sct_register_to_template: Fixed wrong projection in case labels not in same space

[jcohenadad]

Description

In sct_register_to_template.project_labels_on_spinalcord(), the labels are re-oriented to RPI, which can cause bugs in case labels (i) are not in the same voxel space as the input segmentation and (ii) are not RPI. In fact, labels should not be re-oriented, because their coordinates are transformed into physical coordinates.

The implemented fix consisted in removing the re-orientation of labels before projecting them onto the cord centerline.

Fixes #1977

[zougloub]

OK.

realized Travis failed and other

[jcohenadad]

currently breaking because of project_labels_on_spinalcord(). Working on it...

UPDATE 2018-08-06 16.54: I was doing something wrong for the fix. Both the segmentation and the labels need to be re-oriented to RPI. Now checking why this has caused an issue in the particular scan.

UPDATE 2018-08-06 17.33: Nevermind my previous update: i was doing something right, but because of some bugs related to set_orient(), I got wrong results. So: the proposed fix (i.e. do not reorient labels to RPI and work with physical coordinates) should work. The reason it does not work is because sct_image.setorient() sometimes corrupts the physical coordinates of the output images. This is likely related to #1944, hence it would probably be wise to wait until issues with setorient are fixed before moving forward with the present issue.