Tubegen/Obscure Arguments: Difference between revisions
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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 | ||
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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. | | 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> | ||
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! colspan=4 | Output Mesh Control | ! colspan=4 | Output Mesh Control | ||
Latest revision as of 16:30, 24 March 2009
| arg | params | description | defaults |
|---|---|---|---|
| Input Files | |||
| FA | str | Fractional anisotropy image. Note that you don't need this argument unless you've also specified -FASAMPLING 1 or -OUTFA 1. | ./d2mem/FA |
| Output Files | |||
| SAVESM | n | Generate and save the streamtube model VRML file. If you set this to 0, 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 |