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Documentation.SingleTensorFT History
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!!!Basic Usage Pattern:
Specify :
*an input tensor volume using the flag "-in", which takes the file name of the tensor volume as its argument
*a white matter mask using the "-seed", to which the tractography will be limited
*the name of the output file using "-out"
[@
SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -out tensor.vtk
@]
!!!List of Usage
'''-label''' is an option to modify if the value of the binary nifti image is different from 1, in the following case, it is 10
[@
SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -label 10 -out tensor.vtk
@]
\\\
'''-minLength''' and '''-maxLength''' determine the minimum and maximum sizes of the fibers. In the following case, the tractography will only encompass the fibers that measure between 100 and 150mm
[@
SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -minLength 100 -maxLength 150 -out tensor.vtk
@]
\\\
'''-minFA''' and '''maxAngle''' are two stopping criteria. The following example will perform the tractography until very low FA values (0.05) and high angles (with the possibility of tracts turning at right angles)
[@
SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -minFA 0.05 -maxAngle 90 -out tensor.vtk
@]
\\\
'''-stepSize''' defines the length of a step through the diffusion tensor field. The default value is 0.5 but if one is interested in long tracts only, increasing this value increases the speed of the process.
[@
SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -stepSize 2 -out tensor.vtk
@]
\\\
'''-upsample''' can be modified if the initial resolution of the tensor image is very low and the user wants a denser tractography. In the following case, the fiber bundles are 3 times denser than what they would have been with the default value
%center%[@
SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -upsample 3 -out tensor.vtk
@]
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!!!Basic Usage Pattern:
Specify :
*an input tensor volume using the flag "-in", which takes the file name of the tensor volume as its argument
*a white matter mask using the "-seed", to which the tractography will be limited
*the name of the output file using "-out"
%center%[@
SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -out tensor.vtk
@]
!!!List of Usage
'''-label''' is an option to modify if the value of the binary nifti image is different from 1, in the following case, it is 10
%center%[@
SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -label 10 -out tensor.vtk
@]
\\\
'''-minLength''' and '''-maxLength''' determine the minimum and maximum sizes of the fibers. In the following case, the tractography will only encompass the fibers that measure between 100 and 150mm
%center%[@
SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -minLength 100 -maxLength 150 -out tensor.vtk
@]
\\\
'''-minFA''' and '''maxAngle''' are two stopping criteria. The following example will perform the tractography until very low FA values (0.05) and high angles (with the possibility of tracts turning at right angles)
%center%[@
SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -minFA 0.05 -maxAngle 90 -out tensor.vtk
@]
\\\
'''-stepSize''' defines the length of a step through the diffusion tensor field. The default value is 0.5 but if one is interested in long tracts only, increasing this value increases the speed of the process.
%center%[@
SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -stepSize 2 -out tensor.vtk
@]
\\\
'''-upsample''' can be modified if the initial resolution of the tensor image is very low and the user wants a denser tractography. In the following case, the fiber bundles are 3 times denser than what they would have been with the default value
%center%[@
SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -upsample 3 -out tensor.vtk
@]
to:
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'''-upsample''' can be modified if the initial resolution of the tensor image is very low and the user wants a denser tractography. In the following case, the fiber bundles are 3 times densers than what they would have been with the default value to:
'''-upsample''' can be modified if the initial resolution of the tensor image is very low and the user wants a denser tractography. In the following case, the fiber bundles are 3 times denser than what they would have been with the default value
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''' -stepSize''': length of a step through the diffusion tensor field
* upsample: value that needs to be changed for denser tracts in the case of low resolution DTI image
to:
\\\
'''-stepSize''' defines the length of a step through the diffusion tensor field. The default value is 0.5 but if one is interested in long tracts only, increasing this value increases the speed of the process.
