GetMatrix.xml

<?xml version="1.0" encoding="utf-8"?>
<executable>
	<title>Get Connectivity Matrix</title>
	<description>This tool computes the connectivity matrix using a label map. You can either use the connectivity maps corresponding to all of the labels in the label map or a tracts file containing the full brain tractography. The connectivity maps or the tractography and the FA have to be in the same space than the label map. If you give a tracts file and connectivity maps, the connectivity maps will be used. At the end of the process, a text file containing the IDs of all the labels in the way they are used in the matrix will be created in the same folder than the matrix : Matrix_Labels.txt.</description>
	<contributor>Adrien Kaiser</contributor>
	<version>1.0</version>
	<parameters>
		<label>Inputs</label>
		<description>Inputs of the program</description>
		<file fileExtensions="csv">
			<name>ConnecMapsFile</name>
			<longflag>connecMapsFile</longflag>
			<description>This csv file contains the paths to all the connectivity map files, corresponding to all the labels in the Label Map.</description>
			<label>Connec Maps File</label>
		</file>
		<integer>
			<name>ConnecMapsFileIndex</name>
			<longflag>connecMapsFileIndex</longflag>
			<description>The index of the column containing the paths to the connectivity maps (1 for the first column)</description>
			<label>Connec Maps File Index</label>
			<default>1</default>
		</integer>
		<boolean>
			<name>isCostMap</name>
			<longflag>isCostMap</longflag>
			<description>Enable if the given Connectivity maps are cost maps: the values will be inverted.</description>
			<label>is Cost Map</label>
			<default>false</default>
		</boolean>
		<string-vector>
			<name>TractsFiles</name>
			<longflag>tractsFiles</longflag>
			<description>Vector with vtk files containing the tract files. Separate each file with a comma.</description>
			<label>Tracts Files</label>
		</string-vector>
		<image>
			<name>LabelMap</name>
			<longflag>labelMap</longflag>
			<description>Label map 3D image : 1 label for each voxel</description>
			<label>Label Map</label>
		</image>
		<image>
			<name>FA</name>
			<longflag>FA</longflag>
			<description>If you use the tractography, you can give the FA image and the contribution of each tract to the connectivity will be the mean FA along the tract.</description>
			<label>FA</label>
		</image>
	</parameters>
	<parameters>
		<label>Outputs</label>
		<description>Outputs of the program</description>
		<file fileExtensions="txt">
			<name>MatrixFile</name>
			<longflag>matrixFile</longflag>
			<description>The file that will contain the matrix</description>
			<label>Matrix File</label>
		</file>
	</parameters>
	<parameters>
		<label>Options</label>
		<description>Options for the program</description>
		<string-enumeration>
			<name>MatrixMetric</name>
			<longflag>matrixMetric</longflag>
			<description>The way to compute the elements of the matrix. If quantile, please give a quantile value.</description>
			<label>Matrix Metric</label>
			<element>Mean</element>
			<element>Minimum</element>
			<element>Maximum</element>
			<element>Quantile</element>
			<default>Mean</default>
		</string-enumeration>
		<double>
			<name>Quantile</name>
			<longflag>quantile</longflag>
			<description>The quantile value to use. The default value is the median (0.5).</description>
			<label>Quantile</label>
			<default>0.5</default>
		</double>
		<boolean>
			<name>useRegionBoundary</name>
			<longflag>useRegionBoundary</longflag>
			<description>For a given region, the connectivity will be computed only using the voxels on the boundary of each region. Used only with connectivity maps, not with tracts files.</description>
			<label>use Region Boundary</label>
			<default>false</default>
		</boolean>
		<boolean>
			<name>useOnlyReachedVoxels</name>
			<longflag>useOnlyReachedVoxels</longflag>
			<description>For a given set of voxels in a region, only the voxels that are reached (i.e. their connectivity is not 0) will be taken into account.</description>
			<label>use Only Reached Voxels</label>
			<default>false</default>
		</boolean>
		<boolean>
			<name>normalizeFSLConnec</name>
			<longflag>normalizeFSLConnec</longflag>
			<description>If the connectivity maps were generated with FSL, this option will normalize the values by the number of tracts generated, given in the file 'waytotal' in the FSL output folder.</description>
			<label>Normalize FSL Connec</label>
			<default>false</default>
		</boolean>
	</parameters>
</executable>