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comparison diffusion_signal_reconstruction.xml @ 0:fe569aad237c draft

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author greg
date Sun, 05 Nov 2017 09:30:58 -0500
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1 <tool id="diffusion_signal_reconstruction" name="Reconstruct diffusion signal" version="0.13.0">
2 <description>with Tensor model</description>
3 <requirements>
4 <requirement type="package" version="0.13.0">dipy</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 python '$__tool_directory__/diffusion_signal_reconstruction.py'
8 --drmi_dataset $drmi_dataset
9 --output_nifti1_evecs '$output_nifti1_evecs'
10 --output_nifti1_fa '$output_nifti1_fa'
11 --output_nifti1_md '$output_nifti1_md'
12 --output_nifti1_rgb '$output_nifti1_rgb'
13 --output_png_ellipsoids '$output_png_ellipsoids'
14 --output_png_middle_axial_slice '$output_png_middle_axial_slice'
15 --output_png_odfs '$output_png_odfs'
16 ]]></command>
17 <inputs>
18 <param name="drmi_dataset" type="select" label="dRMI dataset">
19 <option value="stanford_hardi" selected="true">stanford_hardi</option>
20 <option value="sherbrooke_3shell">sherbrooke_3shell</option>
21 </param>
22 </inputs>
23 <outputs>
24 <data name="output_png_odfs" format="png" label="${tool.name}: orientation distribution functions" />
25 <data name="output_png_ellipsoids" format="png" label="${tool.name}: colored ellipsoids" />
26 <data name="output_png_middle_axial_slice" format="png" label="${tool.name}: middle axial slice without (left) and with (right) diffusion weighting" />
27 <data name="output_nifti1_fa" format="nifti1" label="${tool.name}: fractional anisotropye" />
28 <data name="output_nifti1_evecs" format="nifti1" label="${tool.name}: eigen vectorse" />
29 <data name="output_nifti1_evecs" format="nifti1" label="${tool.name}: mean diffusivitye" />
30 <data name="output_nifti1_rgb" format="nifti1" label="${tool.name}: RGB-mape" />
31 </outputs>
32 <tests>
33 <test>
34 </test>
35 </tests>
36 <help>
37 **What it does**
38
39 The diffusion tensor model is a model that describes the diffusion within a voxel. It demonstrates
40 the utility of diffusion MRI in characterizing the micro-structure of white matter tissue and of the
41 biophysical properties of tissue, inferred from local diffusion properties.
42 -----
43
44 **Options**
45
46 </help>
47 <citations>
48 </citations>
49 </tool>