Updated pipeline for Zurich/Balgrist group

[jcohenadad]

After discussing with the Zurich group (Maryam, Gergely), a few modifications need to occur on the INSPIRED pipeline. Few things to discuss:

• Data structure. It is supposed to follow that described in the README, but the latest data structure I received was the following:

./diffusion:
ep2d_diff_99dir           ep2d_diff_b0_reversedblip

./diffusion/ep2d_diff_99dir:
DWI_4D.mat DWI_4D.nii

./diffusion/ep2d_diff_b0_reversedblip:
ep2d_diff_b0_reversedblip.nii

./medic:
3D_medic_5mm_C2-C3

./medic/3D_medic_5mm_C2-C3:
avg_medic_HC02.nii  s1_medic_HC02_1.nii s2_medic_HC02-2.nii s3_medic_HC02_3.nii s4_medic_HC02_4.nii

./morpho:
t1_tse_sag_fit t2_tse_sag_fit t2_tse_tra_fit

./morpho/t1_tse_sag_fit:
t1_sag_HC02.nii

./morpho/t2_tse_sag_fit:
t2_sag_HC02.nii

./morpho/t2_tse_tra_fit:
t2_tra_HC02.nii

• diffusion data: there is no bvecs/bvals attached to it
• Derivatives (manual segmentations/labeling): Where are they supposed to be located and packaged? In a separate folder architecture (eg derivatives/labels like in BIDS), or alongside the raw data?