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Diffusion Tensor Imaging ToolKit

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Documentation::DTI-TK::TVtool

Documentation.TVtool History

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March 04, 2011, at 11:12 PM by Caroline -
Changed lines 52-63 from:
 
to:
To compute the principal diffusion direction image
 
->[@ TVtool -in tensor.nii.gz -pd
@]
 
To compute the principal diffusion direction mapped into an RGB image
 
->[@ TVtool -in tensor.nii.gz -rgb
@]
 
 
 
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March 01, 2011, at 10:16 PM by 172.29.30.74 -
Changed lines 193-194 from:
(:cell align=center:) N
to:
(:cell align=center:) N 
(:cell align=center:)
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March 01, 2011, at 10:14 PM by 172.29.30.73 -
Added lines 51-214:


!!!List of options
(:table border=3 cellpadding=5 cellspacing=3 align=center:)
(:head:) specification 
(:head:) type 
(:head:) required
(:head:)  default
(:cellnr align=center:) -in
(:cell align=center:) string(s)
(:cell align=center:) Y
(:cell align=center:)
(:cellnr align=center:) -out
(:cell align=center:) string(s)
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -ad
(:cell align=center:) flag
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -rd
(:cell align=center:) flag
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -tr
(:cell align=center:) flag
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -fa
(:cell align=center:) flag
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -norm
(:cell align=center:) flag
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -dnorm
(:cell align=center:) flag
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -tsp
(:cell align=center:) flag
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -dtsp
(:cell align=center:) flag
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -dydisp
(:cell align=center:) flag
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -dycoh
(:cell align=center:) flag
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -lps
(:cell align=center:) flag
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -eigs
(:cell align=center:) flag
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -pdmp
(:cell align=center:) flag
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -faThreshold
(:cell align=center:) double(s)
(:cell align=center:) N
(:cell align=center:) 0.2
(:cellnr align=center:) -pd 
(:cell align=center:) flag 
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -rgb
(:cell align=center:) flag
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -faWeighting 
(:cell align=center:) integer(s)
(:cell align=center:) N
(:cell align=center:) 1
(:cellnr align=center:) -spd
(:cell align=center:) flag   
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -reorient
(:cell align=center:)  flag 
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -trans
(:cell align=center:) string(s) 
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -euler   
(:cell align=center:) double(s)   
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -dev     
(:cell align=center:) flag     
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -dyadic   
(:cell align=center:) flag     
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -index       
(:cell align=center:) integer(s) 
(:cell align=center:) N
(:cell align=center:) 0
(:cellnr align=center:) -scale 
(:cell align=center:) double(s)
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -add         
(:cell align=center:) string(s)   
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -subtract
(:cell align=center:) string(s) 
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -mosaic   
(:cell align=center:) string(s)   
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -piece     
(:cell align=center:) integer(s) 
(:cell align=center:) N
(:cell align=center:) 16
(:cellnr align=center:) -aop     
(:cell align=center:) string(s) 
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -mask
(:cell align=center:) string(s)   
(:cell align=center:)  N
(:cell align=center:)
(:cellnr align=center:) -nan
(:cell align=center:)  flag   
(:cell align=center:) N
(:cellnr align=center:) -print     
(:cell align=center:) string(s)   
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -vsm     
(:cell align=center:) string(s) 
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -sm       
(:cell align=center:) string(s)
(:cell align=center:) N
(:cell align=center:)
(:cellnr align=center:) -SMOption 
(:cell align=center:) string(s)   
(:cell align=center:) N
(:cell align=center:) EDS, ED, DDS, EDS or GDS
(:cellnr align=center:) -replacement 
(:cell align=center:) string(s) 
(:cell align=center:) N
(:cell align=center:)
(:tableend:)
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March 01, 2011, at 08:18 PM by 172.29.30.67 -
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March 01, 2011, at 08:12 PM by 172.29.30.72 -
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February 25, 2011, at 12:29 PM by 172.29.30.71 -
Changed lines 12-13 from:
* specify an input tensor volume using the flag "-in" which takes the file name of the tensor volume as its argument
 
to:
* Specify an input tensor volume using the flag "-in" which takes the file name of the tensor volume as its argument
 
Changed lines 18-22 from:
* specify a processing task using additional flag(s)
 
