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1 <tool id="diffusion_signal_reconstruction" name="Reconstruct diffusion signal" version="0.13.0">
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2 <description>with Tensor model</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__/diffusion_signal_reconstruction.py'
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8 --drmi_dataset $drmi_dataset
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9 --output_nifti1_evecs '$output_nifti1_evecs'
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10 --output_nifti1_fa '$output_nifti1_fa'
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11 --output_nifti1_md '$output_nifti1_md'
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12 --output_nifti1_rgb '$output_nifti1_rgb'
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13 --output_png_ellipsoids '$output_png_ellipsoids'
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14 --output_png_middle_axial_slice '$output_png_middle_axial_slice'
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15 --output_png_odfs '$output_png_odfs'
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16 ]]></command>
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17 <inputs>
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18 <param name="drmi_dataset" type="select" label="dRMI dataset">
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19 <option value="stanford_hardi" selected="true">stanford_hardi</option>
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20 <option value="sherbrooke_3shell">sherbrooke_3shell</option>
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21 </param>
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22 </inputs>
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23 <outputs>
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24 <data name="output_png_odfs" format="png" label="${tool.name}: orientation distribution functions" />
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25 <data name="output_png_ellipsoids" format="png" label="${tool.name}: colored ellipsoids" />
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26 <data name="output_png_middle_axial_slice" format="png" label="${tool.name}: middle axial slice without (left) and with (right) diffusion weighting" />
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1
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27 <data name="output_nifti1_evecs" format="nifti1" label="${tool.name}: eigen vectors" />
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28 <data name="output_nifti1_fa" format="nifti1" label="${tool.name}: fractional anisotropy" />
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29 <data name="output_nifti1_md" format="nifti1" label="${tool.name}: mean diffusivity" />
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30 <data name="output_nifti1_rgb" format="nifti1" label="${tool.name}: RGB-mape" />
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31 </outputs>
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32 <tests>
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33 <test>
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34 </test>
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35 </tests>
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36 <help>
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37 **What it does**
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38
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39 The diffusion tensor model is a model that describes the diffusion within a voxel. It demonstrates
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40 the utility of diffusion MRI in characterizing the micro-structure of white matter tissue and of the
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41 biophysical properties of tissue, inferred from local diffusion properties.
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42 -----
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43
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44 **Options**
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45
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46 </help>
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47 <citations>
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48 </citations>
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49 </tool>
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