Tubegen - Revision history

Jadrian Miles at 17:05, 24 March 2009

2009-03-24T17:05:44Z

← Older revision		Revision as of 17:05, 24 March 2009
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	We use this program extensively in the [[diffusion MRI]] project and it is generally run at the end of the [[diffusion processing pipeline]].		We use this program extensively in the [[diffusion MRI]] project and it is generally run at the end of the [[diffusion processing pipeline]].

			To submit bugs and feature requests, go to [[/bugs and feature requests\|the bug page]].

	== Code Overview ==		== Code Overview ==

Jadrian Miles: /* Technical Details */

2009-03-24T16:33:26Z

Technical Details

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	== Technical Details ==		== Technical Details ==

	We use 2nd-order Runge-Kutta numerical integration with tricubic b-spline interpolation of the principle eigenvectors; the citation we've used for this process is:		We use 2nd- (or 4th-) order Runge-Kutta numerical integration with tricubic b-spline interpolation of the principle eigenvectors; the citation we've used for this process is:
	{{infobox\|Peter J. Basser, Sinisa Pajevic, Carlo Pierpaoli, Jeffrey Duda, and Akram Aldroubi. '''In vivo fiber tractography using DT-MRI data'''. ''Magnetic Resonance in Medicine'', 44:625632, 2000. ([http://stbb.nichd.nih.gov/bass_paj_pier.pdf PDF])}}		{{infobox\|Peter J. Basser, Sinisa Pajevic, Carlo Pierpaoli, Jeffrey Duda, and Akram Aldroubi. '''In vivo fiber tractography using DT-MRI data'''. ''Magnetic Resonance in Medicine'', 44:625632, 2000. ([http://stbb.nichd.nih.gov/bass_paj_pier.pdf PDF])}}

Jadrian Miles: /* Code Overview */

2009-03-24T16:33:11Z

Code Overview

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	# Throw away the streamlines that are too short, have too low anisotropy (<tt>tubegen</tt> uses linear, not fractional, anisotropy in the current version), etc.		# Throw away the streamlines that are too short, have too low anisotropy (<tt>tubegen</tt> uses linear, not fractional, anisotropy in the current version), etc.
	# Compute a pairwise curve distance between all the remaining curves and throw away curves that are too close to others.		# Compute a pairwise curve distance between all the remaining curves and throw away curves that are too close to others.
	# Generate a streamtube model (a curvy cylindrical shape around each streamline)		# Generate a streamtube model (a curvy cylindrical shape around each streamline).

	== Technical Details ==		== Technical Details ==

Jadrian Miles: /* Code Overview */

2009-03-24T16:32:58Z

Code Overview

← Older revision		Revision as of 16:32, 24 March 2009
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	== Code Overview ==		== Code Overview ==
	The <code>tubegen</code> command may be found in <code>$G/bin/tubegen</code>. The source code for the program lives in <code>$G/src/tubegen</code>, but it is just a simple command-line interface to the [[#streamtube Library\|<tt>streamtube</tt> library]], the source of which is located at <code>$G/src/streamtube</code>. The program generates a <tt>*.sm</tt> file, which [[brainapp]] reads in order to visualize and interact with the streamtubes, as well as several other [[#Output Files\|output files]].		The <code>tubegen</code> command may be found in <code>$G/bin/tubegen</code>. The source code for the program lives in <code>$G/src/tubegen</code>, but it is just a simple command-line interface to the [[#streamtube Library\|<tt>streamtube</tt> library]], the source of which is located at <code>$G/src/streamtube</code>. The program generates a <tt>*.sm</tt> file, which [[brainapp]] reads in order to visualize and interact with the streamtubes, as well as several other [[#Output Files\|output files]].

