Solution for confusion in Spine Generic

[sandrinebedard]

Description

It might be confusing to have space-other in some of the labels but not all of them, also considering that we applided reorientation and resampling, but some of them were already in the right space.

Proposed solution

• Move the data from the root directory in sourcedata folder
• Copy derivatives/data-preprocessed to the root directory
• Remove derivatives/data-preprocessed
• Update the naming to remove space-other:
  • from the raw images
  • from derivatives/data-preprocessed
  • from labels_softseg
  • from labels_softseg_bin
• Fix json to follow our convention:
  • labels_softseg_bin
  • labels_softseg
  • label-SC_seg in labels
    Remove this,

"SpatialReference": {
        "Resampling": "1x1x1",
        "Reorientation": "RPI"

For labels label-SC_seg :

{
    "SpatialReference": "orig",
    "GeneratedBy": [
{
            "Name": "sct_deepseg_sc",
            "Version": "SCT v6.2"
},
            {
              "Name": "Manual",
              "Author": "Sandrine Bedard",
               "Date": "2021-07-25 13:39:39",
            }
]
}

• Temporary: add space-other to the discs labels if they are in different space
• Long term: run totalspineseg on preprocessed data and replace old discs labels
• Test if possible to resample labels
• Keep DWI data in root and source data folder
• Update README, explain how to use source data & update script

TODO

• Edit change log
• Make a release
• Announce in neurostars and sct forum
• Update spinegeneric scripts