neuropoly / spinalcordtoolbox / 10974
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DEFAULT BRANCH: master
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Jobs 2
Files 85
Run time 13min
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10974

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jcohenadad 
Refactoring to allow use of im AND seg in the registration process (#2218)

* Creation of 2 scripts :

sct_axial_rotation will aim to detect the axial rotation (xy plane) of the spinal cord, first version is based on histogram of gradient orientation

sct_test_axial_rotation is a function to process the sct_axial_rotation to multiple subjects and output all figures necessary to quality visualisation in a selected directory

* little script converting to nii (just for testing purpose)

added 3D visualisation of the convolution of histogram

made testing retrieve file and work the sct_axial_rotation script on
a large dataset (sct_large or any with the same structure)

test_sym is just for testing purpose

* corrected errors

added weighting by the gradient magnitude, otherwise we have way too much votes for the 0th degree

* corrected errors

added different filtering

* created script to test on T2* images

* work in progress

* work in progress

* Created new scripts to make the whole thing clearer and easier to use
The old scripts will be deleted in the future

* Modified the "raise" statement

* error in extract_slice

* minor changes, adjustments

* minor changes, adjustments

* minor changes, added figures for debbuguing (and understanding)

* cleaning of old functions

* added weighting map based on segmentation of sc

* added graphical output, safeguards, function to generate 2D dataset,

* changed names for clarity
added possibility to generate a mask

* added new test to compare PCA to hogancest
probability seg map now based on pixdim
angles now translated for visualisation purpose
added mask output

* added angle range

* Created function to compute metrics for the method implemented

* Modified existing scripts to be able to have im + seg on a registration step

* Created script to run evaluate_hogancest in terminal directly

* Added function to directly evaluate angle

* Adde... (continued)

9690 of 14560 relevant lines covered (66.55%)

1.33 hits per line

Jobs
ID Job ID Ran Files Coverage
1 10974.1 (SCT_MINICONDA=2) 85
66.55
 Travis Job 10974.1
2 10974.2 (SCT_MINICONDA=2) 126
67.85
 Travis Job 10974.2
Source Files on build 10974