%center%[@
SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -stepSize 2 -out tensor.vtk
@]
\\\
'''-upsample''' can be modified if the initial resolution of the tensor image is very low and the user wants a denser tractography. In the following case, the fiber bundles are 3 times densers than what they would have been with the default value
%center%[@
SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -upsample 3 -out tensor.vtk
@]
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'''-minLength''' and '''-maxLength''' determine the minimum and maximum sizes of the fibers
to:
'''-minLength''' and '''-maxLength''' determine the minimum and maximum sizes of the fibers. In the following case, the tractography will only encompass the fibers that measure between 100 and 150mm
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SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -minLength 10 -maxLength 10 -out tensor.vtk to:
SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -minLength 100 -maxLength 150 -out tensor.vtk Changed lines 90-94 from:
* minLength:
* maxLength
* minFA: stopping ; FA value under which the tractography will stop
* maxAngle: stopping criteria; Angle over which the tractography will stop
* stepSize: length of a step through the diffusion tensor field
to:
'''-minFA''' and '''maxAngle''' are two stopping criteria. The following example will perform the tractography until very low FA values (0.05) and high angles (with the possibility of tracts turning at right angles)
%center%[@
SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -minFA 0.05 -maxAngle 90 -out tensor.vtk
@]
''' -stepSize''': length of a step through the diffusion tensor field
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'''-minLength''' and '''-maxLength''' determine the minimum and maximum sizes of the fibers
%center%[@
SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -minLength 10 -maxLength 10 -out tensor.vtk
@]
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''-label'' is an option to be modified if the value of the label is different that 1, in this case, the value of the nifti binary image is 10 instead of 1 to:
'''-label''' is an option to modify if the value of the binary nifti image is different from 1, in the following case, it is 10
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* label: to be modified if the value of the label is different that 1
to:
''-label'' is an option to be modified if the value of the label is different that 1, in this case, the value of the nifti binary image is 10 instead of 1
%center%[@
SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -label 10 -out tensor.vtk
@]
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Specify :
*an input tensor volume using the flag "-in", which takes the file name of the tensor volume as its argument
*a white matter mask using the "-seed", to which the tractography will be limited
*the name of the output file using "-out"
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*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
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[@
%center%SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -out tensor.vtk to:
%center%[@
SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -out tensor.vtk
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SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -out tensor.vtk to:
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%block text-align=center% SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -out tensor.vtk
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SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -out tensor.vtk Added lines 73-74:
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%center% SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -out tensor.vtk to:
%block text-align=center% SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -out tensor.vtk
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SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -out tensor.vtk to:
%center% SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -out tensor.vtk
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->'''''SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -out tensor.vtk'''''
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->[@
SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -out tensor.vtk
@]
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!!!Definition
SingleTensorFT is a command that generates white matter tractography of the brain
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!!!About SingleTensorFT
SingleTensorFT is a command line utility for generating white matter tractography of the brain from a DTI volume.
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(:noleft:)(:notitle:)(:title DTI-TK::SingleTensorFT:)
!SingleTensorFT documentation
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'''''SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -out tensor.vtk'''''
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->'''''SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -out tensor.vtk'''''
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* seed:
* label
* minLength to:
* label: to be modified if the value of the label is different that 1
* minLength: Changed lines 76-83 from:
* minFA
* maxAngle
* stepSize
* upsample
to:
* minFA: stopping criteria; FA value under which the tractography will stop
* maxAngle: stopping criteria; Angle over which the tractography will stop
* stepSize: length of a step through the diffusion tensor field
* upsample: value that needs to be changed for denser tracts in the case of low resolution DTI image
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!!!Definition
SingleTensorFT is a command that generates white matter tractography of the brain
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(:cell:) mm
(:cellnr:) -upsample to:
(:cell align=center:) mm
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!!!Further specification
* seed:
* label
* minLength
* maxLength
* minFA
* maxAngle
* stepSize
* upsample
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->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
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*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
