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