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Documentation.TractTool History
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The specifics of the nifti image ''output.nii.gz'' can be defined using '''-target''' followed by an exisiting nifti image, here called target.nii.gz.\\ to:
The specifics of the nifti image ''output.nii.gz'' can be defined using '''-target''' followed by an exisiting nifti image, here called target.nii.gz.
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[-optional overlay volume for tract viewing-] to:
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[-tract rendering mode: 0 for non-interactive-]
[-and 1 for interactive (default)-] to:
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[-tract rendering option: 0 for curve-based and-]
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[--tract rendering option: 0 for curve-based and fast (default) and 1 for tube-based and slow--] Changed line 108 from:
[-tract rendering zoom factor-] to:
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[-number of screenshots to save in-]
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[-DTI volume to retrieve diffusion features for tract annotation-] to:
[--DTI volume to retrieve diffusion features for tract annotation--]
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[-number of screenshots to save in non-interactive viewing mode-] to:
[-number of screenshots to save in-]
[-non-interactive viewing mode-]
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[-tract rendering mode: 0 for non-interactive
and 1 for interactive (default)-] to:
[-tract rendering mode: 0 for non-interactive-]
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[-tract rendering option: 0 for curve-based and
fast (default) and 1 for tube-based and slow-] to:
[-tract rendering option: 0 for curve-based and-]
[-fast (default) and 1 for tube-based and slow-]
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[-tract rendering mode: 0 for non-interactive and 1 for interactive (default)-] to:
[-tract rendering mode: 0 for non-interactive
and 1 for interactive (default)-] Changed lines 104-105 from:
[-tract rendering option: 0 for curve-based and fast (default) and 1 for tube-based and slow-] to:
[-tract rendering option: 0 for curve-based and
fast (default) and 1 for tube-based and slow-]
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[--(optional overlay volume for tract viewing)--] to:
[-optional overlay volume for tract viewing-] Changed line 98 from:
tract rendering mode: 0 for non-interactive and 1 for interactive (default) to:
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tract rendering option: 0 for curve-based and fast (default) and 1 for tube-based and slow to:
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tract rendering zoom factor to:
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number of screenshots to save in non-interactive viewing mode to:
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DTI volume to retrieve diffusion features for tract annotation to:
[-DTI volume to retrieve diffusion features for tract annotation-]
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(optional overlay volume for tract viewing) to:
[--(optional overlay volume for tract viewing)--]
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(:'font-size: smaller':) (optional overlay volume for tract viewing)
to:
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tract rendering mode: 0 for non-interactive and 1 for interactive (default) Changed lines 101-102 from:
(:cell align=center:) 1
(:cellnr align=center:) tract rendering mode: 0 for non-interactive and 1 for interactive (default) to:
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tract rendering option: 0 for curve-based and fast (default) and 1 for tube-based and slow Changed lines 106-107 from:
(:cell align=center:) 0
(:cellnr align=center:) tract rendering option: 0 for curve-based and fast (default) and 1 for tube-based and slow to:
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tract rendering zoom factor Changed lines 111-112 from:
(:cell align=center:) 1.5
(:cellnr align=center:) tract rendering zoom factor to:
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number of screenshots to save in non-interactive viewing mode Deleted line 116:
(:cellnr align=center:) number of screenshots to save in non-interactive viewing mode
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(:cellnr align=center:) prefix for screenshots
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DTI volume to retrieve diffusion features for tract annotation Deleted line 130:
(:cellnr align=center:) DTI volume to retrieve diffusion features for tract annotation
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(:cell style='font-size: smaller':) (optional overlay volume for tract viewing) to:
(:'font-size: smaller':) (optional overlay volume for tract viewing)
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(:div style="font-size:smaller") (optional overlay volume for tract viewing) to:
(:cell style='font-size: smaller':) (optional overlay volume for tract viewing)
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(optional overlay volume for tract viewing) to:
(:div style="font-size:smaller") (optional overlay volume for tract viewing)
