no title derivatives

Author: davidmeunier79

docs/derivatives.rst

@@ -3,7 +3,12 @@
 .. _derivatives:
 
 
-************
+.. _derivatives:
+
+***********
+Derivatives
+***********
+
 Introduction
 ************
 
@@ -13,7 +18,6 @@ Derivatives will be output if option ``-deriv`` is provided to the command line
 
 All files are by default in stereo space; if option ``-pad`` is provided to the command line (See `Commands <commands>`), files in native  will also be output.
 
-****************
 Data Preparation
 ****************
 
@@ -22,16 +26,19 @@ Native
 
 
 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 -pad 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
@@ -41,71 +48,88 @@ Stereo
 
 Original files in template space:
 
-sub-Stevie_ses-01_space-stereo_T1w.nii.gz
-sub-Stevie_ses-01_space-stereo_T2w.nii.gz
+*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
+*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
+*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
+*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-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
+*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-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
+*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
+*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
+*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_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
+*sub-Stevie_ses-01_desc-wmgm_mask.stl*