https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/FinslerBacktracing&feed=atom&action=historyDocumentation/Nightly/Modules/FinslerBacktracing - Revision history2024-03-28T12:12:56ZRevision history for this page on the wikiMediaWiki 1.33.0https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/FinslerBacktracing&diff=37871&oldid=prevAlexy at 16:15, 2 May 20142014-05-02T16:15:42Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 16:15, 2 May 2014</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><!-- ---------------------------- --></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><!-- ---------------------------- --></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>{{documentation/{{documentation/version}}/module-section|Module Description}}</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>{{documentation/{{documentation/version}}/module-section|Module Description}}</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The Backtracing Module uses the output of the Finsler <del class="diffchange diffchange-inline">tractography module </del>to actually trace the estimated fiber bundles. Note that you should have 'Finsler Tractography based on HARDI' installed and working in order to be able to use the present module (see the documentation therein for more details on the Finsler Tractography method). The nomenclature for this module can be a little confusing: contrary to 'Labelmap seeding', this algorithm does not ask for a seeding region. This is because the seeding region is provided when calculating the costs map and the optimal arrival directions with 'Finsler Tractography based on HARDI'. Hence, the seeding region (and also the hypothetic mask used) is now implicit in the costs map. In the present module, we have to choose instead a set of 'target points': the fiber bundles are traced from these target points to the seeding region. Accordingly, no stopping criterion is needed: we stop tracking the bundle just when we hit either the seeding region or a point outside the mask (if used). Nonetheless, we perform some 'sanity checks', avoiding fibers with abnormal length or with excessive curvature. NOTE: If compiled as a stand-alone, this module needs to be linked against both ITK and VTK NOTE2: If compiled as a stand-alone, the fiber bundles computed are written to disk as a VTK file (.vtp/.vtk) that can be loaded with 3D-Slicer or FSL. IMPORTANT: The fibers are always stored in that file in RAS coordinates.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The Backtracing Module uses the output of the <ins class="diffchange diffchange-inline">[[Documentation/{{documentation/version}}/Modules/FinslerTractography|</ins>Finsler <ins class="diffchange diffchange-inline">Tractography Module]] </ins>to actually trace the estimated fiber bundles. Note that you should have 'Finsler Tractography based on HARDI' installed and working in order to be able to use the present module (see the documentation therein for more details on the Finsler Tractography method). The nomenclature for this module can be a little confusing: contrary to 'Labelmap seeding', this algorithm does not ask for a seeding region. This is because the seeding region is provided when calculating the costs map and the optimal arrival directions with 'Finsler Tractography based on HARDI'. Hence, the seeding region (and also the hypothetic mask used) is now implicit in the costs map. In the present module, we have to choose instead a set of 'target points': the fiber bundles are traced from these target points to the seeding region. Accordingly, no stopping criterion is needed: we stop tracking the bundle just when we hit either the seeding region or a point outside the mask (if used). Nonetheless, we perform some 'sanity checks', avoiding fibers with abnormal length or with excessive curvature. NOTE: If compiled as a stand-alone, this module needs to be linked against both ITK and VTK NOTE2: If compiled as a stand-alone, the fiber bundles computed are written to disk as a VTK file (.vtp/.vtk) that can be loaded with 3D-Slicer or FSL. IMPORTANT: The fibers are always stored in that file in RAS coordinates.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><!-- ---------------------------- --></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><!-- ---------------------------- --></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>{{documentation/{{documentation/version}}/extension-section|Use Cases}}</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>{{documentation/{{documentation/version}}/extension-section|Use Cases}}</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">Create fiber tracks from the output of [[Documentation/{{documentation/version}}/Modules/FinslerTractography|Finsler Tractography Module]] </ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><!-- ---------------------------- --></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><!-- ---------------------------- --></div></td></tr>
</table>Alexyhttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/FinslerBacktracing&diff=37870&oldid=prevAlexy at 16:12, 2 May 20142014-05-02T16:12:42Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 16:12, 2 May 2014</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><!-- ---------------------------- --></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><!-- ---------------------------- --></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>{{documentation/{{documentation/version}}/module-section|Module Description}}</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>{{documentation/{{documentation/version}}/module-section|Module Description}}</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">This </del>module <del class="diffchange diffchange-inline">implements </del>the Finsler <del class="diffchange diffchange-inline">tractography </del>method with HARDI <del class="diffchange diffchange-inline">data described by J</del>. <del class="diffchange diffchange-inline">Melonakos et al</del>. <del class="diffchange diffchange-inline">From </del>a set of seeding and <del class="diffchange diffchange-inline">target points</del>, the <del class="diffchange diffchange-inline">paths </del>are <del class="diffchange diffchange-inline">estimated </del>as <del class="diffchange diffchange-inline">the shortest path taking into account </del>a <del class="diffchange diffchange-inline">local, directional dependent cost</del>.