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(:cellnr align=center:) -overlay\\ (optional overlay volume for tract viewing) to:
(:cellnr align=center:) -overlay
(optional overlay volume for tract viewing)
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(:cellnr align=center:) -overlay \\ (optional overlay volume for tract viewing) to:
(:cellnr align=center:) -overlay\\ (optional overlay volume for tract viewing)
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(:cellnr align=center:) -overlay (optional overlay volume for tract viewing) to:
(:cellnr align=center:) -overlay \\ (optional overlay volume for tract viewing)
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(:cellnr align=center:) Comment: optional overlay volume for tract viewing
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(:cell align=center:) optional overlay volume for tract viewing to:
(:cellnr align=center:) Comment: optional overlay volume for tract viewing Changed line 101 from:
(:cell align=center:) tract rendering mode: 0 for non-interactive and 1 for interactive (default) to:
(:cellnr align=center:) tract rendering mode: 0 for non-interactive and 1 for interactive (default) Changed line 106 from:
(:cell align=center:) tract rendering option: 0 for curve-based and fast (default) and 1 for tube-based and slow to:
(:cellnr align=center:) tract rendering option: 0 for curve-based and fast (default) and 1 for tube-based and slow Changed line 111 from:
(:cell align=center:) tract rendering zoom factor to:
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(:cell align=center:) number of screenshots to save in non-interactive viewing mode to:
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(:cell align=center:) DTI volume to retrieve diffusion features for tract annotation to:
(:cellnr align=center:) DTI volume to retrieve diffusion features for tract annotation
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'''-nifti''' is used to transform a .vtk tractography volume into a nifti binary image.\\ to:
'''-nifti''' is used to transform a .vtk tractography volume into a nifti binary image. \\
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The output file name is set using the flag "-filter'''
The value of the ROI can be specified using '''-label''', the default value being 1. ROI.nii.gz can then contain several ROIs corresponding to different labels. to:
The output file name is set using the flag "-filter'''.\\
The value of the ROI can be specified using '''-label''', the default value being 1. ROI.nii.gz can then contain several ROIs corresponding to different labels. \\ Changed line 38 from:
'''-inclusion''' is to be used to find the fibers that do NOT go through a specific ROI. In this case, set this flag to 0. to:
'''-inclusion''' is to be used to find the fibers that do NOT go through a specific ROI. In this case, set this flag to 0. \\ Changed lines 45-46 from:
'''-nifti''' is used to transform a .vtk tractography volume into a nifti binary image.
The specifics of the nifti image ''output.nii.gz'' can be defined using '''-target''' followed by an exisiting nifti image, here called target.nii.gz. to:
'''-nifti''' is used to transform a .vtk tractography volume into a nifti binary image.\\
The specifics of the nifti image ''output.nii.gz'' can be defined using '''-target''' followed by an exisiting nifti image, here called target.nii.gz.\\
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The value of the ROI can be specified using '''-label''', the default value being 1. ROI.nii.gz can then contain several ROIs corresponding to different labels. In the following case, we are just interested in the fibers that intersect the region with the value equal to 10.
to:
The value of the ROI can be specified using '''-label''', the default value being 1. ROI.nii.gz can then contain several ROIs corresponding to different labels.
In the following case, we are just interested in the fibers that intersect the region with the value equal to 10.
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'''-inclusion''' is to be used to find the fibers that do NOT go through a specific ROI. In this case, set this flag to 0. The following example outputs a tractography volume ''output.vtk'' that contains all the fibers from ''tracts.vtk'', except the ones intersecting the ROI with value 10. to:
'''-inclusion''' is to be used to find the fibers that do NOT go through a specific ROI. In this case, set this flag to 0.
The following example outputs a tractography volume ''output.vtk'' that contains all the fibers from ''tracts.vtk'', except the ones intersecting the ROI with value 10. Changed lines 45-46 from:
'''-nifti''' is used to transform a .vtk tractography volume into a nifti binary image. The specifics of the nifti image ''output.nii.gz'' can be defined using '''-target''' followed by an exisiting nifti image, here called target.nii.gz. to:
'''-nifti''' is used to transform a .vtk tractography volume into a nifti binary image.
The specifics of the nifti image ''output.nii.gz'' can be defined using '''-target''' followed by an exisiting nifti image, here called target.nii.gz.
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\\\
'''-nifti''' is used to transform a .vtk tractography volume into a nifti binary image. The specifics of the nifti image ''output.nii.gz'' can be defined using '''-target''' followed by an exisiting nifti image, here called target.nii.gz.