			The basic sequence of the program is as follows:
			# Generate a set of seed points
			# Generate a set of streamlines advected from those points
			# Throw away the streamlines that are too short, have too low anisotropy (<tt>tubegen</tt> uses linear, not fractional, anisotropy in the current version), etc.
			# Compute a pairwise curve distance between all the remaining curves and throw away curves that are too close to others.
			# Generate a streamtube model (a curvy cylindrical shape around each streamline)

	== Technical Details ==		== Technical Details ==

Jadrian Miles: /* Common Arguments */

2009-03-24T16:23:32Z

Common Arguments

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	! style="text-align:left;" \| <tt>t2</tt>		! style="text-align:left;" \| <tt>t2</tt>
	\| str \|\| T2-weighted image path \|\| <tt>/u/sz/diffusion/data/susumu/mri/T2</tt>		\| str \|\| T2-weighted image path \|\| <tt>/u/sz/diffusion/data/susumu/mri/T2</tt>
	\|-
	~~! style="text-align:left;" \| <tt>FA</tt>~~
	~~\| str \|\| Fractional Anisotropy image \|\| <tt>./d2mem/FA</tt>~~
	\|-		\|-
	! colspan=4 \| Output Files		! colspan=4 \| Output Files

Jadrian Miles: /* Common Arguments */

2009-03-24T16:20:34Z

Common Arguments

Jadrian Miles: /* Common Arguments */

2009-03-24T16:17:51Z

Common Arguments

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	\|-		\|-
	! style="text-align:left;" \| <tt>out</tt>		! style="text-align:left;" \| <tt>out</tt>
	\| str \|\| Output sm file \|\| /map/gfx0/common0/diffusion/Interface/bin/tubegen/1.sm		\| str \|\| Output <tt>.sm</tt> file. Note that even if you use the <tt>-SAVESM 0</tt> to avoid generating tubes from the streamlines, this argument still must be specified and must end in "<tt>.sm</tt>". \|\| /map/gfx0/common0/diffusion/Interface/bin/tubegen/1.sm
	\|-		\|-
	! colspan=4 \| Integration Parameters		! colspan=4 \| Integration Parameters

Jadrian Miles: /* Common Arguments */

2009-03-24T15:47:26Z

Common Arguments

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	\|-		\|-
	! style="text-align:left;" \| <tt>cs</tt>		! style="text-align:left;" \| <tt>cs</tt>
	\| n \|\| ~~Max~~ tube length in cm \|\| 20		\| n \|\| Min tube length in mm \|\| 20
	\|-		\|-
	! style="text-align:left;" \| <tt>seed</tt>		! style="text-align:left;" \| <tt>seed</tt>

Jadrian Miles: /* Common Arguments */

2009-03-24T14:30:44Z

Common Arguments

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	! style="text-align:left;" \| <tt>stepsize</tt>		! style="text-align:left;" \| <tt>stepsize</tt>
	\| f \|\| Stepsize in mm \|\| 1.0		\| f \|\| Stepsize in mm \|\| 1.0
	\|-
	~~! style="text-align:left;" \| <tt>radius</tt>~~
	~~\| f \|\| Streamtube radius in mm \|\| 1.0~~
	\|-		\|-
	! style="text-align:left;" \| <tt>al</tt>		! style="text-align:left;" \| <tt>al</tt>
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	! style="text-align:left;" \| <tt>cd</tt>		! style="text-align:left;" \| <tt>cd</tt>
	\| f \|\| Min distance between tubes in mm. Set this to 0 to avoid an O(n<sup>2</sup>) pairwise distance check. \|\| 2.0		\| f \|\| Min distance between tubes in mm. Set this to 0 to avoid an O(n<sup>2</sup>) pairwise distance check. \|\| 2.0
			\|-
			! colspan=4 \| Mesh Generation
			\|-
			! style="text-align:left;" \| <tt>radius</tt>
			\| f \|\| Streamtube radius in mm \|\| 1.0
	\|}		\|}

Jadrian Miles: /* Common Arguments */

2009-03-24T13:55:58Z

Common Arguments

← Older revision		Revision as of 13:55, 24 March 2009
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	\|-		\|-
	! style="text-align:left;" \| <tt>cd</tt>		! style="text-align:left;" \| <tt>cd</tt>
	\| f \|\| Min distance between tubes in mm \|\| 2.0		\| f \|\| Min distance between tubes in mm. Set this to 0 to avoid an O(n<sup>2</sup>) pairwise distance check. \|\| 2.0
	\|}		\|}

