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Fix diffusion mask in voxels outside the FOV #129

Merged
merged 19 commits into from
Oct 29, 2019
Merged

Fix diffusion mask in voxels outside the FOV #129

merged 19 commits into from
Oct 29, 2019

Commits on Oct 6, 2019

  1. BUG: only include voxels fully within the FOV in every volume

    Michiel Cottaar authored and Michiel Cottaar committed Oct 6, 2019
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  2. BUG: only zero-values are outside FOV, not negative values

    Michiel Cottaar authored and Michiel Cottaar committed Oct 6, 2019
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  3. Change threshold for floating point rounding error 

    As suggested by Tim Coalson. Not sure if it is needed, but might as well.
    @MichielCottaar
    MichielCottaar authored and Michiel Cottaar committed Oct 6, 2019
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  4. OPT: use first volume to extract FOV mask 

    Gives equivalent results, but is faster
    Michiel Cottaar authored and Michiel Cottaar committed Oct 6, 2019
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  5. BUG: dilate the diffusion data before spline interpolation

    Michiel Cottaar authored and Michiel Cottaar committed Oct 6, 2019
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  6. Typo: -volume_dilate -> -volume-dilate

    Michiel Cottaar authored and Michiel Cottaar committed Oct 6, 2019
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  7. BUG: added extensions to filenames for wb_command

    Michiel Cottaar authored and Michiel Cottaar committed Oct 6, 2019
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  8. ENH: added text file with percentage of brain mask in final mask

    Michiel Cottaar authored and Michiel Cottaar committed Oct 6, 2019
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  9. BUG: reduce number of voxels to dilate

    Michiel Cottaar authored and Michiel Cottaar committed Oct 6, 2019
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Commits on Oct 11, 2019

  1. BUG: fixed several typos preventing code to run

    Michiel Cottaar authored and Michiel Cottaar committed Oct 11, 2019
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  2. BUG: use fslmaths data -abs -Tmax -bin to only mask out data where al… 

    …l data is zero
    Michiel Cottaar authored and Michiel Cottaar committed Oct 11, 2019
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  3. REF: rename DILATE_DISTANCE to DilateDistance

    Michiel Cottaar authored and Michiel Cottaar committed Oct 11, 2019
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Commits on Oct 12, 2019

  1. Merge branch 'master' into mask_diff

    Michiel Cottaar authored and Michiel Cottaar committed Oct 12, 2019
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  2. Back to using Tmin, but now filling holes 

    Adding -fillh should fill up any internal holes due to voxels
being zero for some other reason than being marked like that by eddy.
    Michiel Cottaar authored and Michiel Cottaar committed Oct 12, 2019
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  3. Fixed comments as suggested by @mharms

    Michiel Cottaar authored and Michiel Cottaar committed Oct 12, 2019
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  4. Do not remove the field of view mask

    Michiel Cottaar authored and Michiel Cottaar committed Oct 12, 2019
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Commits on Oct 17, 2019

  1. REF: compute fov_mask in eddy_postproc rather than Diffusion2Structural

    Michiel Cottaar authored and Michiel Cottaar committed Oct 17, 2019
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Commits on Oct 18, 2019

  1. Updated comments and other minor changes suggested by @mharms

    Michiel Cottaar authored and Michiel Cottaar committed Oct 18, 2019
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Commits on Oct 26, 2019

  1. Several last bug fixes

    Michiel Cottaar authored and Michiel Cottaar committed Oct 26, 2019
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