</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">The Backtracing Module uses the output of the Finsler tractography module to actually trace the estimated fiber bundles. Note that you should have 'Finsler Tractography based on HARDI' installed and working in order to be able to use the present </ins>module <ins class="diffchange diffchange-inline">(see the documentation therein for more details on </ins>the Finsler <ins class="diffchange diffchange-inline">Tractography </ins>method<ins class="diffchange diffchange-inline">). The nomenclature for this module can be a little confusing: contrary to 'Labelmap seeding', this algorithm does not ask for a seeding region. This is because the seeding region is provided when calculating the costs map and the optimal arrival directions </ins>with <ins class="diffchange diffchange-inline">'Finsler Tractography based on </ins>HARDI<ins class="diffchange diffchange-inline">'</ins>. <ins class="diffchange diffchange-inline">Hence, the seeding region (and also the hypothetic mask used) is now implicit in the costs map</ins>. <ins class="diffchange diffchange-inline">In the present module, we have to choose instead </ins>a set of <ins class="diffchange diffchange-inline">'target points': the fiber bundles are traced from these target points to the </ins>seeding <ins class="diffchange diffchange-inline">region. Accordingly, no stopping criterion is needed: we stop tracking the bundle just when we hit either the seeding region or a point outside the mask (if used). Nonetheless, we perform some 'sanity checks', avoiding fibers with abnormal length or with excessive curvature. NOTE: If compiled as a stand-alone, this module needs to be linked against both ITK </ins>and <ins class="diffchange diffchange-inline">VTK NOTE2: If compiled as a stand-alone</ins>, the <ins class="diffchange diffchange-inline">fiber bundles computed </ins>are <ins class="diffchange diffchange-inline">written to disk </ins>as a <ins class="diffchange diffchange-inline">VTK file (.vtp/.vtk) that can be loaded with 3D-Slicer or FSL. IMPORTANT: The fibers are always stored in that file in RAS coordinates</ins>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">The output provided is the connectivity map from each voxel in the volume to the seeding points, plus a vector volume with the directions tangent to the fiber bundles at each point. If the Backtracing module within is built, these directions can be traced back to actually compute the fiber bundles</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><!-- ---------------------------- --></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><!-- ---------------------------- --></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>{{documentation/{{documentation/version}}/extension-section|<del class="diffchange diffchange-inline">Modules</del>}}</div></td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>{{documentation/{{documentation/version}}/extension-section|<ins class="diffchange diffchange-inline">Use Cases</ins>}}</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">*[[Documentation/{{documentation/version}}/Modules/FinslerTractography|Finsler Tractography Module]]</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">*[[Documentation/{{documentation/version}}/Modules/FinslerBacktracing |Backtracing Module]]</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"><!-- ---------------------------- --></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">{{documentation/{{documentation/version}}/extension-section|Use Cases}}</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">The Finsler Tractography Module module uses the fast-sweeping algorithm to find the connectivity from a set of seeding points to each voxel in the input DWI volume (or inside the mask, if provided). This connectivity is the minimum cost of arriving at each voxel from the seeds, following the trajectory of the estimated pathways. The cost is computed as the integral along the pathway of a local directional cost computed from the ODF or some other HARDI-related measurement. A complete description of the algorithm may be found in: J. Melonakos, E. Pichon, S. Angenent, A. Tannenbaum, 'Finsler Active Contours'. IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3):412-423. March 2008. A background-removal mask can be used to accelerate computations. Optionally, the algorithm provides at each voxel an estimation of the vector tangent to the optimal pathway at that point (arrival direction). Fast-sweeping is full multi-threaded, and some other accelerations (checking only those voxels in the causal direction of the solution) have been implemented to obtain a result in a reasonable time. However, an algorithm virtually identical to that in the aforementioned paper may be reproduced fixing the advanced parameters as follows: Cost: (E(q)/Phi(r))^3 Directions: 26 Use threads: deactivate Use accelerated iterations: deactivate (Start accelerated iterations becomes irrelevant). <br></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">The Backtracing Module uses the output of the Finsler tractography module to actually trace the estimated fiber bundles. Note that you should have 'Finsler Tractography based on HARDI' installed and working in order to be able to use the present module (see the documentation therein for more details on the Finsler Tractography method). The nomenclature for this module can be a little confusing: contrary to 'Labelmap seeding', this algorithm does not ask for a seeding region. This is because the seeding region is provided when calculating the costs map and the optimal arrival directions with 'Finsler Tractography based on HARDI'. Hence, the seeding region (and also the hypothetic mask used) is now implicit in the costs map. In the present module, we have to choose instead a set of 'target points': the fiber bundles are traced from these target points to the seeding region. Accordingly, no stopping criterion is needed: we stop tracking the bundle just when we hit either the seeding region or a point outside the mask (if used). Nonetheless, we perform some 'sanity checks', avoiding fibers with abnormal length or with excessive curvature. NOTE: If compiled as a stand-alone, this module needs to be linked against both ITK and VTK NOTE2: If compiled as a stand-alone, the fiber bundles computed are written to disk as a VTK file (.vtp/.vtk) that can be loaded with 3D-Slicer or FSL. IMPORTANT: The fibers are always stored in that file in RAS coordinates..