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.<\/p>\n
For each<\/strong> submission (regardless of sub-challenge), we ask for 3 items.\u00a0This can be compressed (and given any name) and submitted to synapse.<\/p>\n * note that there are several tools available to convert from standard software tools to TRK format, for example\u00a0https:\/\/gist.github.com\/MarcCote\/ebf0ae83a9202eb96d1dfbb949cd98af<\/p>\n Instructions specific to sub-challenges.<\/p>\n 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.<\/em><\/p>\n For the Phantom dataset, each submission will contain 16 track files for each scanner. The nifti file submissions will be named “A.nii.gz<\/strong>” and “B.nii.gz<\/strong>” 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), \u00a0should 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<\/strong>” and “Tracks_B.trk”<\/strong> each containing the 16 bundles for A and B, respectively. The text file must be named “Information.txt<\/strong>“.<\/p>\n *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”.*<\/p>\n Phantom Nifti Header –\u00a0example_phantom_submission<\/a><\/p>\n **Please be sure to change the actual image matrix to your submission matrix in the uploaded Nifti files in the example_phantom_submission<\/p>\n 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<\/strong>“, “Tracks.trk<\/strong>”\u00a0and “Information.txt<\/strong>“. *Note you do not have to enter a submission for each seed size, but multiple submissions are certainly allowed*<\/p>\n Squirrel Monkey Nifti Header –\u00a0HeaderSM<\/a><\/p>\n 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\u00a0include 6\u00a0files, “A.nii.gz<\/strong>” and “B.nii.gz<\/strong>” for the two seeds (see below for seed description), “Tracks_A.trk<\/strong>” and “Tracks_B.trk<\/strong>” and “Information_A.txt<\/strong>” and “Information_B.txt<\/strong>” (please describe in the text file which size seed\u00a0used). *We anticipate that most groups will chose to make submissions for both regular and dilated seeds*.<\/p>\n Macaque Nifti Header –\u00a0HeaderMacaque<\/a><\/p>\n Seed A: contains “144_145_2013_5mm” or\u00a0“144_145_2013_10mm” and is in the PCG.<\/p>\n Seed B: contains “203_79_77_3mm” or\u00a0“203_79_77_5mm” and contains V3\/V4.<\/p>\n For submissions to synapse please read the post on how to submit at the link:\u00a0https:\/\/my.dev.vanderbilt.edu\/votem\/2018\/01\/13\/submission-guidelines-for-synapse\/<\/a><\/p>\n","protected":false},"excerpt":{"rendered":" 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.\u00a0This can be compressed (and given any name) and submitted … Continue reading \n
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