|
0
|
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
|
8 --input $input
|
|
|
9 --input_extra_files_path '$input.extra_files_path'
|
|
0
|
10 --output_nifti1_evecs '$output_nifti1_evecs'
|
|
8
|
11 --output_nifti1_evecs_files_path '$output_nifti1_evecs.files_path'
|
|
0
|
12 --output_nifti1_fa '$output_nifti1_fa'
|
|
8
|
13 --output_nifti1_fa_files_path '$output_nifti1_fa.files_path'
|
|
0
|
14 --output_nifti1_md '$output_nifti1_md'
|
|
8
|
15 --output_nifti1_md_files_path '$output_nifti1_md.files_path'
|
|
0
|
16 --output_nifti1_rgb '$output_nifti1_rgb'
|
|
8
|
17 --output_nifti1_rgb_files_path '$output_nifti1_rgb.files_path'
|
|
0
|
18 --output_png_ellipsoids '$output_png_ellipsoids'
|
|
|
19 --output_png_middle_axial_slice '$output_png_middle_axial_slice'
|
|
|
20 --output_png_odfs '$output_png_odfs'
|
|
7
|
21 &>/dev/null
|
|
0
|
22 ]]></command>
|
|
|
23 <inputs>
|
|
8
|
24 <param name="input" type="data" format="nifti1" label="dRMI dataset"/>
|
|
0
|
25 </inputs>
|
|
|
26 <outputs>
|
|
1
|
27 <data name="output_nifti1_evecs" format="nifti1" label="${tool.name}: eigen vectors" />
|
|
2
|
28 <data name="output_nifti1_fa" format="nifti1" label="${tool.name}: fractional anisotropy" />
|
|
1
|
29 <data name="output_nifti1_md" format="nifti1" label="${tool.name}: mean diffusivity" />
|
|
0
|
30 <data name="output_nifti1_rgb" format="nifti1" label="${tool.name}: RGB-mape" />
|
|
4
|
31 <data name="output_png_middle_axial_slice" format="png" label="${tool.name}: middle axial slice without (left) and with (right) diffusion weighting" />
|
|
|
32 <data name="output_png_odfs" format="png" label="${tool.name}: orientation distribution functions" />
|
|
|
33 <data name="output_png_ellipsoids" format="png" label="${tool.name}: colored ellipsoids" />
|
|
0
|
34 </outputs>
|
|
|
35 <tests>
|
|
|
36 <test>
|
|
|
37 </test>
|
|
|
38 </tests>
|
|
|
39 <help>
|
|
|
40 **What it does**
|
|
|
41
|
|
|
42 The diffusion tensor model is a model that describes the diffusion within a voxel. It demonstrates
|
|
|
43 the utility of diffusion MRI in characterizing the micro-structure of white matter tissue and of the
|
|
|
44 biophysical properties of tissue, inferred from local diffusion properties.
|
|
|
45 -----
|
|
|
46
|
|
|
47 **Options**
|
|
|
48
|
|
|
49 </help>
|
|
|
50 <citations>
|
|
|
51 </citations>
|
|
|
52 </tool>
|