</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><!-- ---------------------------- --></div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><!-- ---------------------------- --></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>{{documentation/{{documentation/version}}/extension-section|Tutorials}}</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>{{documentation/{{documentation/version}}/extension-section|Tutorials}}</div></td></tr>
</table>Alexyhttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/FinslerBacktracing&diff=37869&oldid=prevAlexy: Created page with '<noinclude>{{documentation/versioncheck}}</noinclude> <!-- ---------------------------- --> {{documentation/{{documentation/version}}/module-header}} <!-- -----------------------…'2014-05-02T16:09:45Z<p>Created page with '<noinclude>{{documentation/versioncheck}}</noinclude> <!-- ---------------------------- --> {{documentation/{{documentation/version}}/module-header}} <!-- -----------------------…'</p>
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Acknowledgments:<br />
Supported by grant number FMECD-2010/71131616E from the Spanish Ministry of Education/Fulbright Committee <br><br />
Contributors: Antonio Tristan Vega, Demian Wassermann and Carl-Fredrik Westin. The directional iterators were contributed by Luis Ibanez (Kitware).<br><br />
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This module implements the Finsler tractography method with HARDI data described by J. Melonakos et al. From a set of seeding and target points, the paths are estimated as the shortest path taking into account a local, directional dependent cost.<br />
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The output provided is the connectivity map from each voxel in the volume to the seeding points, plus a vector volume with the directions tangent to the fiber bundles at each point. If the Backtracing module within is built, these directions can be traced back to actually compute the fiber bundles<br />
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*[[Documentation/{{documentation/version}}/Modules/FinslerTractography|Finsler Tractography Module]]<br />
*[[Documentation/{{documentation/version}}/Modules/FinslerBacktracing |Backtracing Module]]<br />
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The Finsler Tractography Module module uses the fast-sweeping algorithm to find the connectivity from a set of seeding points to each voxel in the input DWI volume (or inside the mask, if provided). This connectivity is the minimum cost of arriving at each voxel from the seeds, following the trajectory of the estimated pathways. The cost is computed as the integral along the pathway of a local directional cost computed from the ODF or some other HARDI-related measurement. A complete description of the algorithm may be found in: J. Melonakos, E. Pichon, S. Angenent, A. Tannenbaum, 'Finsler Active Contours'. IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3):412-423. March 2008. A background-removal mask can be used to accelerate computations. Optionally, the algorithm provides at each voxel an estimation of the vector tangent to the optimal pathway at that point (arrival direction). Fast-sweeping is full multi-threaded, and some other accelerations (checking only those voxels in the causal direction of the solution) have been implemented to obtain a result in a reasonable time. However, an algorithm virtually identical to that in the aforementioned paper may be reproduced fixing the advanced parameters as follows: Cost: (E(q)/Phi(r))^3 Directions: 26 Use threads: deactivate Use accelerated iterations: deactivate (Start accelerated iterations becomes irrelevant). <br><br />
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The Backtracing Module uses the output of the Finsler tractography module to actually trace the estimated fiber bundles. Note that you should have 'Finsler Tractography based on HARDI' installed and working in order to be able to use the present module (see the documentation therein for more details on the Finsler Tractography method). The nomenclature for this module can be a little confusing: contrary to 'Labelmap seeding', this algorithm does not ask for a seeding region. This is because the seeding region is provided when calculating the costs map and the optimal arrival directions with 'Finsler Tractography based on HARDI'. Hence, the seeding region (and also the hypothetic mask used) is now implicit in the costs map. In the present module, we have to choose instead a set of 'target points': the fiber bundles are traced from these target points to the seeding region. Accordingly, no stopping criterion is needed: we stop tracking the bundle just when we hit either the seeding region or a point outside the mask (if used). Nonetheless, we perform some 'sanity checks', avoiding fibers with abnormal length or with excessive curvature. NOTE: If compiled as a stand-alone, this module needs to be linked against both ITK and VTK NOTE2: If compiled as a stand-alone, the fiber bundles computed are written to disk as a VTK file (.vtp/.vtk) that can be loaded with 3D-Slicer or FSL. IMPORTANT: The fibers are always stored in that file in RAS coordinates..<br />
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{{documentation/{{documentation/version}}/extension-section|References}}<br />
* GJ. Melonakos, E. Pichon, S. Angenent, A. Tannenbaum, 'Finsler Active Contours'. IEEE Transactions on Pattern Analysis and Machine Intelligence, 30(3):412-423. March 2008<br />
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<!-- ---------------------------- --></div>Alexy