@@ -19,17 +19,15 @@ segmentations in nifti format.
1919 + get the array of values at the voxel below a given label
2020 + symmetrise a segmentation
2121 + [ ...and more] ( https://github.com/SebastianoF/nilabels/wiki/What-you-can-do-with-nilabels )
22- + Facade design pattern to make it easily extendible with new methods (see the [ docs] ( https://github.com/SebastianoF/nilabels/wiki/Design-Pattern ) )
22+ + Facade design pattern (see the [ docs] ( https://github.com/SebastianoF/nilabels/wiki/Design-Pattern ) )
2323
24-
25- ### Non-features (work in progress)
24+ ### Not-features (work in progress)
2625
2726+ Not yet Python 3, back compatible python 2.7
2827+ Not yet 80% coverage
2928+ Not yet pip-installable
3029+ [ ... and more] ( https://github.com/SebastianoF/nilabels/wiki/Work-in-Progress )
3130
32-
3331### Introductory example
3432
3533Given a segmentation ` my_input_folder_path/my_segm.nii.gz ` imagine you want to change the labels values from [ 1, 2, 3, 4, 5, 6] to [ 2, 12, 4, 7, 5, 6]
@@ -38,6 +36,7 @@ and save the result in `my_output_folder_path/my_new_segm.nii.gz`. Then:
3836``` python
3937import nilabels as nis
4038
39+
4140# option 1
4241nis_app = nis.App(' my_input_folder_path' , ' my_output_folder_path' )
4342nis_app.manipulate_labels.relabel(' my_segm.nii.gz' , ' my_new_segm.nii.gz' ,
@@ -53,11 +52,11 @@ nis_app.manipulate_labels.relabel('my_input_folder_path/my_segm.nii.gz', 'my_out
5352
5453
5554+ Install NiLabels: the current version is not (yet) pip installable. It can be installed in development mode.
56- To proceede , initialise a virtual environment and execute the following instructions:
55+ To proceed , initialise a virtual environment and execute the following instructions:
5756```
5857cd <folder where to clone the code>
5958git clone https://github.com/SebastianoF/nilabels.git
60- cd nilabel
59+ cd nilabels
6160pip install -e .
6261```
6362In development mode every change made to your local code will be directly affecting the libray installed in the python distribution
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