Update README.md

README.md

@@ -1,16 +1,34 @@
 # func_processing
-Pipeline used to take functional data from DICOMs through group-level analyses. Organization is as follows:
+Pipeline used to take functional data from DICOMs through group-level analyses. 
 
-- cli: **User-level entrypoint.** Contains scripts to start AFNI, ASHS, fMRIprep, FreeSurfer, refacing, and data checking workflows.
-- cron: Outdated. Automate cli. Can be used to schedule/automate cli usage.
-- dockerfiles: Contains Dockerfile and scripts used for generating, running docker.
-- docs: Resources for formal documentation, via sphinx. Instructions in build_docs.txt.
-- logs: Mainly for completed_preprocessing.tsv, other output logs written here.
-- qc: Files/scripts for conducting qc on pipeline workflows for non-default options. Also serves as example of user-specified timing files.
-- resources: Location of modules for AFNI, ASHS, FreeSurfer, fMRIprep, and reports.
-- tests: Scripts for testing resources and workflows.
-- workflow: Manages resources, controlled by cli.
+## Entry Points
+Following `python setup.py install` or `python setup.py develop`, use the following entry points to trigger cli.
 
-See [Wiki](https://github.com/emu-project/func_processing/wiki) for details and description.
+- `check` : print help, run `cli.checks`
+- `ashs` : trigger help of `cli.ashs`
+- `reface` : trigger help of `cli.reface`
+- `fmriprep` : trigger help of `cli.fmriprep`
+- `task_subj` : trigger help of `cli.afni_task_subj`
+- `rs_subj` : trigger help of `cli.afni_resting_subj`
+- `task_group` : trigger help of `cli.afni_task_group`
+- `rs_group` : trigger help of `cli.afni_resting_group`
 
-Module documentation [here](https://emu-func-processing.readthedocs.io/en/latest/), assuming sphinx is cooperative.
+## Project organization
+
+Top Level
+
+- dockerfiles : Dockerfile, shell script backup
+- docs : Project documentation, for [ReadTheDocs](https://emu-func-processing.readthedocs.io/en/latest/), assuming sphinx is cooperative. Build instruction found in build_docs.txt. 
+- func_processing : Main package
+
+func_processing
+
+- cli : Contains scripts to start AFNI, ASHS, fMRIprep, FreeSurfer, refacing, and data checking workflows.
+- examples : Contains example scripts and files.
+- logs : Mainly for completed_preprocessing.tsv, other output logs written here.
+- resources : Location of modules for AFNI, ASHS, FreeSurfer, fMRIprep, and reports.
+- tests : Scripts for testing resources and workflows.
+- tools : Location for auxiliary/shell scripts. Currently contains (outdated) cron scripts
+- workflow : Manages resources, controlled by cli.
+
+See [Wiki](https://github.com/emu-project/func_processing/wiki) for details and description, now a little outdated due to refactoring.