results are not perfect, so the resulting borders need inspection and tweaking.

There is a command line version available also: caret6_command -surface-border-landmarks

The landmarks identified are:

  Calcarine Sulcus
  Central Sulcus
  Medial Wall
  Superior Temporal Gyrus
  Sylvian Fissure

Inputs Anatomical volume or corpus callosum segmentation (e.g., extracted from Freesurfer aseg.mgz); AC-PC aligned midthickness surface coordinate file; inflated coordinate file; very inflated coord file; ellipsoid coord file; closed topo file; paint file; paint file geography column name or number; surface shape file; surface shape file depth column name or number. The input midthickness surface must be in one of the following stereotaxic spaces (see http://brainvis.wustl.edu/help/pals_volume_normalization):

  AFNI
  FLIRT
  MRITOTAL
  SPM95
  SPM96
  SPM99
  SPM2
  711-2B
  711-2B-111
  711-2C
  711-2C-111
  711-2O
  711-2O-111
  711-2Y
  711-2Y-111

If the space is not already 711-2*, then it is scaled to the 711-2* bounding box (i.e., each axis is scaled to match the corresponding 711-2* axis extent).

The anatomical volume is used to generate the corpus callosum. A corpus callosum segmentation may be used directly, if its filename contains the case insensitive words "corpus" and "callosum" (e.g., if extracted from Freesurfer's aseg.mgz).

Volumetric probabilistic atlases for each of the landmarks are mapped to the scaled input fiducial surface. These atlases were generated using the 12 subjects from the PALS-B12 atlas. Voxel intensity represents the number of subjects whose surface-based parcellation for a landmark intersected that voxel.

Central sulcus: Nodes that intersect with the mapped probabilistic atlas representation of the Central Sulcus that have curvature less than -0.1 are selected in an ROI and geometric min/max values found. Then the curvature threshold is tightened to -0.16 or less, and dilated as needed to include most ventral and medial nodes in the Central Sulcus. A border is drawn geodesically between the most medial and ventral nodes in the ROI. The ends are trimmed to within 19mm of the operculum at the ventral end, 18mm of the medial wall at the dorsal end.

Superior Temporal Gyrus: Nodes that intersect with the mapped probabilistic atlas representation of the Superior Temporal Gyrus, and the coordinates of the z-min and z-max node are found. The posterior extent of the ROI is limited to the y-value of the most inferior point of the Central Sulcus landmark. Then a border is drawn geodesically from the most posterior node in the ROI to the ventral most (temporal pole). Border points are adjusted to the rop of the gyral ridge as needed.

Sylvian Fissure: Nodes that intersect with the mapped probabilistic atlas representation of the sylvian fissure (after removing islands) that have depth less than -7 are intersected with nodes whose curvature on the inflated surface is less than -0.05. A border is drawn from the most posterior node in this ROI to the deepest node in the ROI that is anterior to the temporal pole. From there, the border continues inferiorly, to the deepest node within 10mm anterior and 12mm inferior of the previous point. From there, it continues inferiorly along the fundus toward the node closest to -/+16.0, 12.0, -19.0, but is trimmed to 10mm superior of this node. The inferior branch of the circular sulcus is found by identifying the most inferior nodes in the ROI. The intersection between this border and the superior branch is identified, and the superior branch border is trimmed to 12mm posterior of this intersection along the ellipsoid surface.

Calcarine Sulcus: Nodes that intersect with the mapped probabilistic atlas representation of the calcarine sulcus are intersected with nodes whose inflated mean curvature is less than or equal to -0.07. The posterior and anterior limits of this ROI are found, and then the ROI is intersected with nodes whose fiducial mean curvature is less than or equal to -0.16. The border is drawn geodesically along the inflated surface using the more stringent ROI, but the less stringent anterior/posterior limits. The posterior end of the border is trimmed to with 24mm of the occipital pole.

Medial Wall:

Dorsal: Find intersection of frontal and medial wall; move frontal/medial wall intersection a little bit dorsal; find intersection of calcarine and medial wall. If anatomy volume is named like CorpusCallosum, skip corpus callosum generation. Else segment CorpusCallosum. Place foci along top of corpus callosum. Draw border connecting foci; find and fix spikes.

Ventral: Nodes that intersect with the mapped probabilistic atlas representation of the hippocampal fissure are intersected with nodes whose depth is 10mm or more. Mark a point A at the most superior node in this ROI, or the splenium ventral node -- whichever is more superior. Mark a point B 35mm posterior to the most inferior node in the ROI node, and 12mm lateral along parahippocampal gyrus (ensuring positive z-normals to keep from mapping to the wrong side of the gyrus). Mark a point C 8mm anterior to the most inferior ROI node and 12mm lateral along parahippocampal gyrus. Mark point D 30mm posterior to temporal pole along path toward most inferior ROI node. Mark point E just inferior and posterior to the genu. Draw a border from A to B to C to D to E.

A template frontal cut is intersected with the merged medial wall border, and points are deleted near the intersection, until the gap between the dorsal and ventral is 19mm. Points near the calcarine junction are deleted to make a 16mm gap between the calcarine, medial wall dorsal, and medial wall ventral borders.

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