img2track
=========

maps image values on a tractogram

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**Usage**

.. code-block:: bash

    ./trekker img2track [OPTIONS] <input image> <input tractogram> <output file name>

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**Positionals**

- `<input image> TEXT:FILE REQUIRED`
  Input image (.nii, .nii.gz)

- `<input tractogram> TEXT:FILE REQUIRED`
  Input tractogram (.vtk, .tck)

- `<output file name> TEXT REQUIRED`
  Output file name. Output is a float32 type binary file.

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**Options**

.. raw:: html

   <table style="width: 100%; border-collapse: collapse;">
       <tr style="background-color: #f2f2f2;">
           <th style="padding: 8px; border-bottom: 1px solid #000; border-top: 1px solid #000;">Option</th>
           <th style="padding: 8px; border-bottom: 1px solid #000; border-top: 1px solid #000;">Description</th>
       </tr>
       <tr>
           <td style="padding: 8px; font-weight: 500;">--SH</td>
           <td style="padding: 8px;">Treat the image as a 4D spherical harmonics image.</td>
       </tr>
       <tr style="background-color: #f2f2f2;">
           <td style="padding: 8px; font-weight: 500;">--SF</td>
           <td style="padding: 8px;">Treat the image as a 4D spherical function image.</td>
       </tr>
       <tr>
           <td style="padding: 8px; font-weight: 500;">--SF_smoothing FLOAT</td>
           <td style="padding: 8px;">Apply spherical smoothing before using the spherical function.</td>
       </tr>
   </table>

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**General options**

.. raw:: html

   <table style="width: 100%; border-collapse: collapse;">
       <tr style="background-color: #f2f2f2;">
           <th style="padding: 8px; border-bottom: 1px solid #000; border-top: 1px solid #000;">Option</th>
           <th style="padding: 8px; border-bottom: 1px solid #000; border-top: 1px solid #000;">Description</th>
       </tr>
       <tr>
           <td style="padding: 8px; font-weight: 500;">-h, --help</td>
           <td style="padding: 8px;">Print this help message and exit.</td>
       </tr>
       <tr>
           <td style="padding: 8px; font-weight: 500;">-n, --numberOfThreads INT</td>
           <td style="padding: 8px;">Number of threads.</td>
       </tr>
       <tr style="background-color: #f2f2f2;">
           <td style="padding: 8px; font-weight: 500;">-v, --verbose TEXT</td>
           <td style="padding: 8px;">Verbose level. Options are "quiet", "fatal", "error", "warn", "info", and "debug". Default=info.</td>
       </tr>
       <tr>
           <td style="padding: 8px; font-weight: 500; border-bottom: 1px solid #000;">-f, --force</td>
           <td style="padding: 8px; border-bottom: 1px solid #000;">Force overwriting of existing file.</td>
       </tr>
   </table>