FreeSurfer 7

[MatthieuJoulot]

Here are shown the results of the tests and changes to make in order to use FreeSurfer 7 with Clinica (Which currently uses FreeSurfer 6).

Tests:

• t1-freesurfer : tested, works; basis of the next pipelines. FreeSurfer 7 brings more files, but the one which existed in FreeSurfer 6 still do.
• t1-freesurfer-template: tested, works
• t1-freesurfer-longitudinal: tested, works
• dwi-connectome: tested, works
• pet-surface: tested, works
• pet-surface-longitudinal: tested, works
• stat-surface : tested, works.

Changes to make:

There is one change to make on t1-freesurfer-atlas: the additionnal atlas have a specific format in which the version is specified. Currently the version of FreeSurfer being 6, the code for the atlases is 6p0. It'll have to be updated to 7p1.

[omar-rifai]

Great! thanks for the effort. It might be worthwhile to also mark the outputs that have been visually compared with the current references so as to ensure stability.