Tubegen/Obscure Arguments: Difference between revisions

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

Revision as of 16:20, 24 March 2009

arg params description defaults
Output Files
SAVESM n Generate and save the streamtube model VRML file. Without this, the program only generates streamlines. 1
Output Mesh Control
NUMPTR n Number of points on a ring 6
MESHNOVSIZE n Mesh coords not affected by vsize 0
OUTFA n output FA as red color 0
Integration
USROI n use region of interest for seed points generation 0
ROI 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
chi0thresh f isotropy model Chisqr threshold 2.0
chi1thresh f isotropy model Chisqr threshold 2.0
chi2thresh f isotropy model Chisqr threshold 2.0
Culling
wd n Gaussian weighted distance: end points get higher weight. 0
USECUTOFFROI n use cutoff ROI 0
ROICUTOFF 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
Statistical Options
chi0 str chisqr for isotropic model /u/sz/diffusion/data/susumu/mri/Diff
Partial Volume
pv str Partial volume between iso and wm image path /u/sz/diffusion/data/susumu/mri/Diff
pv1thresh f partial volume threshold for tracking 0.5
pvwm str Partial volume between wm image path /u/sz/diffusion/data/susumu/mri/Diff
Unknown
cr f Compress ratio, 0 means no compression 0.3
randlen f random jittering diameter, coupled with seed 1.0
randseed f srand? 0: no srand, -1 srand(time), other:srand(other) 0.0
ColSeed n seed ColA data mask for seeds 0
Colmask str Col mask image path nomask
ColmaskVx f f f Vx of the mask Coord 0.0 0.0 0.0
ColmaskVy f f f Vx of the mask Coord 0.0 0.0 0.0
ColmaskCtr f f f Ctr of the mask Coord 0.0 0.0 0.0
ColDTICtr f f f Ctr of the DTI Coord 0.0 0.0 0.0
ColDTIvsize f f f vsize of the DTI Coord 0.0 0.0 0.0
Colmaskvsize f f f vsize of the mask Coord 0.859376 0.859376 3.0
ColS n Number of random points used in a voxel in Colseeding 4
SS n Using the tubes generated for the seed points of the Second Start 0
flatdir n trace on a plane perpendicular to flatdir. 0: 1 0 0; 1: 0 1 0; 2: 0 0 1 -1
SEG str Segmentation image NoSegFile
SF str Seed-points file NoSeedsFile
OUTSF str Output seed-points file NoSeesFile
USESF n Use seed-points file 0
GMCON n GM constaint extension step, 0 means no constraint 0
CROSSMIDBRAIN n Col lesion test, keep only the tubes across midbrain 0
MIDBRAIN n n n Definition of midbrain 0 45 45
FASAMPLING n sample according to FA 0
Multicompartment Input Files
MC n Multicompartment 0
dt1 str First diffusion tensor image path in multi compartemnt model /u/sz/diffusion/data/susumu/mri/Diff
dt2 str Second diffusion tensor image path in multi compartment model /u/sz/diffusion/data/susumu/mri/Diff
Multicompartment Statistical Options
chi1 str chisqr for single compartemnt model /u/sz/diffusion/data/susumu/mri/Diff
chi2 str chisqr multi compartemnt model /u/sz/diffusion/data/susumu/mri/Diff
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