[@
TractTool -in tracts.vtk -nifti output.nii.gz -target target.nii.gz
@]
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'''-inclusion''' is to be used to find the fibers that do NOT go through a specific ROI. In this case, set this flag to 0. The following example outputs a tractography volume '''output.vtk'' that contains all the fibers from '''tracts.vtk''', except the ones intersecting the ROI with value 10. to:
'''-inclusion''' is to be used to find the fibers that do NOT go through a specific ROI. In this case, set this flag to 0. The following example outputs a tractography volume ''output.vtk'' that contains all the fibers from ''tracts.vtk'', except the ones intersecting the ROI with value 10.
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\\\
'''-inclusion''' is to be used to find the fibers that do NOT go through a specific ROI. In this case, set this flag to 0. The following example outputs a tractography volume '''output.vtk'' that contains all the fibers from '''tracts.vtk''', except the ones intersecting the ROI with value 10.
[@
TractTool -in tracts.vtk -filter output.vtk -roi ROI.nii.gz -label 10 -inclusion 0
@]
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!!!Basic usage pattern
Specify :
*an input tractography volume using the flag "-in", which takes the file name of the .vtk fiber volume as its argument
Output:
*number of fibers in this volume
[@
TractTool -in tracts.vtk
@]
Example of Output
[@
Reading the input tract ... Done in 0.58s
Number of input fibers = 52615
@]
\\\
'''-roi''' is used to define a specific region of interest (a binary image called ROI.nii.gz), through which a set of fibers go
The output file name is set using the flag "-filter'''
The value of the ROI can be specified using '''-label''', the default value being 1. ROI.nii.gz can then contain several ROIs corresponding to different labels. In the following case, we are just interested in the fibers that intersect the region with the value equal to 10.
[@
TractTool -in tracts.vtk -filter output.vtk -roi ROI.nii.gz -label 10
@]
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!!!Basic usage pattern
Specify :
*an input tractography volume using the flag "-in", which takes the file name of the .vtk fiber volume as its argument
Output:
*number of fibers in this volume
%center%[@
TractTool -in tracts.vtk
@]
Example of Output
[@
Reading the input tract ... Done in 0.58s
Number of input fibers = 52615
@]
!!!List of usage
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Specify :
*an input tractography volume using the flag "-in", which takes the file name of the .vtk fiber volume as its argument
Output:
*number of fibers in this volume
%center%[@
TractTool -in tracts.vtk
Example of Output:
Reading the input tract ... Done in 0.58s
Number of input fibers = 52615
@]
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!!!Simple Example:
!!!Further specification to:
!!!Basic usage pattern
!!!List of usage
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!!!Definition
TractTool limits the tractography using ROIs
to:
(:noleft:)(:notitle:)(:title DTI-TK::TractTool:)
!TractTool documentation
!!!About TractTool
TractTool is a command line utility for identifying, from an input set of fibers, a subset that either intersects or avoids specified regions-of-interest (ROIs).
