Ivadomed: Make gm_challenge_16 dataset BIDS-compatible

Created on 21 Jun 2019  路  2Comments  路  Source: ivadomed/ivadomed

I was formatting the gm_challenge_16 dataset to be BIDS-compatible.
See on internal path:
duke/projects/ivado-medical-imaging/gm_challenge_16/

@jcohenadad, I was wondering:

  • Would you like me to take the folder duke/sct_testing/bids/spineGeneric_multiSubjects/ as example? ie format it in the same way (eg sub-ucl01)
  • For the segmentation files: Are we keeping the previous organization? i.e. duke/projects/ivado-medical-imaging/gm_challenge_16/derivatives/labels/sub-ucl01/anat/
  • For some subjects, we have the segmentation of several raters --> I was thinking of keeping GM voxels where at least half of raters agreed (majority voting). Does that sound okay?
help wanted

Most helpful comment

Update: duke/projects/ivado-medical-imaging/gm_challenge_16/ is formatted / ready for review.
@jcohenadad could you please let me know what you think?

this is perfect!! thank you so much :-)

All 2 comments

Update: duke/projects/ivado-medical-imaging/gm_challenge_16/ is formatted / ready for review.
@jcohenadad could you please let me know what you think?

Update: duke/projects/ivado-medical-imaging/gm_challenge_16/ is formatted / ready for review.
@jcohenadad could you please let me know what you think?

this is perfect!! thank you so much :-)

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