# Preproccesing pipeline

1. Please download the data
- /misc/rhesus/rrios/noBackup/MRI_stuff/dMRI-for-preprocessing-best-practices/Release
3. Preprocess the DWI images with your typical image preprocessing pipeline.
- [ ] Denoising. Mrtrix3 Cordero-grande
- Default parameters
- [x] ~~Gibbs~~
- [x] Bias field
- N4 correction to b0
- Apply correction to all images
- [ ] Eddy
5. Upload the preprocessed data to a personalized upload server
- Link to upload: https://nyulangone-my.sharepoint.com/:f:/g/personal/jelle_veraart_nyulangone_org/Eq5fmhsnobJCtvKWbI_obGcBoVbr33tdfw81f6KT8T6-Tw

4. Provide details on the used preprocessing pipeline using an online form (https://nyu.qualtrics.com/jfe/form/SV_doPv2gyQwsfYLAi)

## Data notes
For each scan, we provide the following data:

T1-weighted MPRAGE image [defaced]
./*/anat/t1w_anat.nii.gz

Multi-shell diffusion-weighted images
./*/dwi/dwi.nii.gz

The diffusion-weighted gradient scheme used in the acquisition in FSL bvecs/bvals format files
./*/dwi/dwi.bvec/bval

Non-diffusion-weighted images, acquired with reversed phase encoding
./*/dwi/b0rpe.nii.gz

B0 field map
either
./*/fmap/B0_fieldmap.nii.gz
or both
./*/fmap/gre_magnitude.nii.gz and ./*/fmap/gre_phasediff.nii.gz

## Steps