IronTract Challenge - Round II - How to Participate

Transcript

1. How to participate
   IronTract Challenge Round II
   

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2. Step 1: Register to the Challenge
   https://irontract.mgh.harvard.edu/register/
   Request challenge-specific access codes for
   your team
   Submitted only once per team
   

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3. Step 2: Register on the QMENTA Platform
   https://client.qmenta.com/
   

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4. Step 2: Register on the QMENTA Platform
   

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5. Step 3: Sign in the QMENTA Platform
   

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6. Step 3: Sign in the QMENTA Platform
   

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7. Step 3: Sign in the QMENTA Platform
   

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8. Step 4: Download the training data
   

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9. Step 5: Run your favorite tractography method!
   ROUND I PARTICIPANTS ROUND II PARTICIPANTS
   Use the same orientation
   reconstruction and tractography
   methods that you used in Round I
   Use any orientation reconstruction
   and tractography method of your
   choice
   

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10. Step 5: Run your favorite tractography method!
    ROUND I PARTICIPANTS ROUND II PARTICIPANTS
    Use the same orientation
    reconstruction and tractography
    methods that you used in Round I
    Use any orientation reconstruction
    and tractography method of your
    choice
    Both previous and new participants must use the harmonized
    pre-processing and seed region
    

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11. Step 6: Postprocessing of the training data
    •Post-processing 1: spatial filtering, from EPFL
    team compute_density_volumes_EPFL.py.
    Trk files use the script as is
    Tract Volumes apply the first step (length
    thresholding) on the fly in your own tractography
    code, and you can then use the rest of the script on
    your output volumes.
    • Post-processing 2: anatomical ROIs, from
    VUMC team
    compute_density_volumes_VUMC.py
    + two inclusion masks
    Trk files use the script as is
    Tract Volumes apply inclusion masks on the fly
    in your tractography code, and you can then use
    the rest of the script on your output volumes
    You will receive a link to access the following scripts upon registering to the challenge
    Email us if you have any question!
    

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12. Step 6: Postprocessing of the training data
    •Post-processing 1: spatial filtering, from EPFL
    team compute_density_volumes_EPFL.py.
    Trk files use the script as is
    Tract Volumes apply the first step (length
    thresholding) on the fly in your own tractography
    code, and you can then use the rest of the script on
    your output volumes.
    • Post-processing 2: anatomical ROIs, from
    VUMC team
    compute_density_volumes_VUMC.py
    + two inclusion masks
    Trk files use the script as is
    Tract Volumes apply inclusion masks on the
    fly in your tractography code, and you can then
    use the rest of the script on your output
    volumes
    You will receive a link to access the following scripts upon registering to the challenge
    Include all the NIfTI volumes produced by this method at all the different thresholds in a single zip file.
    Submit results separately for each of these two post-processing approaches
    

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13. Step 6: Upload the training data
    

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14. Step 6: Upload the training data
    

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15. Step 6: Upload the training data
    

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16. Step 6: Upload the training data
    

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17. Step 6: Upload the training data: check results
    Max 10 Uploads
    If you need more, contact us
    

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18. Step 7: Download the validation data
    

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19. Step 8: Postprocessing of the validation data
    •Post-processing 1: spatial filtering, from EPFL
    team compute_density_volumes_EPFL.py.
    Trk files use the script as is
    Tract Volumes apply the first step (length
    thresholding) on the fly in your own tractography
    code, and you can then use the rest of the script on
    your output volumes.
    • Post-processing 2: anatomical ROIs, from
    VUMC team
    compute_density_volumes_VUMC.py
    + two inclusion masks
    Trk files use the script as is
    Tract Volumes apply inclusion masks on the
    fly in your tractography code, and you can then
    use the rest of the script on your output
    volumes
    You will receive a link to access the following scripts upon registering to the challenge
    Include all the NIfTI volumes produced by this method at all the different thresholds in a single zip file.
    1-2 pages description of your methods. PDF included in the zip file of your validation
    results.
    - must include any information that one would need to replicate your results independently.
    Submit results separately for each of these two post-processing approaches
    

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20. Step 8: Upload the validation data
    

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21. Step 8: Upload the validation data
    

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22. By November 8th you need to upload:
    1.Results from the training data.
    1.Results from the validation data.
    1.A 1-2 page description of your methods.
    - PDF included in the zip file of your validation results.
    - must include any information that one would need to
    replicate your results independently.
    All of the above must be the same for the training and
    validation data.
    SHARE YOUR CODE
    +
    Finalize your submission
    

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23. Subscribe to the mailing list:
    ayendiki@mgh.havard.edu
    cmaffei@mgh.Harvard.edu
    Questions?
    

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