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Description update for CLI usage
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@zhangfanmark
zhangfanmark committed Jan 20, 2022
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38 changes: 18 additions & 20 deletions UKFTractography/UKFTractography.xml
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<contributor>Yogesh Rathi, Stefan Lienhard, Yinpeng Li, Martin Styner, Ipek Oguz, Yundi Shi, Christian Baumgartner, Kent Williams, Hans Johnson, Peter Savadjiev, Carl-Fredrik Westin, Lauren O'Donnell, Jessica Lee.</contributor>
<acknowledgements><![CDATA[The development of this module was supported by NIH grants R01 MH097979 (PI Rathi), R01 MH092862 (PIs Westin and Verma), U01 NS083223 (PI Westin), R01 MH074794 (PI Westin) and P41 EB015902 (PI Kikinis), U01 CA199459 (PI O'Donnell), and P41 EB015898 (NCIGT).]]></acknowledgements>


<parameters>
<label>IO</label>
<description>Input/output parameters</description>
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<parameters>

<label>Seeding Options (pick one option)</label>
<description>Options for seeding tractography. Only one of the three provided options will be used. If none of these options are specified, full brain tractography will be performed, and the algorithm will start from every voxel in Input Brain Mask where the fractional anisotropy is greater than 0.18.</description>
<description>Options for seeding tractography. Only one of the three provided options will be used. Option 1 (Minimum Seed FA) is the default.</description>

<double>
<name>seedingThreshold</name>
<longflag deprecatedalias="seedFALimit">
seedingThreshold
</longflag>
<label>Option 1: Minimum Seed FA</label>
<description>Tractography parameter used in all models. Seed points whose fractional anisotropy (FA) are below this value are excluded. This option will not be used if Seeding Option 2 or 3 is provided. Default: 0.18. Range: 0-1.</description>
<description>(Seeding Option 1) Tractography parameter used in all models. Seed points whose fractional anisotropy (FA) are below this value are excluded. This seeding option is default and will not be used if Seeding Option 2 or 3 is used. Default: 0.18. Range: 0-1.</description>
<default>0.18</default>
<constraints>
<minimum>0</minimum>
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<longflag alias="wmData">wmFile</longflag>
<label>Option 2: WM Segmentation Map</label>
<channel>input</channel>
<description>A probabilistic segmentation map of the White Matter (WM). The values in the map should be between 0 and 1. Voxels with a probability over WM Probability Threshold will be used for seeding. This option will not be used if Seeding Option 3 is provided.</description>
<description>(Seeding Option 2) A probabilistic segmentation map of the White Matter (WM). The values in the map should be between 0 and 1. Voxels with a probability over WM Probability Threshold (--wmProbThreshold) will be used for seeding. This seeding option will not be used if Seeding Option 3 is used.</description>
</image>

<double>
<name>wmProbThreshold</name>
<longflag>wmProbThreshold</longflag>
<label>Option 2: WM Probability Threshold</label>
<description>When a WM segmentation map is provided, tracking will be seeded in voxels with values over this threshold. Default: 0.3. Range: 0-1.</description>
<description>(Seeding Option 2) When a WM Segmentation Map (--wmFile) is provided, tracking will be seeded in voxels with values over this threshold. Default: 0.3. Range: 0-1.</description>
<default>0.3</default>
<constraints>
<minimum>0</minimum>
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<longflag alias="seedsData">seedsFile</longflag>
<label>Option 3: Seeding Label Map</label>
<channel>input</channel>
<description>Voxels in this map with a label defined in ROI Labels for Seeding will be used for seeding. If this option is provided, Seeding Options 1 and 2 will not be used.</description>
<description>(Seeding Option 3) Voxels in this map with a label defined in ROI Labels (--seedLabels) for Seeding will be used for seeding. If this option is used, Seeding Options 1 and 2 will not be used.</description>
</image>

<integer-vector>
<name>seedLabels</name>
<longflag>seedLabels</longflag>
<label>Option 3: ROI Labels for Seeding</label>
<description>A list of the ROI labels to be used. There are the voxel values where tractography should be seeded.</description>
<description>(Seeding Option 3) A list of the ROI labels to be used when Seeding Label Map (--seedsFile) is provided. There are the voxel values where tractography should be seeded.</description>
<default>1</default>
</integer-vector>

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<parameters>

<label>Stopping Options (pick one option)</label>
<description>Options for stopping tractography. Only one of the three provided options will be used. If none of these options are specified, the algorithm will stop when the tracking reaches the boundary of Input Brain Mask.</description>
<description>Options for stopping tractography. Only one of the three provided options will be used. Option 1 (Terminating Mean Signal) is the default.</description>

