Inputs

Default input format - BIDS

sf-tractomics input folder must follow a valid BIDS format, that minimally contains diffusion (dwi) and T1-weighted (T1w) MRI acquisitions :

Directoryinput_bids_directory
- dataset_description.json
- Directorysub-01
  - Directorydwi
    sub-01_dwi.nii.gz
    sub-01_dwi.bval
    sub-01_dwi.bvec
    sub-01_dwi.json
  - Directoryanat
    sub-01_T1w.nii.gz
    sub-01_T1w.json
- Directorysub-02
  - Directorydwi
    sub-02_dwi.nii.gz
    sub-02_dwi.bval
    sub-02_dwi.bvec
    sub-02_dwi.json
  - Directoryanat
    sub-02_T1w.nii.gz
    sub-02_T1w.json

Perform Motion and Eddy currents correction

sf-tractomics automatically detects reverse-phase acquired images and epi references from the BIDS dataset organization. To be detected, those images need to have a valid direction entity. The same is expected for the main diffusion volume as well (AP and PA are used as example) :

Reverse b0
Reverse DWI

Directoryinput_bids_directory
- dataset_description.json
- Directorysub-01
  - Directorydwi
    sub-01_dir-AP_dwi.nii.gz
    sub-01_dir-AP_dwi.bval
    sub-01_dir-AP_dwi.bvec
    sub-01_dir-AP_dwi.json
  - Directoryanat
    sub-01_T1w.nii.gz
    sub-01_T1w.json
  - Directoryepi
    sub-01_dir-PA_sbref.nii.gz
    sub-01_dir-PA_sbref.json
- Directorysub-02
  - Directorydwi
    sub-02_dir-AP_dwi.nii.gz
    sub-02_dir-AP_dwi.bval
    sub-02_dir-AP_dwi.bvec
    sub-02_dir-AP_dwi.json
  - Directoryanat
    sub-02_T1w.nii.gz
    sub-02_T1w.json
  - Directoryepi
    sub-02_dir-PA_sbref.nii.gz
    sub-02_dir-PA_sbref.json

Unstructured datasets

sf-tractomics also supports parsing its input from a samplesheet.csv in Comma Separated Values format, in case your dataset doesn’t follow the BIDS format yet. The samplesheet must respect the header below :

subject,dwi,bval,bvec,sbref,rev_dwi,rev_bval,rev_bvec,rev_sbref,t1,wmparc,aparc_aseg


subject	Identifier to tag the subject’s files when producing outputs
dwi	Diffusion Weighted volume in Nifti format
bval	b-values file following FSL format
bvec	b-vectors file following FSL format
sbref	Single-band b0 reference for the DWI volume in Nifti format
rev_dwi	Reverse-phase acquired Diffusion Weighted volume in Nifti format
rev_bval	b-values file for the reverse-phase DWI following FSL format
rev_bvec	b-vectors file for the reverse-phase DWI following FSL format
rev_sbref	Single-band b0 reference for the reverse-phase DWI volume in Nifti format
t1	Anatomical T1-Weighted volume in Nifti format
wmparc	White matter parcellation from FreeSurfer
aparc_aseg	Tissue segmentation and cortical parcellation from FreeSurfer