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← Revision 14 as of 2019-07-26 10:48:16 ⇥
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| [[fswiki|top]] | = AnatomiCuts correspondences = This method finds corresponding clusters across subjects. Currently, only one-to-one cluster's correspondences are available using the Hungarian algorithm. Our implementation uses our anatomical similarity metric which allows us to find correspondences without the need of registration, comparing clusters of streamlines in each subject's native space. |
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| = AnatomiCuts correspondences = This method finds corresponding clusters across subjects. Currently only one-to-one cluster's correspondences are available using the Hungarian algorithm. |
{{attachment:hungarian_babies.png||height="360px"}}{ |
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| A use case analysis merely addresses the most obvious of questions: who needs the software, and what are they going to do with it. | The Hungarian algorithm finds corresponding clusters between two subjects. |
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| === Actors (Users) === In UML terminology, the persons (or software agents) external to a software component are called the actors. |
{{{ bash /space/erebus/2/users/vsiless/code/freesurfer/anatomicuts/dmri_ac.sh preGA SUBJECT TARGET_SUBJECT MIN_STREMLINE_LENGHT STD_CLUSTER_CLEANING |
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| ==== Research ==== === Scenarios (Use Cases) === These establish the framework for test cases. They also bring out the vocabulary of the system. This vocabulary is defined in the Terms section following these scenarios. |
bash /space/erebus/2/users/vsiless/code/freesurfer/anatomicuts/dmri_ac.sh forAll preGA TARGET_SUBJECT MIN_STREMLINE_LENGHT STD_CLUSTER_CLEANING - "pbsubmit_-n_1_-c_" |
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| ==== Use Case #1 ==== ==== Use Case #2 ==== ==== Use Case #3 ==== ==== Use Case #4 ==== === Terms === The following is a list of some of the vocabulary used in the preceding scenarios, plus terms that are common across the system in which the software is used. |
AnatomiCuts_correspondences -s1 segmentation1.nii.gz -s2 segmentation2.nii.gz -c numClusters -h1 clusteringPath1 -h2 clusteringPath2 -m metric -o output.csv }}} |
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| == Requirements == === General Requirements === === Specific Requirements === == Implementation == === API === === System Architecture and Primary Components === === Classes === === Collaboration and Sequence Diagrams === UML diagrams describing the time-course of the objects composing the executable. |
Where |
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| === Properties === Here are listed the configurable properties of the executable. These can be configurables read from a configuration file, or configurables hard-coded into the source code. |
-s1 the segmentation to be used for anatomical similarity in subject one. |
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| == Test Plan == === Introduction === Tests should cover the following categories of testing. |
-s2 the segmentation to be used for anatomical similarity in subject two. |
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| ==== Functional ==== This type of test ascertains whether the software executes its basic functionality under optimal conditions. |
-h1 the path to the AnatomiCuts folder to be used for subject one. |
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| ==== Boundary ==== This type of test determines the breaking points of the software, and whether the software gracefully handles input near and beyond these boundaries. |
-h2 the path to the AnatomiCuts folder to be used for subject two. |
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| ==== Stability ==== This type of test determines long-term behavior of the software: whether is has a memory leak, or prone to crashes which are not repeatable in any single run of any of the other tests. |
-m metric to be used: labels (anatomical similarity) or euclid (euclidean similarity). |
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| ==== Performance ==== These tests produce benchmarks on the performance of the software. |
-sym (under development) this flag will mirror the segmentation in subject two to find between hemisphere correspondences. -o output csv file == Output == The output will be a csv file: {{{ Subject one, Subject two 100000,11111 1010101, 100010 }}} Where cluster 100000.trk from Subject one corresponds to cluster 11111.trk from Subject two |
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V. Siless, J. Y. Davidow, J. Nielsen, Q. Fan, T. Hedden, M. Hollinshead, C. V. Bustamante, M. K. Drews, K. R. A. Van Dijk, M.A. Sheridan, R. L. Buckner, B. Fischl, L. Somerville, and A. Yendiki. 2017. “Registration-free analysis of diffusion MRI tractography data across subjects through the human lifespan.” V. Siless, K. Chang, B. Fischl, and A. Yendiki. 2018. “AnatomiCuts: Hierarchical clustering of tractography streamlines based on anatomical similarity.” NeuroImage, 166, Pp. 32-45. |
AnatomiCuts correspondences
This method finds corresponding clusters across subjects. Currently, only one-to-one cluster's correspondences are available using the Hungarian algorithm. Our implementation uses our anatomical similarity metric which allows us to find correspondences without the need of registration, comparing clusters of streamlines in each subject's native space.
{
The Hungarian algorithm
The Hungarian algorithm finds corresponding clusters between two subjects.
bash /space/erebus/2/users/vsiless/code/freesurfer/anatomicuts/dmri_ac.sh preGA SUBJECT TARGET_SUBJECT MIN_STREMLINE_LENGHT STD_CLUSTER_CLEANING bash /space/erebus/2/users/vsiless/code/freesurfer/anatomicuts/dmri_ac.sh forAll preGA TARGET_SUBJECT MIN_STREMLINE_LENGHT STD_CLUSTER_CLEANING - "pbsubmit_-n_1_-c_" AnatomiCuts_correspondences -s1 segmentation1.nii.gz -s2 segmentation2.nii.gz -c numClusters -h1 clusteringPath1 -h2 clusteringPath2 -m metric -o output.csv
Where
-s1 the segmentation to be used for anatomical similarity in subject one.
-s2 the segmentation to be used for anatomical similarity in subject two.
-h1 the path to the AnatomiCuts folder to be used for subject one.
-h2 the path to the AnatomiCuts folder to be used for subject two.
-m metric to be used: labels (anatomical similarity) or euclid (euclidean similarity).
-sym (under development) this flag will mirror the segmentation in subject two to find between hemisphere correspondences.
-o output csv file
Output
The output will be a csv file:
Subject one, Subject two 100000,11111 1010101, 100010
Where cluster 100000.trk from Subject one corresponds to cluster 11111.trk from Subject two
References
V. Siless, J. Y. Davidow, J. Nielsen, Q. Fan, T. Hedden, M. Hollinshead, C. V. Bustamante, M. K. Drews, K. R. A. Van Dijk, M.A. Sheridan, R. L. Buckner, B. Fischl, L. Somerville, and A. Yendiki. 2017. “Registration-free analysis of diffusion MRI tractography data across subjects through the human lifespan.”
V. Siless, K. Chang, B. Fischl, and A. Yendiki. 2018. “AnatomiCuts: Hierarchical clustering of tractography streamlines based on anatomical similarity.” NeuroImage, 166, Pp. 32-45.