Submissions

Example submissions have been posted with the data (https://www.synapse.org/). Please see “Registration and Data Access” Tab for step-by-step download instructions.

For each submission (regardless of sub-challenge), we ask for 3 items. This can be compressed (and given any name) and submitted to synapse.

  1. A tractography file, in TRACKVIS “.trk” format*
  2. A NIFTI file that contains the voxel-wise “visitation counts”. This is identical to the tract count per voxel. If you plan to threshold your results at a certain visitation count (as is common in probabilistic techniques) please ensure that your visitation NIFTI has been thresholded appropriately.
  3. A text file that contains the following:
    1. Submissions unique name or identifier (can be chosen by submitter)
    2. Submitter name and contact information (as well as team members and affiliations)
    3. Data: which data was used (to avoid sub-challenge confusion), and which subset of data (b-value, number of directions, etc) was utilized
    4. Pre-processing done, if any
    5. Reconstruction technique (i.e. DTI, CSD, Qball, etc.)
    6. Software utilized (if exists)
    7. Tracking method: deterministic, probabilistic, or other (briefly describe if other)
    8. Algorithm: for example, FACT
    9. Constraints: any constraints: FA, Angular threshold, logical constraints
    10. Seeds/ROI: which Seed was used and how it was used (for example as a pure seed, or as an AND/OR Region of interest)
    11. Miscellaneous: other interesting information, more detailed description of algorithm, appropriate citations, recommended visitation count threshold, etc.
    12. Please include any citations / references to your own work or the work of others that we should include when discussing your work in the challenge summary journal article. Additional descriptor files (e.g., Word documents) are welcome.

* note that there are several tools available to convert from standard software tools to TRK format, for example https://gist.github.com/MarcCote/ebf0ae83a9202eb96d1dfbb949cd98af

Instructions specific to sub-challenges.

For all submissions please use the Nifti header files provided at the link below specific to the sub-challenges. Please ensure that no changes are made to the headers of the Nifti files.

For the Phantom dataset, each submission will contain 16 track files for each scanner. The nifti file submissions will be named “A.nii.gz” and “B.nii.gz” for scanner A and B, respectively. Both of the mentioned submission files should be in a single .zip file as a single submission. The submissions containing two nifti files (one for A and one for B),  should each be of size X*Y*Z*16, where each volume contains the visitation counts associated with the appropriately numbered seed. The track files will be named “Tracks_A.trk” and “Tracks_B.trk” each containing the 16 bundles for A and B, respectively. The text file must be named “Information.txt“.

*Note that you are free to use as little or as much of the 3080 image volumes per scanner as you would like. But please indicate which was used in the text file, for example, “all b1000 data” or “all data from both b-values” or “3 repeats of b1000”.*

Phantom Nifti Header – example_phantom_submission

**Please be sure to change the actual image matrix to your submission matrix in the uploaded Nifti files in the example_phantom_submission

For the squirrel monkey dataset, because there is only a single injection region, each submission will simply contain the 3 files described above. These must be named “SM.nii.gz“, “Tracks.trk” and “Information.txt“. *Note you do not have to enter a submission for each seed size, but multiple submissions are certainly allowed*

Squirrel Monkey Nifti Header – HeaderSM

For the Macaque, because there are two white matter pathways of interest (two seeds), there will be two datasets for each submission (one for each seed). Each submission will then include 6 files, “A.nii.gz” and “B.nii.gz” for the two seeds (see below for seed description), “Tracks_A.trk” and “Tracks_B.trk” and “Information_A.txt” and “Information_B.txt” (please describe in the text file which size seed used). *We anticipate that most groups will chose to make submissions for both regular and dilated seeds*.

Macaque Nifti Header – HeaderMacaque

Seed A: contains “144_145_2013_5mm” or “144_145_2013_10mm” and is in the PCG.

Seed B: contains “203_79_77_3mm” or “203_79_77_5mm” and contains V3/V4.

For submissions to synapse please read the post on how to submit at the link: https://my.vanderbilt.edu/votem/2018/01/13/submission-guidelines-for-synapse/