Jadrian Miles at 16:30, 24 March 2009

2009-03-24T16:30:42Z

← Older revision		Revision as of 16:30, 24 March 2009
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	! style="text-align:left;" \| <tt>FA</tt>		! style="text-align:left;" \| <tt>FA</tt>
	\| str \|\| Fractional anisotropy image. Note that you don't need this argument unless you've also specified <tt>-FASAMPLING 1</tt>. \|\| <tt>./d2mem/FA</tt>		\| str \|\| Fractional anisotropy image. Note that you don't need this argument unless you've also specified <tt>-FASAMPLING 1</tt> or <tt>-OUTFA 1</tt>. \|\| <tt>./d2mem/FA</tt>
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	! colspan=4 \| Output Files		! colspan=4 \| Output Files

Jadrian Miles at 16:24, 24 March 2009

2009-03-24T16:24:16Z

← Older revision		Revision as of 16:24, 24 March 2009
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	! style="text-align:left;" \| <tt>SAVESM</tt>		! style="text-align:left;" \| <tt>SAVESM</tt>
	\| n \|\| Generate and save the streamtube model VRML file. ~~Without~~ this, the program only generates streamlines. \|\| <tt>1</tt>		\| n \|\| Generate and save the streamtube model VRML file. If you set this to <tt>0</tt>, the program only generates streamlines. \|\| <tt>1</tt>
	\|-		\|-
	! colspan=4 \| Output Mesh Control		! colspan=4 \| Output Mesh Control

Jadrian Miles at 16:23, 24 March 2009

2009-03-24T16:23:53Z

← Older revision		Revision as of 16:23, 24 March 2009
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	! {{Hl2}} \| description		! {{Hl2}} \| description
	! {{Hl2}} \| defaults		! {{Hl2}} \| defaults
			\|-
			! colspan=4 \| Input Files
			\|-
			! style="text-align:left;" \| <tt>FA</tt>
			\| str \|\| Fractional anisotropy image. Note that you don't need this argument unless you've also specified <tt>-FASAMPLING 1</tt>. \|\| <tt>./d2mem/FA</tt>
	\|-		\|-
	! colspan=4 \| Output Files		! colspan=4 \| Output Files

Jadrian Miles at 16:20, 24 March 2009

2009-03-24T16:20:55Z

Show changes

Jadrian Miles at 16:15, 24 March 2009

2009-03-24T16:15:21Z

← Older revision		Revision as of 16:15, 24 March 2009
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	! style="text-align:left;" \| <tt>SAVESM</tt>		! style="text-align:left;" \| <tt>SAVESM</tt>
	\| n \|\| ~~Save sm~~ file \|\| 1		\| n \|\| Generate and save the streamtube model VRML file. Without this, the program only generates streamlines. \|\| 1
	\|-		\|-
	! colspan=4 \| Output Mesh Control		! colspan=4 \| Output Mesh Control

Jadrian Miles: New page: {| {{prettytable}} |- ! {{Hl2}} | arg ! {{Hl2}} | params ! {{Hl2}} | description ! {{Hl2}} | defaults |- ! colspan=4 | Output Files |- ! style="text-align:left;" | `SAVESM` | n || S...

2009-02-11T05:40:41Z

New page: {| {{prettytable}} |- ! {{Hl2}} | arg ! {{Hl2}} | params ! {{Hl2}} | description ! {{Hl2}} | defaults |- ! colspan=4 | Output Files |- ! style="text-align:left;" | <tt>SAVESM</tt> | n || S...

