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toads-cruise:Segmentation

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1 Segmentation Plugins

Segmentation Plugins

TOADS

TOADS (TOpology-preserving Anatomy Driven Segmentation) is an algorithm which generates a detailed and topologically consistent segmentation of brain into its sub-structures. TOADS incorporates statistical and topological atlases into a fuzzy clustering framework to segment the brain into cortical gray matter, cerebral white matter, putamen, thalamus, caudate, brainstem, sulcal csf, vetricular csf, cerebellar white and gray matter.

Example on an MPRAGE Brain MRI

The process below was used to segment a T1_MPRAGE image :

Input Image

1) Select the TOADS_2008 Plugin from Plugins > TOADS-CRUISE > Segmentation > TOADS_2008

TOADS_2008 plugin in mipav

2)The TOADS 2008 GUI will open. Specify input image and choose parameters as follows:

TOADS GUI

   2.1) Specify the image to be segmented either as a file (using Browse button) or as an open image.

   2.2) Specify the image pulse sequence using Image modality option. Note that you should distinguish between T1_MPRAGE and T1_SPGR.

   2.3) Specify which result images you want the plugin to output using Output images option.

3) Click OK

4) A save dialog box will open, asking you for the location to save all the results

5) Once the algorithm is complete, a summary screen will open showing all the files created. You can use the View button next to each output image to open it.

TOADS output

6) Default option only generates the hard segmentation of the structures

TOADS results

LongCRUISE

Full Surface Reconstruction Algorithm Using SPECTRE for skullstripping, TOADS for classification and CRUISE for cortical surface reconstruction

Example on an MPRAGE Brain MRI

Fig. 1 LongCRUISE in Mipav Menu

The process below was used to produce the following central surface reconstruction(viewed in Paraview):

Fig. 2 Specifying a target volume to segment its cortical surface

Fig. 3 LongCRUISE Results Summary Screen

Select the LongCruise Plugin with Plugins > TOADS-CRUISE > Segmentation > LongCRUISE (see Fig. 1)
Specify the target of the cortical surface reconstruction, either as a file or as an opened volume(see Fig. 2)
Click OK
A save dialog box will open, asking you for the location to save all the results
Once the algorithm is complete, a summary screen will open showing all the files created(see Fig 3.)
"TGDM Inner Surface", "TGDM Central Surface", "TGDM Outer Surface" lists the output vtk files for the reconstructed inner, central and outer surface.

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SPECTRE

Simple Paradigm for Extra-Cerebral Tissue Removal. Fully automated brain extraction - or skull stripping - algorithm that uses registration, segmentation, and morphological operators.

Example on an MPRAGE Brain MRI

The process below was used to produce the brain extraction in Fig. 1:

Fig.1: Input image on the left and an extracted brain image after running SPECTRE on the right.

1. Open the SPECTRE plugin by selecting Plugins > TOADS-CRUISE > Segmentation > SPECTRE_2009 (See Fig. 2)

Fig.2: Selecting the SPECTRE_2009 plugin

2. Specify the volume to be segmented, either as a file or as an opened volume (see Fig. 3).

Fig.3: Selecting input image

3. Click OK.
4. A Save dialog box will open. Specify the directory in the File Name box where the output should be saved (see Fig. 4).

Fig.4: Specify directory for outputs

5. Click Save.
6. Once the algorithm is complete, a window of all results created will appear (see Fig. 5).

Fig.5: Summary of results

7. Each of the result volumes can be viewed by clicking the view button on the right of the result file name (see Fig. 6).

Fig.6: Click view to show each result volume

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Fantasms

Fantasms applies a "fuzzy" spatial regularization to reduce the effects of image noise. It also compensates for MR intensity inhomogeneities by estimating a gain field along with the segmentation.

Example on an MPRAGE Brain MRI

The process below was used to produce the following classification:

Fig. 1 Loading a skull-stripped image

Fig. 2 Finding Fantasms

Fig. 3 Tuning parameters

Fig. 4 Classificantion result

Load a skull-stripped image. (see Fig. 1)
Select the Fantasms Plugin with Plugins > TOADS-CRUISE > Segmentation > Fantasms (see Fig. 2)
Tune the parameters in the interface (the default setting should work)(see Fig. 3)
Click OK
When the algorithm is complete, a calssification result will show up(see Fig. 4)

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CRUISE

Cortical Reconstruction Using Implicit Surface Evolution. It yields accurate brain surface reconstructions that are guaranteed to be topologically correct and free from self-intersections

Example on an MPRAGE Brain MRI

The process below was used to produce the following reconstruction (viewed in another plugin:StandAloneSurfaceViewer ):

Fig. 1 Finding CRUISE plugin

Fig. 2 CRUISE interface

Fig. 3 Loading images

Fig. 4 Output target

Fig. 5 Summary after algorithm is complete

Fig. 6 Finding StandAloneSurfaceViewer plugin

Fig. 7 Opening .vtk files

Fig. 8 Inner surface

Fig. 9 Central surface

Fig. 10 Outer surface

Select the CRUISE Plugin with Plugins > TOADS-CRUISE > Segmentation > CRUISE (see Fig. 1)
Then the interface shows(see Fig. 2)
Select the image to segment(see Fig. 3) and tune the parameters in the interface (the default setting should work)
Choose the ouput target(see Fig. 4)
Click OK
When the algorithm is complete, a summary window will show up(see Fig. 5)
The reconstructed surface can be viewed in StandAloneSurfaceViewer(see Fig. 6). Select the \CRUISE\nested_tgdm directory in the output target. Then open .vtk files(see Fig. 7).
The results are shown in Fig.8-10

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