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sct_propseg: Now possible to rescale data header to be able to segment non-human spinal cord (mice, rats, etc.) #1903

Merged
merged 19 commits into from Jul 7, 2018
Merged

sct_propseg: Now possible to rescale data header to be able to segment non-human spinal cord (mice, rats, etc.) #1903

merged 19 commits into from Jul 7, 2018

Commits on Jul 3, 2018

  1. reorganized usage

    @jcohenadad
    jcohenadad committed Jul 3, 2018
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  2. minor usage update

    @jcohenadad
    jcohenadad committed Jul 3, 2018
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  3. started to implement header-based rescaling (WIP)

    @jcohenadad
    jcohenadad committed Jul 3, 2018
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Commits on Jul 4, 2018

  1. now creating file in temp folder, and fixed input to propseg function

    @jcohenadad
    jcohenadad committed Jul 4, 2018
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  2. added flag to enable/disable the algorithm that corrects the segmenta… 

    …tion
    @jcohenadad
    jcohenadad committed Jul 4, 2018
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Commits on Jul 5, 2018

  1. added doc

    @jcohenadad
    jcohenadad committed Jul 5, 2018
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  2. refactored to follow variable conventions

    @jcohenadad
    jcohenadad committed Jul 5, 2018
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Commits on Jul 6, 2018

  1. finished implementing the major part of the rescaling

    @jcohenadad
    jcohenadad committed Jul 6, 2018
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  2. fixed issue with output file name

    @jcohenadad
    jcohenadad committed Jul 6, 2018
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  3. moved import at the beginning

    @jcohenadad
    jcohenadad committed Jul 6, 2018
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  4. added flag -rescale

    @jcohenadad
    jcohenadad committed Jul 6, 2018
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  5. Merge branch 'master' into enh/1406

    @jcohenadad
    jcohenadad committed Jul 6, 2018
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  6. Merge branch 'master' into enh/1406

    @jcohenadad
    jcohenadad committed Jul 6, 2018
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  7. fixing output path issues (unfinished)

    @jcohenadad
    jcohenadad committed Jul 6, 2018
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Commits on Jul 7, 2018

  1. fixed output filename

    @jcohenadad
    jcohenadad committed Jul 7, 2018
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  2. fixed typo in usage

    @jcohenadad
    jcohenadad committed Jul 7, 2018
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  3. does not rename the centerline if rescaled is on

    @jcohenadad
    jcohenadad committed Jul 7, 2018
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  4. removed TODO

    @jcohenadad
    jcohenadad committed Jul 7, 2018
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  5. added TODO to deal with removal of temp file (not urgent)

    @jcohenadad
    jcohenadad committed Jul 7, 2018
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