New page

{| {{prettytable}}
|-
! {{Hl2}} | arg
! {{Hl2}} | params
! {{Hl2}} | description
! {{Hl2}} | defaults
|-
! colspan=4 | Output Files
|-
! style="text-align:left;" | <tt>SAVESM</tt>
| n || Save sm file || 1
|-
! colspan=4 | Output Mesh Control
|-
! style="text-align:left;" | <tt>NUMPTR</tt>
| n || Number of points on a ring || 6
|-
! style="text-align:left;" | <tt>MESHNOVSIZE</tt>
| n || Mesh coords not affected by vsize || 0
|-
! style="text-align:left;" | <tt>OUTFA</tt>
| n || output FA as red color || 0
|-
! colspan=4 | Integration
|-
! style="text-align:left;" | <tt>USROI</tt>
| n || use region of interest for seed points generation || 0
|-
! style="text-align:left;" | <tt>ROI</tt>
| f f f f f f || region of interest, specify center point and edge length || 0.0 0.0 0.0 0.0 0.0 0.0
|-
! style="text-align:left;" | <tt>chi0thresh</tt>
| f || isotropy model Chisqr threshold || 2.0
|-
! style="text-align:left;" | <tt>chi1thresh</tt>
| f || isotropy model Chisqr threshold || 2.0
|-
! style="text-align:left;" | <tt>chi2thresh</tt>
| f || isotropy model Chisqr threshold || 2.0
|-
! colspan=4 | Culling
|-
! style="text-align:left;" | <tt>wd</tt>
| n || Gaussian weighted distance: end points get higher weight. || 0
|-
! style="text-align:left;" | <tt>USECUTOFFROI</tt>
| n || use cutoff ROI || 0
|-
! style="text-align:left;" | <tt>ROICUTOFF</tt>
| f f f f f f || Cut off ROI, only streamtubes running through this ROI are kept || 0.0 0.0 0.0 0.0 0.0 0.0
|-
! colspan=4 | Statistical Options
|-
! style="text-align:left;" | <tt>chi0</tt>
| str || chisqr for isotropic model || /u/sz/diffusion/data/susumu/mri/Diff
|-
! colspan=4 | Partial Volume
|-
! style="text-align:left;" | <tt>pv</tt>
| str || Partial volume between iso and wm image path || /u/sz/diffusion/data/susumu/mri/Diff
|-
! style="text-align:left;" | <tt>pv1thresh</tt>
| f || partial volume threshold for tracking || 0.5
|-
! style="text-align:left;" | <tt>pvwm</tt>
| str || Partial volume between wm image path || /u/sz/diffusion/data/susumu/mri/Diff
|-
! colspan=4 | Unknown
|-
! style="text-align:left;" | <tt>cr</tt>
| f || Compress ratio, 0 means no compression || 0.3
|-
! style="text-align:left;" | <tt>randlen</tt>
| f || random jittering diameter, coupled with seed || 1.0
|-
! style="text-align:left;" | <tt>randseed</tt>
| f || srand? 0: no srand, -1 srand(time), other:srand(other) || 0.0
|-
! style="text-align:left;" | <tt>ColSeed</tt>
| n || seed ColA data mask for seeds || 0
|-
! style="text-align:left;" | <tt>Colmask</tt>
| str || Col mask image path || nomask
|-
! style="text-align:left;" | <tt>ColmaskVx</tt>
| f f f || Vx of the mask Coord || 0.0 0.0 0.0
|-
! style="text-align:left;" | <tt>ColmaskVy</tt>
| f f f || Vx of the mask Coord || 0.0 0.0 0.0
|-
! style="text-align:left;" | <tt>ColmaskCtr</tt>
| f f f || Ctr of the mask Coord || 0.0 0.0 0.0
|-
! style="text-align:left;" | <tt>ColDTICtr</tt>
| f f f || Ctr of the DTI Coord || 0.0 0.0 0.0
|-
! style="text-align:left;" | <tt>ColDTIvsize</tt>
| f f f || vsize of the DTI Coord || 0.0 0.0 0.0
|-
! style="text-align:left;" | <tt>Colmaskvsize</tt>
| f f f || vsize of the mask Coord || 0.859376 0.859376 3.0
|-
! style="text-align:left;" | <tt>ColS</tt>
| n || Number of random points used in a voxel in Colseeding || 4
|-
! style="text-align:left;" | <tt>SS</tt>
| n || Using the tubes generated for the seed points of the Second Start || 0
|-
! style="text-align:left;" | <tt>flatdir</tt>
| n || trace on a plane perpendicular to flatdir. 0: 1 0 0; 1: 0 1 0; 2: 0 0 1 || -1
|-
! style="text-align:left;" | <tt>SEG</tt>
| str || Segmentation image || NoSegFile
|-
! style="text-align:left;" | <tt>SF</tt>
| str || Seed-points file || NoSeedsFile
|-
! style="text-align:left;" | <tt>OUTSF</tt>
| str || Output seed-points file || NoSeesFile
|-
! style="text-align:left;" | <tt>USESF</tt>
| n || Use seed-points file || 0
|-
! style="text-align:left;" | <tt>GMCON</tt>
| n || GM constaint extension step, 0 means no constraint || 0
|-
! style="text-align:left;" | <tt>CROSSMIDBRAIN</tt>
| n || Col lesion test, keep only the tubes across midbrain || 0
|-
! style="text-align:left;" | <tt>MIDBRAIN</tt>
| n n n || Definition of midbrain || 0 45 45
|-
! style="text-align:left;" | <tt>FASAMPLING</tt>
| n || sample according to FA || 0
|-
! colspan=4 | Multicompartment Input Files
|-
! style="text-align:left;" | <tt>MC</tt>
| n || Multicompartment || 0
|-
! style="text-align:left;" | <tt>dt1</tt>
| str || First diffusion tensor image path in multi compartemnt model || /u/sz/diffusion/data/susumu/mri/Diff
|-
! style="text-align:left;" | <tt>dt2</tt>
| str || Second diffusion tensor image path in multi compartment model || /u/sz/diffusion/data/susumu/mri/Diff
|-
! colspan=4 | Multicompartment Statistical Options
|-
! style="text-align:left;" | <tt>chi1</tt>
| str || chisqr for single compartemnt model || /u/sz/diffusion/data/susumu/mri/Diff
|-
! style="text-align:left;" | <tt>chi2</tt>
| str || chisqr multi compartemnt model || /u/sz/diffusion/data/susumu/mri/Diff
|}