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!!!Definition
SingleTensorFT is a command that generates white matter tractography of the brain
!!!Usage
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->'''''SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -out tensor.vtk'''''
*tensor.nii.gz: DTI image
*wm.nii.gz: white matter mask that limits the tractography
*tensor.vtk: output file containing the tractography defined by wm.nii.gz
to:
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(:cell align=center:) N
(:cell align=center:)
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(:cell align=center:) -mode to:
(:cellnr align=center:) -mode
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(:cellnr align=center:) N
(:cell align=center:) -view
(:cell align=center:) flag
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(:cellnr align=center:) -view
(:cell align=center:) flag
(:cell align=center:) N
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(:cellr align=center:) -label to:
(:cellnr align=center:) -label
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(:table border=3 cellpadding=5 cellspacing=3 align=center:)
(:head:) specification
(:head:) type
(:head:) required
(:head:) default
(:head:) unit
(:cellnr align=center:) -in
(:cell align=center:) string(s)
(:cell align=center:) Y
(:cell align=center:)
(:cell align=center:)
(:cellnr align=center:) -seed
(:cell align=center:) string(s)
(:cell align=center:) Y
(:cell align=center:)
(:cell align=center:)
(:cellnr align=center:) -label
(:cell align=center:) integer(s)
(:cell align=center:) N
(:cell align=center:) 1
(:cell align=center:)
(:cellnr align=center:) -minLength
(:cell align=center:) double(s)
(:cell align=center:) N
(:cell align=center:) 10
(:cell align=center:) mm
(:cellnr align=center:) -maxLength
(:cell align=center:) double(s)
(:cell align=center:) N
(:cell align=center:) 1000
(:cell align=center:) mm
(:cellnr align=center:) -minFA
(:cell align=center:) double(s)
(:cell align=center:) N
(:cell align=center:) 0.15
(:cell align=center:)
(:cellnr align=center:) -maxAngle
(:cell align=center:) double(s)
(:cell align=center:) N
(:cell align=center:) 45
(:cell align=center:) degrees
(:cellnr align=center:) -stepSize
(:cell align=center:) double(s)
(:cell align=center:) N
(:cell align=center:) 0.5
(:cell align=center:) mm
(:cellnr align=center:) -upsample
(:cell align=center:) integer(s)
(:cell align=center:) N
(:cell align=center:) 1
(:cell align=center:)
(:cellnr align=center:) -out
(:cell align=center:) string(s)
(:cell align=center:) Y
(:cell align=center:)
(:cell align=center:)
(:tableend:)
to:
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(:cellnr align=center:) string(s)
(:cellnr align=center:) Y
(:cellnr align=center:) -filter
(:cellnr align=center:) string(s)
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(:cell align=center:) string(s)
(:cell align=center:) Y
(:cell align=center:) -filter
(:cell align=center:) string(s)
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(:cellnr align=center:) string(s)
(:cellnr align=center:) N
(:cellnr align=center:) -label
(:cellnr align=center:) integer(s)
(:cellnr align=center:) N
(:cellnr align=center:) 1 to:
(:cell align=center:) string(s)
(:cell align=center:) N
(:cellr align=center:) -label
(:cell align=center:) integer(s)
(:cell align=center:) N
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(:cellnr align=center:) integer(s)
(:cellnr align=center:) N
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(:cell align=center:) integer(s)
(:cell align=center:) N
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(:cellnr align=center:) string(s)
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(:cell align=center:) string(s)
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(:cellnr align=center:) -view
(:cellnr align=center:) flag
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(:cell align=center:) -view
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(:cellnr align=center:) string(s)
(:cellnr align=center:) N
(:cellnr align=center:) optional overlay volume for tract viewing
(:cellnr align=center:) -mode
(:cellnr align=center:) integer(s)
(:cellnr align=center:) N
(:cellnr align=center:) 1
(:cellnr align=center:) tract rendering mode: 0 for non-interactive and 1 for interactive (default) to:
(:cell align=center:) string(s)
(:cell align=center:) N
(:cell align=center:) optional overlay volume for tract viewing
(:cell align=center:) -mode
(:cell align=center:) integer(s)
(:cell align=center:) N
(:cell align=center:) 1
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(:cellnr align=center:) integer(s)
(:cellnr align=center:) N
(:cellnr align=center:) 0
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(:cell align=center:) integer(s)
