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Register NIST phantom data to ROI for subsequent quantification #10

Merged
merged 21 commits into from
Aug 4, 2020
Merged

Register NIST phantom data to ROI for subsequent quantification #10

merged 21 commits into from
Aug 4, 2020

Commits on Jul 27, 2020

  1. Added download ROIs routine 

    TODO: do this download outside of this CLI (ie should be part of another "install required data" CLI)
    @jcohenadad
    jcohenadad committed Jul 27, 2020
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  2. Created labels for the NIST ROI files 

    These labels {1, 2, 3} are used for the first affine transformation between the ROI image and each NIST site
    @jcohenadad
    jcohenadad committed Jul 27, 2020
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  3. Creating 3x3 labels instead of 1x1 

    Related to: #1 (comment)
    @jcohenadad
    jcohenadad committed Jul 27, 2020
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  4. Fixed label value assignment

    @jcohenadad
    jcohenadad committed Jul 27, 2020
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Commits on Jul 28, 2020

  1. Removed fsl dependency; Fixed bug related to image dim 

    - now using nibabel
- fixed bug that happened when using fslsplit on 4d single-slice data --> the output image was 2d instead of 3d, which created a blanck image when applying the transfo obtained from the 3d labels
    @jcohenadad
    jcohenadad committed Jul 28, 2020
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  2. Fixed bug due to the .nii (vs. nii.gz) extension of the roi mask

    @jcohenadad
    jcohenadad committed Jul 28, 2020
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  3. Now including ref mask at the beginning of the gif

    @jcohenadad
    jcohenadad committed Jul 28, 2020
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  4. Cleanup

    @jcohenadad
    jcohenadad committed Jul 28, 2020
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  5. APIfied some code: create_labels(), copy_header()

    @jcohenadad
    jcohenadad committed Jul 28, 2020
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  6. Removed 'reference' field in json (no more used)

    @jcohenadad
    jcohenadad committed Jul 28, 2020
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  7. Updated doc with new procedure for registration

    @jcohenadad
    jcohenadad committed Jul 28, 2020
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  8. Removed comma

    @jcohenadad
    jcohenadad committed Jul 28, 2020
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  9. Refactored to construct gif based on exact jpg file names 

    Instead of using the ugly glob.glob
    @jcohenadad
    jcohenadad committed Jul 28, 2020
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  10. Removed unused deps

    @jcohenadad
    jcohenadad committed Jul 28, 2020
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  11. Apply inverse transformation of adjusted mask to T1map native space

    @jcohenadad
    jcohenadad committed Jul 28, 2020
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  12. Removed FSL dependency

    @jcohenadad
    jcohenadad committed Jul 28, 2020
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  13. Added ANTs version

    @jcohenadad
    jcohenadad committed Jul 28, 2020
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Commits on Aug 3, 2020

  1. Enforce 2d output when copying header from mask

    @jcohenadad
    jcohenadad committed Aug 3, 2020
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  2. REMOVE datasets acquired on the T2 plate instead of T1 plate

    @mathieuboudreau
    mathieuboudreau committed Aug 3, 2020
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  3. Add nearest neighbor interpolation

    @mathieuboudreau
    mathieuboudreau committed Aug 3, 2020
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Commits on Aug 4, 2020

  1. Add JSON for ROIs on OSF

    @mathieuboudreau
    mathieuboudreau committed Aug 4, 2020
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