← Older revision		Revision as of 16:23, 24 March 2009
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	! style="text-align:left;" \| <tt>t2</tt>		! style="text-align:left;" \| <tt>t2</tt>
	\| str \|\| T2-weighted image path \|\| <tt>/u/sz/diffusion/data/susumu/mri/T2</tt>		\| str \|\| T2-weighted image path \|\| <tt>/u/sz/diffusion/data/susumu/mri/T2</tt>
	\|-
	~~! style="text-align:left;" \| <tt>FA</tt>~~
	~~\| str \|\| Fractional Anisotropy image \|\| <tt>./d2mem/FA</tt>~~
	\|-		\|-
	! colspan=4 \| Output Files		! colspan=4 \| Output Files

← Older revision		Revision as of 14:30, 24 March 2009
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	! style="text-align:left;" \| <tt>stepsize</tt>		! style="text-align:left;" \| <tt>stepsize</tt>
	\| f \|\| Stepsize in mm \|\| 1.0		\| f \|\| Stepsize in mm \|\| 1.0
	\|-
	~~! style="text-align:left;" \| <tt>radius</tt>~~
	~~\| f \|\| Streamtube radius in mm \|\| 1.0~~
	\|-		\|-
	! style="text-align:left;" \| <tt>al</tt>		! style="text-align:left;" \| <tt>al</tt>
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	! style="text-align:left;" \| <tt>cd</tt>		! style="text-align:left;" \| <tt>cd</tt>
	\| f \|\| Min distance between tubes in mm. Set this to 0 to avoid an O(n<sup>2</sup>) pairwise distance check. \|\| 2.0		\| f \|\| Min distance between tubes in mm. Set this to 0 to avoid an O(n<sup>2</sup>) pairwise distance check. \|\| 2.0
			\|-
			! colspan=4 \| Mesh Generation
			\|-
			! style="text-align:left;" \| <tt>radius</tt>
			\| f \|\| Streamtube radius in mm \|\| 1.0
	\|}		\|}