!!!List of Usages
To compute the map of fractional anisotropy (FA)
 
to:
* Specify a processing task using additional flag(s), e.g. the flag "-fa" without any arguments is used to compute the FA map
 
Added lines 22-31:
@]
->The computed FA map will be saved as tensor_fa.nii.gz
 
* Output file name is set to some default value based on the input file name (like the example above) but can be customized using the flag "-out" with an argument
 
!!!List of Usages
To compute the map of fractional anisotropy (FA)
 
->[@
TVtool -in tensor.nii.gz -fa
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February 25, 2011, at 12:08 PM by 172.29.30.66 -
Changed lines 9-10 from:
 
to:
** computing arithmetic of two tensor volumes, such as addition
 
Changed lines 12-13 from:
* provide an input tensor volume using the flag "-in" followed by the file name of the tensor volume
 
to:
* specify an input tensor volume using the flag "-in" which takes the file name of the tensor volume as its argument
 
Changed lines 18-19 from:
* provide additional flag(s) to specify a processing task
 
to:
* specify a processing task using additional flag(s)
 
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February 25, 2011, at 12:01 PM by 172.29.30.75 -
Changed lines 4-6 from:
!!!List of Usages
To compute the map of fractional anisotropy (FA)
 
to:
!!!About TVtool
* TVtool is a command line utility for basic processing of tensor volumes, including
** computing maps of tensor-derived scalar indices, such as fractional anisotropy (FA)
** computing maps of tensor-derived vectors, such as the eigenvectors
** computing maps of related tensors, such as the deviatoric tensors
 
!!!Basic Usage Pattern
* provide an input tensor volume using the flag "-in" followed by the file name of the tensor volume
 
Added lines 14-22:
TVtool -in tensor.nii.gz
@]
 
* provide additional flag(s) to specify a processing task
 
!!!List of Usages
To compute the map of fractional anisotropy (FA)
 
->[@
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February 23, 2011, at 11:36 PM by 172.29.30.67 -
Changed lines 11-12 from:
To compute the map of trace (TR) (Trace is equal to 3 times the mean diffusivity)
 
to:
To compute the map of trace (TR) (equal to 3 times the mean diffusivity)
 
Changed lines 15-27 from:
@]\\
to:
@]\\ 
 
To compute the map of axial diffusivity (AD)
 
->[@
TVtool -in tensor.nii.gz -ad
@]\\
 
To compute the map of radial diffusivity (RD)
 
->[@
TVtool -in tensor.nii.gz -rd
@]
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February 23, 2011, at 11:34 PM by 172.29.30.69 -
Changed lines 5-6 from:
To compute the Fractional Anisotropy (FA)
 
to:
To compute the map of fractional anisotropy (FA)
 
Changed lines 9-15 from:
@]
to:
@]\\
 
To compute the map of trace (TR) (Trace is equal to 3 times the mean diffusivity)
 
->[@
TVtool -in tensor.nii.gz -tr
@]\\
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February 23, 2011, at 11:28 PM by 172.29.30.72 -
Changed lines 4-5 from:
!!!Usage of TVtool
*To compute the Fractional Anisotropy (FA)
to:
!!!List of Usages
To compute the Fractional Anisotropy (FA) 
 
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February 23, 2011, at 11:24 PM by 172.29.30.74 -
Changed lines 4-8 from:
!!Usage of TVtool
to:
!!!Usage of TVtool 
*To compute the Fractional Anisotropy (FA)
->[@
TVtool -in tensor.nii.gz -fa
@]
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February 23, 2011, at 11:15 PM by 172.29.30.65 -
Changed lines 2-4 from:
!TVtool documentation
to:
!TVtool documentation 
 
!!Usage of TVtool
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February 23, 2011, at 11:14 PM by 172.29.30.73 -
Changed line 1 from:
(:noside:)(:notitle:)(:title DTI-TK::TVtool:)
to:
(:noleft:)(:notitle:)(:title DTI-TK::TVtool:)
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February 23, 2011, at 11:12 PM by 172.29.30.67 -
Added lines 1-2:
(:noside:)(:notitle:)(:title DTI-TK::TVtool:)
!TVtool documentation
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February 23, 2011, at 10:36 PM by 172.29.30.69 -
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