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(:cellnr align=center:) double(s)
(:cellnr align=center:) N
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(:cellnr align=center:) string(s)
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(:cellnr align=center:) DTI volume to retrieve diffusion features for tract annotation
to:
(:cell align=center:) string(s)
(:cell align=center:) N
(:cell align=center:) DTI volume to retrieve diffusion features for tract annotation
!!!Definition
SingleTensorFT is a command that generates white matter tractography of the brain
!!!Usage
(:table border=3 cellpadding=5 cellspacing=3 align=center:)
(:head:) specification
(:head:) type
(:head:) required
(:head:) default
(:head:) unit
(:cellnr align=center:) -in
(:cell align=center:) string(s)
(:cell align=center:) Y
(:cell align=center:)
(:cell align=center:)
(:cellnr align=center:) -seed
(:cell align=center:) string(s)
(:cell align=center:) Y
(:cell align=center:)
(:cell align=center:)
(:cellnr align=center:) -label
(:cell align=center:) integer(s)
(:cell align=center:) N
(:cell align=center:) 1
(:cell align=center:)
(:cellnr align=center:) -minLength
(:cell align=center:) double(s)
(:cell align=center:) N
(:cell align=center:) 10
(:cell align=center:) mm
(:cellnr align=center:) -maxLength
(:cell align=center:) double(s)
(:cell align=center:) N
(:cell align=center:) 1000
(:cell align=center:) mm
(:cellnr align=center:) -minFA
(:cell align=center:) double(s)
(:cell align=center:) N
(:cell align=center:) 0.15
(:cell align=center:)
(:cellnr align=center:) -maxAngle
(:cell align=center:) double(s)
(:cell align=center:) N
(:cell align=center:) 45
(:cell align=center:) degrees
(:cellnr align=center:) -stepSize
(:cell align=center:) double(s)
(:cell align=center:) N
(:cell align=center:) 0.5
(:cell align=center:) mm
(:cellnr align=center:) -upsample
(:cell align=center:) integer(s)
(:cell align=center:) N
(:cell align=center:) 1
(:cell align=center:)
(:cellnr align=center:) -out
(:cell align=center:) string(s)
(:cell align=center:) Y
(:cell align=center:)
(:cell align=center:)
(:tableend:)
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!!!Definition
TractTool limits the tractography using ROIs
!!!Usage
(:table border=3 cellpadding=5 cellspacing=3 align=center:)
(:head:) specification
(:head:) type
(:head:) required
(:head:) default
(:cellnr align=center:) -in
(:cellnr align=center:) string(s)
(:cellnr align=center:) Y
(:cellnr align=center:) -filter
(:cellnr align=center:) string(s)
(:cellnr align=center:) N
(:cellnr align=center:) -roi
(:cellnr align=center:) string(s)
(:cellnr align=center:) N
(:cellnr align=center:) -label
(:cellnr align=center:) integer(s)
(:cellnr align=center:) N
(:cellnr align=center:) 1
(:cellnr align=center:) -inclusion
(:cellnr align=center:) integer(s)
(:cellnr align=center:) N
(:cellnr align=center:) 1
(:cellnr align=center:) -nifti
(:cellnr align=center:) string(s)
(:cellnr align=center:) N
(:cellnr align=center:) -target
(:cellnr align=center:) string(s)
(:cellnr align=center:) N
(:cellnr align=center:) -view
(:cellnr align=center:) flag
(:cellnr align=center:) N
(:cellnr align=center:) -overlay
(:cellnr align=center:) string(s)
(:cellnr align=center:) N
(:cellnr align=center:) optional overlay volume for tract viewing
(:cellnr align=center:) -mode
(:cellnr align=center:) integer(s)
(:cellnr align=center:) N
(:cellnr align=center:) 1
(:cellnr align=center:) tract rendering mode: 0 for non-interactive and 1 for interactive (default)
(:cellnr align=center:) -useTube
(:cellnr align=center:) integer(s)
(:cellnr align=center:) N
(:cellnr align=center:) 0
(:cellnr align=center:) tract rendering option: 0 for curve-based and fast (default) and 1 for tube-based and slow
(:cellnr align=center:) -zoom
(:cellnr align=center:) double(s)
(:cellnr align=center:) N
(:cellnr align=center:) 1.5
(:cellnr align=center:) tract rendering zoom factor
(:cellnr align=center:) -png
(:cellnr align=center:) integer(s)
(:cellnr align=center:) N
(:cellnr align=center:) 20
(:cellnr align=center:) number of screenshots to save in non-interactive viewing mode
(:cellnr align=center:) -prefix
(:cellnr align=center:) string(s)
(:cellnr align=center:) N
(:cellnr align=center:) prefix for screenshots
(:cellnr align=center:) -annotate
(:cellnr align=center:) string(s)
(:cellnr align=center:) N
(:cellnr align=center:) -source
(:cellnr align=center:) string(s)
(:cellnr align=center:) N
(:cellnr align=center:) DTI volume to retrieve diffusion features for tract annotation
!!!Simple Example:
->'''''SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -out tensor.vtk'''''
*tensor.nii.gz: DTI image
*wm.nii.gz: white matter mask that limits the tractography
*tensor.vtk: output file containing the tractography defined by wm.nii.gz
!!!Further specification
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