← Older revision		Revision as of 16:20, 24 March 2009
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	\|-		\|-
	! style="text-align:left;" \| <tt>dt</tt>		! style="text-align:left;" \| <tt>dt</tt>
	\| str \|\| Diffusion tensor image path \|\| /u/sz/diffusion/data/susumu/mri/Diff		\| str \|\| Diffusion tensor image path \|\| <tt>/u/sz/diffusion/data/susumu/mri/Diff</tt>
	\|-		\|-
	! style="text-align:left;" \| <tt>t2</tt>		! style="text-align:left;" \| <tt>t2</tt>
	\| str \|\| T2-weighted image path \|\| /u/sz/diffusion/data/susumu/mri/T2		\| str \|\| T2-weighted image path \|\| <tt>/u/sz/diffusion/data/susumu/mri/T2</tt>
	\|-		\|-
	! style="text-align:left;" \| <tt>FA</tt>		! style="text-align:left;" \| <tt>FA</tt>
	\| str \|\| Fractional Anisotropy image \|\| ./d2mem/FA		\| str \|\| Fractional Anisotropy image \|\| <tt>./d2mem/FA</tt>
	\|-		\|-
	! colspan=4 \| Output Files		! colspan=4 \| Output Files
	\|-		\|-
	! style="text-align:left;" \| <tt>out</tt>		! style="text-align:left;" \| <tt>out</tt>
	\| str \|\| Output <tt>.sm</tt> file. Note that even if you use the <tt>-SAVESM 0</tt> to avoid generating tubes from the streamlines, this argument still must be specified and must end in "<tt>.sm</tt>". \|\| /map/gfx0/common0/diffusion/Interface/bin/tubegen/1.sm		\| str \|\| Output <tt>.sm</tt> file. Note that even if you use the <tt>-SAVESM 0</tt> to avoid generating tubes from the streamlines, this argument still must be specified and must end in "<tt>.sm</tt>". \|\| <tt>/map/gfx0/common0/diffusion/Interface/bin/tubegen/1.sm</tt>
	\|-		\|-
	! colspan=4 \| Integration Parameters		! colspan=4 \| Integration Parameters
	\|-		\|-
	! style="text-align:left;" \| <tt>ODE</tt>		! style="text-align:left;" \| <tt>ODE</tt>
	\| n \|\| ODE method. n=0 ⇒ rk2; n=1 ⇒ rk4 \|\| 0		\| n \|\| ODE method. n=0 ⇒ rk2; n=1 ⇒ rk4 \|\| <tt>0</tt>
	\|-		\|-
	! style="text-align:left;" \| <tt>cs</tt>		! style="text-align:left;" \| <tt>cs</tt>
	\| n \|\| Min tube length in mm \|\| 20		\| n \|\| Min tube length in mm \|\| <tt>20</tt>
	\|-		\|-
	! style="text-align:left;" \| <tt>seed</tt>		! style="text-align:left;" \| <tt>seed</tt>
	\| f f f \|\| Size of voxel group in the imaging volume in which to place one integration seed each. ''i.e.'' <tt>1 1 1</tt> generates one streamtube per voxel; <tt>0.5 0.5 0.5</tt> generates 8 streamtubes per voxel, <tt>2 2 2</tt> generates one streamtube per cube of 8 voxels. \|\| 10.0 10.0 5.0		\| f f f \|\| Size of voxel group in the imaging volume in which to place one integration seed each. ''i.e.'' <tt>1 1 1</tt> generates one streamtube per voxel; <tt>0.5 0.5 0.5</tt> generates 8 streamtubes per voxel, <tt>2 2 2</tt> generates one streamtube per cube of 8 voxels. \|\| <tt>10.0 10.0 5.0</tt>
	\|-		\|-
	! style="text-align:left;" \| <tt>stepsize</tt>		! style="text-align:left;" \| <tt>stepsize</tt>
	\| f \|\| Stepsize in mm \|\| 1.0		\| f \|\| Stepsize in mm \|\| <tt>1.0</tt>
	\|-		\|-
	! style="text-align:left;" \| <tt>al</tt>		! style="text-align:left;" \| <tt>al</tt>
	\| f \|\| Low threshold for linear anisotropy for terminating integration \|\| 0.1		\| f \|\| Low threshold for linear anisotropy for terminating integration \|\| <tt>0.1</tt>
	\|-		\|-
	! style="text-align:left;" \| <tt>dth</tt>		! style="text-align:left;" \| <tt>dth</tt>
	\| f \|\| Low threshold on inter-tube distances, in mm, for terminating integration \|\| 0.5		\| f \|\| Low threshold on inter-tube distances, in mm, for terminating integration \|\| <tt>0.5</tt>
	\|-		\|-
	! style="text-align:left;" \| <tt>t2thresh</tt>		! style="text-align:left;" \| <tt>t2thresh</tt>
	\| f \|\| T2 low threshold for terminating integration \|\| -1.0		\| f \|\| T2 low threshold for terminating integration \|\| <tt>-1.0</tt>
	\|-		\|-
	! style="text-align:left;" \| <tt>Longshort</tt>		! style="text-align:left;" \| <tt>Longshort</tt>
	\| n \|\| For integration, start from long one? (1) or short one(0), or longest of the two (2), or mean of the two (3) \|\| 0		\| n \|\| For integration, start from long one? (1) or short one(0), or longest of the two (2), or mean of the two (3) \|\| <tt>0</tt>
	\|-		\|-
	! colspan=4 \| Streamtube Culling		! colspan=4 \| Streamtube Culling
	\|-		\|-
	! style="text-align:left;" \| <tt>cl</tt>		! style="text-align:left;" \| <tt>cl</tt>
	\| f \|\| Min average Linear Anisotropy \|\| 0.3		\| f \|\| Min average Linear Anisotropy \|\| <tt>0.3</tt>
	\|-		\|-
	! style="text-align:left;" \| <tt>cd</tt>		! style="text-align:left;" \| <tt>cd</tt>
	\| f \|\| Min distance between tubes in mm. Set this to 0 to avoid an O(n<sup>2</sup>) pairwise distance check. \|\| 2.0		\| f \|\| Min distance between tubes in mm. Set this to 0 to avoid an O(n<sup>2</sup>) pairwise distance check. \|\| <tt>2.0</tt>
	\|-		\|-
	! colspan=4 \| Mesh Generation		! colspan=4 \| Mesh Generation
	\|-		\|-
	! style="text-align:left;" \| <tt>radius</tt>		! style="text-align:left;" \| <tt>radius</tt>
	\| f \|\| Streamtube radius in mm \|\| 1.0		\| f \|\| Streamtube radius in mm \|\| <tt>1.0</tt>
	\|}		\|}