Data Requirements

Data for freesurfer

Data for CIVET

Data for Tractoflow

[root folder as input]
├── S1
│   ├── brain_mask.nii.gz
│   ├── bval
│   ├── bvec
│   ├── dwi.nii.gz
│   ├── t1.nii.gz
│   ├── rev_b0.nii.gz  (optional)
│   └── pve_wm.nii.gz*  (with civet_pve or fsl_pve)
│   └── pve_gm.nii.gz*  (with civet_pve or fsl_pve)
│   └── pve_csf.nii.gz* (with civet_pve or fsl_pve)
│   └── pve_sc.nii.gz*  (with civet_pve)
└── S2
    ├── brain_mask.nii.gz
    ├── ...

Standard profile

-profile brain_mask_only

-profile civet_pve

-profile fsl_pve