<double>
<name>stoppingFA</name>
<longflag deprecatedalias="minFA">
stoppingFA
</longflag>
<label>Option 1: Terminating FA</label>
<description>Tractography parameter used in tensor model. Tractography will stop when the fractional anisotropy (FA) of the tensor being tracked is less than this value. Note: make sure to also decrease the GA to track through lower anisotropy areas. This parameter is used only in tensor models. This parameter will be applied whether stopping maps (i.e., stopFile, gmFile and/or csfFile) are provided or not. (If one wants to only use the stopping maps as Stopping Criterion, stoppingFA and stoppingThreshold need to be set to 0.) Default: 0.15. Range: 0-1.</description>
<description>(Stopping Option 1) Tractography parameter used only in tensor models. Tractography will stop when the fractional anisotropy (FA) of the tensor being tracked is less than this value. Note: make sure to also decrease the Terminating Mean Signal (--stoppingThreshold) to track through lower anisotropy areas. This option will not be used if Stopping Option 2 or 3 is provided. Default: 0.15. Range: 0-1.</description>
<default>0.15</default>
<constraints>
<minimum>0</minimum>
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<name>stoppingThreshold</name>
<longflag>stoppingThreshold</longflag>
<label>Option 1: Terminating Mean Signal</label>
<description>Tractography parameter used in all models. Tractography will stop when the mean signal is below this value. This option will not be used if Stopping Option 2 or 3 is provided. Default: 0.1. Range: 0-1.</description>
<description>(Stopping Option 1) Tractography parameter used by default in all models. Tractography will stop when the mean signal is below this value. This option will not be used if Stopping Option 2 or 3 is provided. Default: 0.1. Range: 0-1.</description>
<default>0.1</default>
<constraints>
<minimum>0</minimum>
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<longflag alias="gmData">gmFile</longflag>
<label>Option 2: GM Segmentation Map</label>
<channel>input</channel>
<description>A probabilistic segmentation map of the Gray Matter (GM). The values in the map should be between 0 and 1. Tracking will stop in the voxels with a probability over GM Probability Threshold. This option will not be used if Stopping Option 3 is provided.</description>
<description>(Stopping Option 2) A probabilistic segmentation map of the Gray Matter (GM). The values in the map should be between 0 and 1. Tracking will stop in the voxels with a probability over GM Probability Threshold (--gmProbThreshold). This option will not be used if Stopping Option 3 is used.</description>
</image>

<double>
<name>gmProbThreshold</name>
<longflag>gmProbThreshold</longflag>
<label>Option 2: GM Probability Threshold </label>
<description>TWhen a GM segmentation map is provided, tracking will stop in voxels with values over this threshold. Default: 0.99. Range: 0-1.</description>
<default>0.95</default>
<description> (Stopping Option 2) When a GM Segmentation Map (--gmFile) is provided, tracking will stop in voxels with values over this threshold. Default: 0.99. Range: 0-1.</description>
<default>0.99</default>
<constraints>
<minimum>0</minimum>
<maximum>1</maximum>
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<longflag alias="csfData">csfFile</longflag>
<label>Option 2: CSF Segmentation Map</label>
<channel>input</channel>
<description>A probabilistic segmentation map of the Cerebrospinal Fluid (CSF). The values in the map should be between 0 and 1. Tracking will stop in voxels with a probability over CSF Probability Threshold. This option will not be used if Stopping Option 3 is provided.</description>
<description> (Stopping Option 2) A probabilistic segmentation map of the Cerebrospinal Fluid (CSF). The values in the map should be between 0 and 1. Tracking will stop in voxels with a probability over CSF Probability Threshold (--csfProbThreshold). This option will not be used if Stopping Option 3 is used.</description>
</image>

<double>
<name>csfProbThreshold</name>
<longflag>csfProbThreshold</longflag>
<label>Option 2: CSF Probability Threshold</label>
<description>When a CSF segmentation map is provided, tracking will stop in voxels with values over this threshold. Default: 0.6. Range: 0-1.</description>
<default>0.95</default>
<description>(Stopping Option 2) When a CSF Segmentation Map (--csfFile) is provided, tracking will stop in voxels with values over this threshold. Default: 0.5. Range: 0-1.</description>
<default>0.5</default>
<constraints>
<minimum>0</minimum>
<maximum>1</maximum>
<step>0.01</step>
</constraints>
</double>


<image type="scalar" fileExtensions=".nhdr,.nrrd">
<name>stopFile</name>
<longflag alias="stopData">stopFile</longflag>
<label>Option 3: Input Stopping Label Map</label>
<channel>input</channel>
<description>Label map that defines where tracking should stop. Voxels in this map with a label listed in ROI Labels for Stopping will be used for stopping. If this option is provided, Stopping Options 1 and 2 will not be used.</description>
<description>(Stopping Option 3) Label map that defines where tracking should stop. Voxels in this map with a label listed in ROI Labels for Stopping (--stopLabels) will be used for stopping. If this option is provided, Stopping Options 1 and 2 will not be used.</description>
</image>

<integer-vector>
<name>stopLabels</name>
<longflag>stopLabels</longflag>
<label>Option 3: ROI Labels for stopping</label>
<description>A list of the ROI labels to be used. There are the voxel values where tractography should stop.</description>
<description>(Stopping Option 3) A list of the ROI labels to be used when Stopping Label Map (--stopFile) is provided. There are the voxel values where tractography should stop. </description>
<default>1</default>
</integer-vector>

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<name>freeWater</name>
<longflag>freeWater</longflag>
<label>Tensor Model: Estimate term for free water</label>
<description>Adds a term for free water diffusion to the model. The free water model is a tensor with all 3 eigenvalues equal to the diffusivity of free water (0.003). To output the free water fraction, make sure to use the "save free water" parameter. </description>
<description>Adds a term for free water diffusion to the model. The free water model is a tensor with all 3 eigenvalues equal to the diffusivity of free water (0.003). To output the free water fraction, make sure to use the "save free water" parameter.</description>
<default>false</default>
</boolean>

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