Derivatives

Introduction

Depending on the options provided by command line and params.json, different files will ouput

Derivatives will be output if option -deriv is provided to the command line (See Commands <commands>):

All files are by default in stereo space; if option -padback is provided to the command line (See Commands <commands>), files in native will also be output.

Data Preparation

Original files (possibly after reorientation and avereging):

sub-Stevie_ses-01_space-native_T1w.nii.gz

sub-Stevie_ses-01_space-native_T2w.nii.gz

If -padback is defined in command line (See Commands <commands>):

sub-Stevie_ses-01_space-native_desc-denoised_T1w.nii.gz

sub-Stevie_ses-01_space-native_desc-denoised_T2w.nii.gz

sub-Stevie_ses-01_space-native_desc-debiased_T1w.nii.gz

sub-Stevie_ses-01_space-native_desc-debiased_T2w.nii.gz

NB: Both denoise and debias are optional

Original files in stereo space:

sub-Stevie_ses-01_space-stereo_T1w.nii.gz

sub-Stevie_ses-01_space-stereo_T2w.nii.gz

After some preprocessing :

sub-Stevie_ses-01_space-stereo_desc-denoised_T1w.nii.gz

sub-Stevie_ses-01_space-stereo_desc-denoised_T2w.nii.gz

sub-Stevie_ses-01_space-stereo_desc-debiased_T1w.nii.gz

sub-Stevie_ses-01_space-stereo_desc-debiased_T2w.nii.gz

NB: Both denoise and debias are optional

Transformations:

sub-Stevie_ses-01_space-native_target-stereo_affine.txt

sub-Stevie_ses-01_space-stereo_target-native_affine.txt

Brain extraction

Brain mask:

sub-Stevie_ses-01_space-stereo_desc-brain_mask.nii.gz

sub-Stevie_ses-01_space-native_desc-brain_mask.nii.gz

Brain segmentation

Brainmasked files after T1*T2 Bias correction:

sub-Stevie_ses-01_space-stereo_desc-debiased_desc-brain_T1w.nii.gz

sub-Stevie_ses-01_space-stereo_desc-debiased_desc-brain_T2w.nii.gz

sub-Stevie_ses-01_space-native_desc-debiased_desc-brain_T2w.nii.gz

sub-Stevie_ses-01_space-native_desc-debiased_desc-brain_T1w.nii.gz

Segmentated files as probability tisses:

sub-Stevie_ses-01_space-stereo_label-WM_probseg.nii.gz

sub-Stevie_ses-01_space-stereo_label-GM_probseg.nii.gz

sub-Stevie_ses-01_space-stereo_label-CSF_probseg.nii.gz

sub-Stevie_ses-01_space-native_label-WM_probseg.nii.gz

sub-Stevie_ses-01_space-native_label-GM_probseg.nii.gz

sub-Stevie_ses-01_space-native_label-CSF_probseg.nii.gz

Segmentated files as indexed tisses:

sub-Stevie_ses-01_space-stereo_desc-brain_dseg.nii.gz

sub-Stevie_ses-01_space-native_desc-brain_dseg.nii.gz

Optional Post brain segmentation

Segmented files in mrtrix format:

sub-Stevie_ses-01_space-stereo_desc-5tt_dseg.nii.gz

sub-Stevie_ses-01_space-native_desc-5tt_dseg.nii.gz

White matter + Gray matter binary mask and corresponding mesh:

sub-Stevie_ses-01_space-stereo_desc-wmgm_mask.nii.gz

sub-Stevie_ses-01_space-native_desc-wmgm_mask.nii.gz

sub-Stevie_ses-01_desc-wmgm_mask.stl