Add some info while looking at results

README.md

@@ -1,5 +1,5 @@
-# extractor_flow_documentation[![Documentation Status](https://readthedocs.org/projects/extractor_flow-documentation/badge/?version=latest)](https://extractor_flow-documentation.readthedocs.io/en/latest/?badge=latest)
+# extractor_flow_documentation[![Documentation Status](https://readthedocs.org/projects/extractor-flow-documentation/badge/?version=latest)](https://extractor-flow-documentation.readthedocs.io/en/latest/?badge=latest)
 
 # Extractor_Flow-documentation
 
-https://extractor_flow-documentation.readthedocs.io/en/latest/
+https://extractor-flow-documentation.readthedocs.io/en/latest/

source/index.rst

@@ -1,6 +1,5 @@
-Test
 Welcome to the Extractor_flow user documentation!
-=============================================
+=================================================
 
 .. note::
     New release available: 1.0.0.

source/pipeline/output.rst

@@ -1,5 +1,69 @@
+Outputs
+=======
+
 Output structure
-===============
+----------------
+
+The output contains the final outputs, and, if option --keep_intermediate was added, a folder intermediates. That folder is useful is you want to re-run your nextflow command with option --resume, but can be safely deleted once you are satisfied with the results.
+
+::
+
+    [root_outputs]
+    ├── final_outputs
+    ├── S1
+    │   ├── bundles_mni
+    │   ├── mni_space
+    │   └── ...
+    └── S2
+    │   ├── ...
+    ├── intermediates
+    │   ├── ...
+
+
+The exact list of outputs per subject depends on your options.
+
+
+Output bundles
+--------------
+
+*toDo: This doc has yet to be completed. Note: See figures in the doc file. Add them here?*
+
+If you have chosen profile extract_bundles, you will have a list of bundles as output:
+
+**Association bundles**
+
+- AF_L, AF_R: Arcuate Fasciculus
+- cing_L, cing_R: cingulum
+- ifof_L, ifof_R: Inferior fronto-occipital fasciculus
+- ilf_L, ilf_R: Inferior longitudinal fasciculus
+- slf_L, slf_R: Superior longitudinal fasciculus
+- uf_L, uf_R: Uncinate fasciculus
+
+**U-shaped (short association fibers)**
+
+- ushape_L, ushape_R
+
+**Commissural bundles**
+
+- accx: anterior commissure
+- CC: Corpus callosum. Separated into:
+    - cc_homotopic_cingulum
+    - cc_homotopic_frontal
+    - cc_homotopic_insular
+    - cc_homotopic_occipital
+    - cc_homotopic_parietal
+    - cc_homotopic_temporal
+- cerebellum: Cerebellar streamlines. A mix of MCP (Middle cerebellar peduncle) and (??).
+
+
+**Projection bundles**
 
+- Brainstem: all streamlines starting in the brainstem. Includes:
+    - corticopontine_frontal_L, corticopontine_frontal_R
+    - corticopontine_POT_L, corticopontine_POT_R
+    - cst_L, cst_R: corticospinal tract
+- coronaradiata_L, coronaradiata_R: the corona radiata, covering most of the superior part of the brain. Note that it could include portions of the optic radiation.
+- corticostriatal: very similar to corona radiata!
+- fornix
+- optic radiation L, R: see figure for difference with corona radiata!
 
-BLABLA BLA BLA

source/reference/references.rst

@@ -6,9 +6,7 @@ How to cite extractor_flow
 .. tip::
     If needed
 
-If Extractor_flow is used in a publication, please cite the following references:
-
-.. [Theaud20] Theaud, G., Houde, J.-C., Boré, A., Rheault, F., Morency, F., Descoteaux, M.,extractor_flow: A robust, efficient and reproducible diffusion MRI pipeline leveraging Nextflow & Singularity, NeuroImage,  https://doi.org/10.1016/j.neuroimage.2020.116889.
+There is no official reference paper yet. Please add the link to the GitHub instead: https://github.com/scilus/extractor_flow.
 
 Download: