DOC: Review layout in outputs.rst [skip ci]

docs/outputs.rst

@@ -29,19 +29,29 @@ BIDS derivatives entities
 
 See `Original BIDS Entities Appendix <https://bids-specification.readthedocs.io/en/v1.4.1/99-appendices/09-entities.html>`_ for more description.
 
-.. note:: A new BIDS entity `atlas-<atlas_label>` (where ``<atlas_label>``: ``Desikan``/ ``L2008``/ ``L2018``) has been introduced, that is used in combination
- with the ``res-<atlas_scale>`` (where ``<atlas_scale>``: ``scale1`` / ``scale2`` / ``scale3`` / ``scale4`` / ``scale5``) entity to distinguish
- data derived from different parcellation atlases and different scales.
+.. note:: Connectome Mapper 3 introduced a new BIDS entity ``atlas-<atlas_label>``
+ (where ``<atlas_label>``: ``Desikan``/ ``L2008``/ ``L2018``), that is used
+ in combination with the ``res-<atlas_scale>`` (where ``<atlas_scale>``:
+ ``scale1`` / ``scale2`` / ``scale3`` / ``scale4`` / ``scale5``) entity to
+ distinguish data derived from different parcellation atlases and
+ different scales.
 
 
 Main Connectome Mapper Derivatives
 ==========================================
 
-Main outputs produced by Connectome Mapper 3 are written to ``<bids_dataset/derivatives>/cmp/sub-<subject_label>/``. In this folder, a configuration file generated for each modality pipeline (i.e. anatomical/diffusion/fMRI) and used for processing each participant is saved as ``sub-<subject_label>_anatomical/diffusion/fMRI_config.ini``. It summarizes pipeline workflow options and parameters used for processing. An execution log of the full workflow is saved as `sub-<subject_label>_log.txt``
+Main outputs produced by Connectome Mapper 3 are written to
+``cmp/sub-<subject_label>/``. In this folder, a configuration file
+generated for each modality pipeline (i.e. anatomical/diffusion/fMRI)
+and used for processing each participant is saved as
+``sub-<subject_label>_anatomical/diffusion/fMRI_config.ini``.
+It summarizes pipeline workflow options and parameters used for processing.
+An execution log of the full workflow is saved as `sub-<subject_label>_log.txt``.
 
 Anatomical derivatives
 ------------------------
-* Anatomical derivatives in the individual ``T1w`` space are placed in each subject's ``anat/`` subfolder, including:
+* Anatomical derivatives in the individual ``T1w`` space are placed
+ in each subject's ``anat/`` subfolder, including:
 
  * The original T1w image:
 
@@ -62,12 +72,12 @@ Anatomical derivatives
 
  - ``anat/sub-<subject_label>_atlas-<atlas_label>[_res-<scale_label>]_dseg.nii.gz``
 
- where:
+  where:
 
- - ``<atlas_label>``:``Desikan``/``L2008``/``L2018``
- is the parcellation scheme used
- - ``<scale_label>``: ``scale1``, ``scale2``, ``scale3``, ``scale4``, ``scale5``
- corresponds to the parcellation scale if applicable
+  - ``<atlas_label>``:``Desikan``/``L2008``/``L2018``
+  is the parcellation scheme used
+  - ``<scale_label>``: ``scale1``, ``scale2``, ``scale3``, ``scale4``, ``scale5``
+  corresponds to the parcellation scale if applicable
 
  with the description of parcel labels and the updated FreeSurfer color lookup table:
 
@@ -93,12 +103,12 @@ Anatomical derivatives
 
  - ``anat/sub-<subject_label>_space-DWI_atlas-<atlas_label>[_res-<scale_label>]_dseg.nii.gz``
 
- where:
+  where:
 
- - ``<atlas_label>``:``Desikan``/``L2008``/``L2018``
- is the parcellation scheme used
- - ``<scale_label>``: ``scale1``, ``scale2``, ``scale3``, ``scale4``, ``scale5``
- corresponds to the parcellation scale if applicable
+  - ``<atlas_label>``:``Desikan``/``L2008``/``L2018``
+  is the parcellation scheme used
+  - ``<scale_label>``: ``scale1``, ``scale2``, ``scale3``, ``scale4``, ``scale5``
+  corresponds to the parcellation scale if applicable
 
  * The 5TT image used for Anatomically Constrained Tractorgaphy (ACT):
 
@@ -134,7 +144,7 @@ each subject's ``dwi/`` subfolder, including:
 
  - ``dwi/sub-<subject_label>]_desc-WLS_model-DTI_diffmodel.nii.gz``
 
- with derived Fractional Anisotropic (FA) and Mean Diffusivity (MD) maps:
+  with derived Fractional Anisotropic (FA) and Mean Diffusivity (MD) maps:
 
  - ``dwi/sub-<subject_label>]_model-DTI_FA.nii.gz``
  - ``dwi/sub-<subject_label>]_model-DTI_MD.nii.gz``
@@ -174,25 +184,25 @@ each subject's ``dwi/`` subfolder, including:
 
  - ``dwi/sub-<subject_label>_model-<model_label>_desc-<label>_tractogram.trk``
 
- where:
+  where:
 
- - ``<model_label>`` is the diffusion model used to drive tractography
- (DTI, CSD, SHORE)
- - ``<label>`` is the type of tractography algorithm employed
- (DET for deterministic, PROB for probabilistic)
+  - ``<model_label>`` is the diffusion model used to drive tractography
+  (DTI, CSD, SHORE)
+  - ``<label>`` is the type of tractography algorithm employed
+  (DET for deterministic, PROB for probabilistic)
 
 * The structural connectivity (SC) graphs:
 
  - ``dwi/sub-<subject_label>_atlas-<atlas_label>[_res-<scale_label>]_conndata-network_connectivity.<format>``
 
- where:
+  where:
 
- - ``<atlas_label>``:``Desikan``/``L2008``/``L2018``
- is the parcellation scheme used
- - ``<scale_label>``: ``scale1``, ``scale2``, ``scale3``, ``scale4``, ``scale5``
- corresponds to the parcellation scale if applicable
- - ``<format>``: ``mat``/``gpickle``/``tsv``/``graphml`` is the preferred format
- employed to stored the graph.
+  - ``<atlas_label>``:``Desikan``/``L2008``/``L2018``
+  is the parcellation scheme used
+  - ``<scale_label>``: ``scale1``, ``scale2``, ``scale3``, ``scale4``, ``scale5``
+  corresponds to the parcellation scale if applicable
+  - ``<format>``: ``mat``/``gpickle``/``tsv``/``graphml`` is the preferred format
+  employed to stored the graph.
 
 
 Functional derivatives
@@ -233,21 +243,25 @@ each subject's ``func/`` subfolder including:
  - ``func/sub-<subject_label>_atlas-<atlas_label>[_res-<scale_label>]_timeseries.npy``
  - ``func/sub-<subject_label>_atlas-<atlas_label>[_res-<scale_label>]_timeseries.mat``
 
- where ``<scale_label>`` : ``scale1``, ``scale2``, ``scale3``, ``scale4``, ``scale5``
- corresponds to the parcellation scale if applicable
+ where:
+
+ - ``<atlas_label>``:``Desikan``/``L2008``/``L2018``
+ is the parcellation scheme used
+ - ``<scale_label>``: ``scale1``, ``scale2``, ``scale3``, ``scale4``, ``scale5``
+ corresponds to the parcellation scale if applicable
 
 * The functional connectivity (FC) graphs:
 
  - ``func/sub-<subject_label>_atlas-<atlas_label>[_res-<scale_label>]_conndata-network_connectivity.<format>``
 
- where:
+  where:
 
- - ``<atlas_label>``:``Desikan``/``L2008``/``L2018``
- is the parcellation scheme used
- - ``<scale_label>``: ``scale1``, ``scale2``, ``scale3``, ``scale4``, ``scale5``
- corresponds to the parcellation scale if applicable
- - ``<format>``: ``mat``, ``gpickle``, ``tsv``, ``graphml`` is
- the preferred format employed to stored the graph
+  - ``<atlas_label>``:``Desikan``/``L2008``/``L2018``
+  is the parcellation scheme used
+  - ``<scale_label>``: ``scale1``, ``scale2``, ``scale3``, ``scale4``, ``scale5``
+  corresponds to the parcellation scale if applicable
+  - ``<format>``: ``mat``, ``gpickle``, ``tsv``, ``graphml`` is
+  the preferred format employed to stored the graph
 
 
 FreeSurfer Derivatives