Bring stuff from frheault work

[arnaudbore]

• new module modules/local/segmentation/fs_utils/main.nf : EXTRACT_FSRECONALL_PARCELLATION

• new module modules/local/segmentation/lobes_parcellation/main.nf : GENERATE_LOBES_PARCELLATION MERGED

• new module modules/local/tractogram/math/main.nf: TRACTOGRAM_MATH

• See REGISTRATION overhaul ! #175 . If needed port fixes for TRACTOGRAM_REGISTRATION from modules/local/tractogram/registration +

  subworkflow subworkflows/nf-neuro/registration I had to flip fixed and moving to fix the results (fixed and moving are not in an harmonize order, compared to the modules for example). In its own PR, need to look at transform modules as well, and it touches a lot of subworkflows +

  subworkflows/nf-neuro/registration/main.nf
        transfo_image       = transfo_image           // channel: [ val(meta), [ warp ], [ <affine> ] ]
        transfo_trk         = transfo_trk             // channel: [ val(meta), [ <inverse-affine> ], [ inverse-warp ] ]
  Pour moi je ferais 4 emit au lieu de les mettre ensemble, OU je changerais les noms parce que c'est possible de vouloir le inverse pour en image. Et c'est intuitif pour un expert de mettre warp et affine pour direct et affine et inversewarp pour l'inverse, mais c'est pas evident que les affine/warp sont pas dans le meme ordre selon la direction. Bref, 4 emit serait mieux
  

• Ajout de paramètre pour le choix de segmentation de WM si on prend FSL vs freesurfer (et si le channel est vide, parce que ca process on doit attendre) dans subworkflows/nf-neuro/anatomical_segmentation/main.nf
  Si on fourni un channel freesurfer il FAUT attendre le résultat pour avoir des bons MASK, mais on peut aller de l'avant et utiliser FSL pour les MAPS (on AlexVCaron/hotfix). MERGED

• modules/nf-neuro/segmentation/freesurferseg/main.nf dans SEGMENTATION_FREESURFERSEG : swap addition to union, uint8 (quand on merge les GM et WM ensemble) +

  subworkflows/nf-neuro/tractoflow/modules.config (changé le default)
        ext.interpolation   = "MultiLabel"
        ext.output_dtype    = "short"
  
  
  

  All on (on AlexVCaron/hotfix) MERGED

[frheault]

https://github.com/scilus/nf-neuro/blob/main/modules/nf-neuro/registration/tractogram/main.nf Already exist, so that's already done ! But I just saw that the cut_invalid parameters is unused (must be added to the first OR second script call)

[AlexVCaron]

anatomical segmentation is already fixed as well with the join method I was talking about

[arnaudbore]

I'm taking care of EXTRACT_FSRECONALL_PARCELLATION

[arnaudbore]

erratum -> no need for EXTRACT_FSRECONALL_PARCELLATION

[AlexVCaron]

Tractogram registration is already in nf-neuro, we only have to port fixes if needed.

[AlexVCaron]

Closed by #175