Introductory Bet Flashcards

Front 1

By default bet just...

Back 1

...calls the bet2 program for simple brain extraction.

Front 2

bet syntax is

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bet <input> <output> [options]

Front 3

Bet GUI - firstly,

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...set the input image filename and the output image filename. The output name is also used to generate the filenames for any optional outputs that are turned on.

Front 4

Fractional intensity threshold must...

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...must like between 0 and 1.

Front 5

Changing Fractional intensity threshold from its default value of 0.5...

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will cause the overall segmented brain to become larger (<0.5) or smaller (>0.5).

Front 6

If you change the options menu from the default setting of "run standard brain extraction using bet 2", then...

Back 6

...you will get one of the variations on default bet2 functionality.

Front 7

Output brain-extracted image:

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by default the only output from BET, an image with all non-brain matter removed.

Front 8

Output binary brain mask image:

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outpit a binary brain mask (0 outside of the brain and 1 inside). This can be used in later processing to mask other images derived from the original.

Front 9

Apply thresholding to brain and mask image

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BET applies thresholding to the segmented brain image (and also the brain mask if selected). Thus, inside the estimated brain, some voxels can be "zeroed" after segmentation, if their intensity falls below an automatically estimated threshold.

Front 10

Output exterior skull surface image

Back 10

BET produces an image estimate of the exterior surface of the skull. All non-skull-surface poitns are 0 in this image, skull-surface points are 100.

Front 11

Output brain surface overlaid onto original image

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Output is a copy of the original image, with additionally an outline of the brain's surface drawn on top.

Front 12

Changing threshold gradient from its default value of 0

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causes a gradient to be applied to the previous threshold. Thus setting a +ve value here causes the primary threshold to be reduced at the bottom of the brain, giving a larger brain estimate there, and a smaller estimate towards the top of the image.

Front 13

Threshold gradient must lie between

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-1 and 1.

Front 14

Main bet2 option -o:

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generate brain surface outline overlaid onto original image

Front 15

Main bet2 option -m:

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Generate binary brain mask.

Front 16

Main bet2 option -s:

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Generate rough skull image (not as clean as what betsurf generates)

Front 17

Main bet2 option -n:

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Don't generate the default brain image output

Front 18

Main bet2 option -f <f>:

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Fractiona intensity threshold (0 - >1); default =0.5; smaller values give larger brain outline estimates

Front 19

Main bet2 option -g <g>:

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vertical gradient in fractional intensity threshold (-1 - >1); default=0; positive values give larger brain outline at bottom, smaller at top

Front 20

Main bet2 option -r <r>

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Head radius (mm not voxels); initial surface sphere is set to half of this

Front 21

Main bet2 option -c < x y z>

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Centre-of-gravity (voxels not mm) of initial mesh surface.

Front 22

Main bet2 option -t

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apply thresholding to segmented brain image and mask

Front 23

Main bet2 option -e

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Generates brain surface as mesh in .vtk format

Front 24

Variations on default bet2 functionality (mutually exclusive options): -R

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This option runs more "robust" brain centre estimation; The primary purpose is to improve the brain extraction
when the input data contains a lot of non-brain matter - most likely when there is a lot of neck
included in the input image.

Front 25

Variations on default bet2 functionality (mutually exclusive options): -S

Back 25

This attempts to cleanup residual eye and optic nerve voxels which bet2 can sometimes
leave behind.

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Variations on default bet2 functionality (mutually exclusive options): -B

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This attempts to reduce image bias, and residual neck voxels. This

Front 27

Variations on default bet2 functionality (mutually exclusive options): -Z

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This can improve the brain extraction if only a few slices are present in the data (i.e., a
small field of view in the Z direction). This is achieved by padding the end slices in both
directions, copying the end slices several times, running bet2 and then removing the added
slices.

Front 28

Variations on default bet2 functionality (mutually exclusive options): -F

Back 28

This option uses bet2 to determine a brain mask on the basis of the first volume in a 4D
data set, and applies this to the whole data set. This is principally intended for use on FMRI
data, for example to remove eyeballs. Because it is normally important (in this application)
that masking be liberal (ie that there be little risk of cutting out valid brain voxels) the -f
threshold is reduced to 0.3, and also the brain mask is "dilated" slightly before being used.

Front 29

Variations on default bet2 functionality (mutually exclusive options): -A

Back 29

This runs both bet2 and betsurf programs in order to get the additional skull and scalp
surfaces created by betsurf. This involves registering to standard space in order to allow
betsurf to find the standard space masks it needs.

Front 30

Variations on default bet2 functionality (mutually exclusive options): -A2 <T2>

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This is the same as -A except that a T2 image is also input, to further improve
the estimated skull and scalp surfaces. As well as carrying out the standard space registration
this also registers the T2 to the T1 input image.

Front 31

Option -b

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This uses flirt to register the input image to a standard space whole-head image; the resulting
transform is then inverted and a standard-space brain mask is transformed into the space of
the input image, and then applied to this to create the output.