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1 <tool id="create_streamlines" name="Create streamlines" version="0.13.0">
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2 <description>within brain images</description>
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3 <requirements>
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4 <requirement type="package" version="0.13.0">dipy</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 python '$__tool_directory__/create_streamlines.py'
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8 --output_trackvis_header '$output_trackvis_header'
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9 --output_superiorfrontal_nifti '$output_superiorfrontal_nifti'
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10 --output_connectivity '$output_connectivity'
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11 --output_corpuscallosum_sagittal '$output_corpuscallosum_sagittal'
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12 --output_corpuscallosum_axial 'output_corpuscallosum_axial'
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13 ]]></command>
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14 <inputs>
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15 <param name="drmi_dataset" type="select" label="dRMI dataset">
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16 <option value="stanford_t1" selected="true">stanford_t1</option>
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17 </param>
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18 </inputs>
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19 <outputs>
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20 <data name="output_trackvis_header" format="txt" label="${tool.name}: Superiorfrontal Track Visualization Header" />
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21 <data name="output_superiorfrontal_nifti" format="nifti1" label="${tool.name}: Superiorfrontal" />
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22 <data name="output_connectivity" format="png" label="${tool.name}: Connectivity" />
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23 <data name="output_corpuscallosum_sagittal" format="png" label="${tool.name}: Corpuscallosum Sagittal" />
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24 <data name="output_corpuscallosum_axial" format="png" label="${tool.name}: Corpuscallosum Axial" />
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25 </outputs>
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26 <tests>
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27 <test>
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28 </test>
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29 </tests>
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30 <help>
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31 **What it does**
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32
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33 Uses the target function to target streamlines that either pass through or do
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34 not pass through some region of the brain, the connectivity_matrix groups function
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35 to count streamlines based on where in the brain they begin and end and the density
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36 map function to count the number of streamlines that pass though every voxel of some image.
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37
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38 -----
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39
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40 **Options**
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41
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42 </help>
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43 <citations>
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44 </citations>
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45 </tool>
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