Project4/segment Seg3D tutorial lv

From CVRG Wiki

Return to Project 4 Home

Contents 1 Segmenting Left Ventricle using Seg3D 1.1 Start Software 1.2 Load Cardiac Volume 1.3 Apply Median Filter 1.3.1 Select: Filter - Median Filter 1.3.2 Accept Default Values by selecting Start push button 1.3.3 New volume created by median filter 1.4 Apply Discreet Gaussian Filter 1.4.1 Select: Filter - Discreet Gaussian 1.4.2 Accept Default Values by selecting Start push button 1.4.3 New volume created by discreet gaussian filter 1.5 Use Threshold Tool to create mask with general interior and exterior limits of cardiac wall 1.5.1 Select: Tools - Threshold Tool 1.5.2 Threshold minimum and maximum initially set to default values 1.5.3 Adjust minimum and maximum threshold values to define interior and exterior limits of cardiac wall 1.5.4 Create mask 1.6 Remove Mask voxels that are outside extents of maximum slices in Coronal plane 1.6.1 Create duplicate mask 1.6.2 Use Polyline Tool to define outer boundary of cardiac wall 1.6.3 Combine Masks with Logical And 1.6.4 Delete Intermediate Masks 1.7 Remove Mask voxels that are outside extents of maximum slices in Axial Plane 1.7.1 Create duplicate mask, Use Polyline Tool to define outer boundary of cardiac wall 1.7.2 Combine Masks with Logical And 1.7.3 Delete Intermediate Masks 1.8 Remove Mask voxels that are outside extents of maximum slices in Sagittal Plane 1.8.1 Create duplicate mask, Use Polyline Tool to define outer boundary of cardiac wall 1.8.2 Combine Masks with Logical And 1.8.3 Delete Intermediate Masks 1.9 Remove Mask voxels that are within the interior boundaries of cardiac wall Plane 1.9.1 Adjust Opacity of Initial Mask 1.9.2 Display Initial Volume with mask 1.9.3 Display Single Plane for Editing using View - Single 1.9.4 Use Polyline Tool to Erase Undesired Voxels 1.10 Use Polyline Tool to Include Desired Voxels 1.11 Create Segmentation using Mask Data 1.12 Save Segmentation

Segmenting Left Ventricle using Seg3D

Start Software

Seg3D is available for both Linux and Windows at [:http.software.sci.utah.edu:http.software.sci.utah.edu]

Load Cardiac Volume

Load Cardiac Volume (Analyze Image) using File - Open Volume. Browse to file and select.

Apply Median Filter

Select: Filter - Median Filter

Accept Default Values by selecting Start push button

New volume created by median filter

This volume is currently selected on right side of screen

Apply Discreet Gaussian Filter

Select: Filter - Discreet Gaussian

Accept Default Values by selecting Start push button

New volume created by discreet gaussian filter

This volume is currently selected on right side of screen

Use Threshold Tool to create mask with general interior and exterior limits of cardiac wall

Select: Tools - Threshold Tool

Threshold minimum and maximum initially set to default values

Adjust minimum and maximum threshold values to define interior and exterior limits of cardiac wall

The slide controls can be used to adjust the lower and upper threshold. The user can navigate through triplanar slices to see the effects of threshold selection by moving cursor to desired plane, and using scroll control on mouse to view other slices.

Create mask

Selecting the "Complete" push button on the screen displayed above will create new mask (shown below).

Remove Mask voxels that are outside extents of maximum slices in Coronal plane

Create duplicate mask

Select "plus" icon on right side of screen to create duplicate mask, resulting in:

Use Polyline Tool to define outer boundary of cardiac wall

Select Tools Polyline

Move cursor above the Coronal Slice. Use scroll button on mouse to navigate to slice that appears to have largest area of cardiac muscle (shown below)

Draw polyline by clicking left mouse button at successive parts of slice.

After polyline is complete, scroll through all coronal slices to check that no part of desired cardiac muscle is inside polyline

When user is satisfied that polyline includes all of desired cardiac muscle, select Fill push button on left side of screen. This will fill the polyline on coronal plane.

Move the cursor over the filled area of the polyline. Press the "P" button on the keyboard. This will propogate the filled polyline to the two other planes.

Combine Masks with Logical And

Select Filters - Combine Labels with Logical And

Press "Set Mask Label" at upper left of screen:

Select other mask on right side of screen:

Press "Start" button on upper left of screen. This will generate a new mask, in which only voxels which are common to selected masks will be non-zero.

Delete Intermediate Masks

Delete the two previous masks by selecting the red X icon of each mask on the right side of the screen. The user will be prompted to confirm each deletion.

Remove Mask voxels that are outside extents of maximum slices in Axial Plane

Repeat the procedure that was used for the coronal planes in Axial planes.

Create duplicate mask, Use Polyline Tool to define outer boundary of cardiac wall

Create duplicate mask, create polyline to outline cardiac muscle at largest section in axial plane. Propogate to other planes using P on keyboard:

Combine Masks with Logical And

Delete Intermediate Masks

Remove Mask voxels that are outside extents of maximum slices in Sagittal Plane

Repeat the procedure that was used for the coronal planes in sagittal plane.

Create duplicate mask, Use Polyline Tool to define outer boundary of cardiac wall

Combine Masks with Logical And

Delete Intermediate Masks

Remove Mask voxels that are within the interior boundaries of cardiac wall Plane

Adjust Opacity of Initial Mask

Use opacity icon on right side of screen (fourth icon from left under Volumes). Opacity icon has two arrows facing opposite directions. Adjust the opacity so that the underlying greyscale volume can be clearly seen.

Display Initial Volume with mask

Use the leftmost icon on right side of screen to hide all volumes except the initial volume and mask.

Display Single Plane for Editing using View - Single

If desired, a singe plane can be displayed using View - Single

Use Polyline Tool to Erase Undesired Voxels

Draw polyline around undesired voxels.

Press Erase button to remove undesired voxels.

Use mouse scroll bar to navigate to adjacent slice. The polyline will be displayed on following slice. Adjust polyline if necessary.

Press Erase button to remove undesired voxels.

Use Polyline Tool to Include Desired Voxels

Draw polyline surrounding area to include in mask.

Press Fill button to add area to mask.

Create Segmentation using Mask Data

Select the Mask Data Filter - Filters - Mask Data

With the current mask selected on the right side of the screen, press the Set Mask Label button on the left side of the screen.

Select the original volume on the right side of the screen.

Press the Start button on the left side of the screen. This will apply the mask to the original volume, the resulting segmentation will be displayed.

Save Segmentation

Select the Masked Volume (greyscale with non cardiac muscle removed) on right hand side. Select File - Save Volume.

Enter file name, press Save button. Volume will be saved in nrrd format.