Mercurial > repos > greg > create_streamlines
comparison create_streamlines.xml @ 0:1c5508f627ec draft
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| author | greg |
|---|---|
| date | Tue, 28 Nov 2017 14:15:52 -0500 |
| parents | |
| children | 5bdd56ba7187 |
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| -1:000000000000 | 0:1c5508f627ec |
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| 1 <tool id="create_streamlines" name="Create streamlines" version="0.13.0"> | |
| 2 <description>within brain images</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.13.0">dipy</requirement> | |
| 5 </requirements> | |
| 6 <command detect_errors="exit_code"><![CDATA[ | |
| 7 python '$__tool_directory__/linear_fascile_evaluation.py' | |
| 8 --candidates '$candidates' | |
| 9 --output_trackvis_header '$output_trackvis_header' | |
| 10 --output_superiorfrontal_nifti '$output_superiorfrontal_nifti' | |
| 11 --output_connectivity '$output_connectivity' | |
| 12 --output_corpuscallosum_sagittal '$output_corpuscallosum_sagittal' | |
| 13 --output_corpuscallosum_axial 'output_corpuscallosum_axial' | |
| 14 ]]></command> | |
| 15 <inputs> | |
| 16 <param name="drmi_dataset" type="select" label="dRMI dataset"> | |
| 17 <option value="stanford_t1" selected="true">stanford_t1</option> | |
| 18 </param> | |
| 19 </inputs> | |
| 20 <outputs> | |
| 21 <data name="output_trackvis_header" format="txt" label="${tool.name}: Superiorfrontal Track Visualization Header" /> | |
| 22 <data name="output_superiorfrontal_nifti" format="nifti1" label="${tool.name}: Superiorfrontal" /> | |
| 23 <data name="output_connectivity" format="png" label="${tool.name}: Connectivity" /> | |
| 24 <data name="output_corpuscallosum_sagittal" format="png" label="${tool.name}: Corpuscallosum Sagittal" /> | |
| 25 <data name="output_corpuscallosum_axial" format="png" label="${tool.name}: Corpuscallosum Axial" /> | |
| 26 </outputs> | |
| 27 <tests> | |
| 28 <test> | |
| 29 </test> | |
| 30 </tests> | |
| 31 <help> | |
| 32 **What it does** | |
| 33 | |
| 34 Uses the target function to target streamlines that either pass through or do | |
| 35 not pass through some region of the brain, the connectivity_matrix groups function | |
| 36 to count streamlines based on where in the brain they begin and end and the density | |
| 37 map function to count the number of streamlines that pass though every voxel of some image. | |
| 38 | |
| 39 ----- | |
| 40 | |
| 41 **Options** | |
| 42 | |
| 43 </help> | |
| 44 <citations> | |
| 45 </citations> | |
| 46 </tool> |