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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
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->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
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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
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!!!Usage of SingleTensorFT
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!!!Usage of SingleTensorFT
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Simple Example:
->'''''SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -out tensor.vtk''''' to:
!!!Simple Example:
'''''SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -out tensor.vtk'''''
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->''SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -out tensor.vtk''<- to:
->'''''SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -out tensor.vtk'''''
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(:tableend:)
Simple Example:
->''SingleTensorFT -in tensor.nii.gz -seed wm.nii.gz -out tensor.vtk''<-
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(:cellnr align=center:) -in
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(:cell:) string(s)
(:cell:) Y
(:cell:)
(:cell:)
(:cellnr:) -seed
(:cell:) string(s)
:cell:) Y
:)
(:cell:)
(:cellnr:) -label
:) integer(s)
:) N
:cell:) 1
:)
(:cellnr:) -minLength
:) double(s)
:) N
(:cell:) 10 to:
(: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
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(:cellnr:) -maxLength
(:cell:) double(s)
(:cell:) N
(:cell:) 1000
(:cell:) mm
(:cellnr:) -minFA
(:cell:) double(s)
(:cell:) N
(:cell:) 0.15
(:cell:)
(:cellnr:) -maxAngle
(:cell:) double(s)
(:cell:) N
(:cell:) 45
(:cell:) degrees
(:cellnr:) -stepSize
(:cell:) double(s)
(:cell:) N
(:cell:) 0.5
(:cell:) mm
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(:cell:)
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(: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:)
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(:cell:) required
(:cell:) default
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(:head:) required
(:head:) default
(:head:) unit
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(:table border=3 cellpadding=5 cellspacing=3:) to:
(:table border=3 cellpadding=5 cellspacing=3 align=center:)
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(:table border=3 cellpadding=5 cellspacing=3:)
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(:table border=3 cellpadding=5 cellspacing=0:)
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(:headnr:) -in (:cell:) string(s) (:cell:) Y (:cell:) (:cell:)
(:headnr:) -seed (:cell:) string(s) (:cell:) Y (:cell:) (:cell:)
(:headnr:) -label (:cell:) integer(s) (:cell:) N (:cell:) 1 (:cell:)
(:headnr:) -minLength (:cell:) double(s) (:cell:) N (:cell:) 10 (:cell:)mm
(:headnr:) -maxLength (:cell:) double(s) (:cell:) N (:cell:) 1000 (:cell:) mm
(:headnr:) -minFA (:cell:) double(s) (:cell:) N (:cell:) 0.15 (:cell:)
(:headnr:) -maxAngle (:cell:) double(s) (:cell:) N (:cell:) 45 (:cell:) degrees
(:headnr:) -stepSize (:cell:) double(s) (:cell:) N (:cell:) 0.5 (:cell:) mm
(:headnr:) -upsample (:cell:) integer(s) (:cell:) N (:cell:) 1 (:cell:)
(:headnr:) -out (:cell:) string(s) (:cell:) Y (:cell:) (:cell:)
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(:headnr:) -in
(:cell:) string(s)
(:cell:) Y
(:cell:)
(:cell:)
(:headnr:) -seed
(:cell:) string(s)
(:cell:) Y
(:cell:)
(:cell:)
(:headnr:) -label
(:cell:) integer(s)
(:cell:) N
(:cell:) 1
(:cell:)
(:headnr:) -minLength
(:cell:) double(s)
(:cell:) N
(:cell:) 10
(:cell:) mm
(:headnr:) -maxLength
(:cell:) double(s)
(:cell:) N
(:cell:) 1000
(:cell:) mm
(:headnr:) -minFA
(:cell:) double(s)
(:cell:) N
(:cell:) 0.15
(:cell:)
(:headnr:) -maxAngle
(:cell:) double(s)
(:cell:) N
(:cell:) 45
(:cell:) degrees
(:headnr:) -stepSize
(:cell:) double(s)
(:cell:) N
(:cell:) 0.5
(:cell:) mm
(:headnr:) -upsample
(:cell:) integer(s)
(:cell:) N
(:cell:) 1
(:cell:)
(:headnr:) -out
(:cell:) string(s)
(:cell:) Y
(:cell:)
(:cell:)
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(:head:) specification (:cell:) type (:cell:) required (:cell:) default (:cell:) unit to:
(:head:) specification
(:cell:) type
(:cell:) required
(:cell:) default
(:cell:) unit
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-in type: string(s) required: Y
-seed type: string(s) required: Y
-label type: integer(s) required: N default: 1
-minLengthtype: double(s) required: N default: 10 in mm
-maxLength type: double(s) required: N default: 1000 in mm
-minFA type: double(s) required: N default: 0.15
-maxAngle type: double(s) required: N default: 45 in degrees
stepSize type: double(s) required: N default: 0.5 in mm
-upsample type: integer(s) required: N default: 1
-out type: string(s) required: Y
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(:table border=1 cellpadding=5 cellspacing=0:)
(:head:) specification (:cell:) type (:cell:) required (:cell:) default (:cell:) unit
(:headnr:) -in (:cell:) string(s) (:cell:) Y (:cell:) (:cell:)
(:headnr:) -seed (:cell:) string(s) (:cell:) Y (:cell:) (:cell:)
(:headnr:) -label (:cell:) integer(s) (:cell:) N (:cell:) 1 (:cell:)
(:headnr:) -minLength (:cell:) double(s) (:cell:) N (:cell:) 10 (:cell:)mm
(:headnr:) -maxLength (:cell:) double(s) (:cell:) N (:cell:) 1000 (:cell:) mm
(:headnr:) -minFA (:cell:) double(s) (:cell:) N (:cell:) 0.15 (:cell:)
(:headnr:) -maxAngle (:cell:) double(s) (:cell:) N (:cell:) 45 (:cell:) degrees
(:headnr:) -stepSize (:cell:) double(s) (:cell:) N (:cell:) 0.5 (:cell:) mm
(:headnr:) -upsample (:cell:) integer(s) (:cell:) N (:cell:) 1 (:cell:)
(:headnr:) -out (:cell:) string(s) (:cell:) Y (:cell:) (:cell:)
(:tableend:)
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Usage of SingleTensorFT
-in type: string(s) required: Y
-seed type: string(s) required: Y
-label type: integer(s) required: N default: 1
-minLength type: double(s) required: N default: 10 in mm
-maxLength type: double(s) required: N default: 1000 in mm
-minFA type: double(s) required: N default: 0.15
-maxAngle type: double(s) required: N default: 45 in degrees
-stepSize type: double(s) required: N default: 0.5 in mm
-upsample type: integer(s) required: N default: 1
-out type: string(s) required: Y
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