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):

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

For all files provided by macapype, see Derivatives and see Derivatives

Data Preparation (Padded files)

If pad_template is defined in params (normalily used to coregister stereo to petra, T1w and CT):

sub-Stevie_ses-01_space-stereo_desc-pad_T1w.nii.gz

sub-Stevie_ses-01_space-stereo_desc-pad_T2w.nii.gz

Some files computed with macapype are put in the same space after pad:

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

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

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

sub-Stevie_ses-01_space-native_desc-pad_T1w.nii.gz

sub-Stevie_ses-01_space-native_desc-pad_T2w.nii.gz

Petra Skull extraction

Petra in stereo space:

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

Headmask in stereo and native (normally corresponding to native T1w) spaces:

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

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

Skullmask in stereo and native (normally corresponding to native T1w) spaces:

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

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

Meshes of headmask and skullmask:

sub-Stevie_ses-01_desc-petra_skullmask.stl

sub-Stevie_ses-01_desc-petra_headmask.stl

T1w Skull extraction

Headmask in stereo and native spaces:

sub-Stevie_ses-01_space-stereo_desc-t1_headmask.nii.gz

sub-Stevie_ses-01_space-native_desc-t1_headmask.nii.gz

Skullmask in stereo and native spaces:

sub-Stevie_ses-01_space-stereo_desc-t1_skullmask.nii.gz

sub-Stevie_ses-01_space-native_desc-t1_skullmask.nii.gz

Meshes of headmask and skullmask:

sub-Stevie_ses-01_desc-t1_skullmask.stl

sub-Stevie_ses-01_desc-t1_headmask.stl (is missing so far)

CT Skull extraction

CT file in stereo space:

sub-Stevie_ses-01_space-stereo_desc-ct_T2star.nii.gz

Skullmask in stereo and native spaces:

sub-Stevie_ses-01_space-stereo-ct_skullmask.nii.gz

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

Mesh of skullmask:

sub-Stevie_ses-01_desc-ct_skullmask.stl

NB if pad_template is defined (as normally is by default in all skullTo3d parameter files…) , stereo corresponds to desc-pad files for macapype processing.