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preprocessing with SCT #5

Merged
merged 30 commits into from
Dec 2, 2022
Merged

preprocessing with SCT #5

merged 30 commits into from
Dec 2, 2022

Commits on Nov 17, 2022

  1. initial preprocess script

    @kiristern
    kiristern committed Nov 17, 2022
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Commits on Nov 18, 2022

  1. Update .gitignore

    @valosekj
    valosekj committed Nov 18, 2022
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  2. Update preprocessing for T2w image (add reorientation, resampling, se… 

    …gmentation by propseg and deepseg, labeling, and lesions segmentation); update README
    @valosekj
    valosekj committed Nov 18, 2022
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  3. Add TODO to consider 3D kernel for sct_deepseg_sc

    @valosekj
    valosekj committed Nov 18, 2022
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Commits on Nov 19, 2022

  1. Allow kernel specification (2d, 3d) for segment_if_does_not_exist fun… 

    …ction
    @valosekj
    valosekj committed Nov 19, 2022
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Commits on Nov 22, 2022

  1. Add info how to run analysis in virtual terminal

    @valosekj
    valosekj committed Nov 22, 2022
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Commits on Nov 24, 2022

  1. Keep only sct_deepseg_sc 2d.

    @valosekj
    valosekj committed Nov 24, 2022
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  2. initial commit

    @sandrinebedard
    sandrinebedard committed Nov 24, 2022
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  3. Keep only sct_deepseg_sc within the segment_if_does_not_exist function.

    @valosekj
    valosekj committed Nov 24, 2022
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  4. adjust manual correction script for sc segmentation

    @sandrinebedard
    sandrinebedard committed Nov 24, 2022
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  5. add instructions for manual corrections

    @sandrinebedard
    sandrinebedard authored Nov 24, 2022
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Commits on Nov 28, 2022

  1. add pycache

    @sandrinebedard
    sandrinebedard committed Nov 28, 2022
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  2. add script to package data to correct

    @sandrinebedard
    sandrinebedard committed Nov 28, 2022
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  3. Merge branch 'sb/manual_correction_script' of github.com:ivadomed/can… 

    …proco into sb/manual_correction_script
    @sandrinebedard
    sandrinebedard committed Nov 28, 2022
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  4. Allow specifying deepseg/propseg for the segment_if_does_not_exist fu… 

    …nction
    @valosekj
    valosekj committed Nov 28, 2022
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  5. Implement _raw suffix to have BIDS compliant derivatives

    @valosekj
    valosekj committed Nov 28, 2022
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  6. Comment out T2w labeling and lesion seg

    @valosekj
    valosekj committed Nov 28, 2022
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  7. Add check if T2w file exists

    @valosekj
    valosekj committed Nov 28, 2022
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  8. Remove unused processing steps for T2w

    @valosekj
    valosekj committed Nov 28, 2022
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  9. Add PSIR, STIR and T2star preprocessing (reorientation, segmentation).

    @valosekj
    valosekj committed Nov 28, 2022
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  10. Switch from mv to ln -s to allow easier file renaming tracking

    @valosekj
    valosekj committed Nov 28, 2022
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  11. fix typos

    @sandrinebedard
    sandrinebedard authored Nov 28, 2022
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  12. Fix typo in YouTube 

    Co-authored-by: Julien Cohen-Adad <[email protected]>
    @valosekj @jcohenadad
    valosekj and jcohenadad authored Nov 28, 2022
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Commits on Nov 30, 2022

  1. Merge branch 'ks/preprocess' into sb/manual_correction_script

    @sandrinebedard
    sandrinebedard authored Nov 30, 2022
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  2. Merge pull request #9 from ivadomed/sb/manual_correction_script 

    Add manual correction script
    @sandrinebedard
    sandrinebedard authored Nov 30, 2022
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Commits on Dec 1, 2022

  1. Update label_if_does_not_exist function

    @valosekj
    valosekj committed Dec 1, 2022
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  2. Do vertebral labeling for T2w

    @valosekj
    valosekj committed Dec 1, 2022
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  3. Delete temporary files

    @valosekj
    valosekj committed Dec 1, 2022
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  4. Update script description

    @valosekj
    valosekj committed Dec 1, 2022
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  5. Merge branch 'ks/preprocess' of https:/ivadomed/canproco … 

    …into ks/preprocess
    @valosekj
    valosekj committed Dec 1, 2022
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