update aim1 and aim2 modeling

.gitignore

@@ -19,3 +19,14 @@ nilearn_data*
 nipype_mem*
 .spyproject
 dockerfile_old
+.vscode/
+behavioral_data_prep/Untitled.ipynb
+docker_path.txt
+fmri_analysis/scripts/Untitled.ipynb
+*Untitled*.ipynb
+*/*Untitled*.ipynb
+*/*/*Untitled*.ipynb
+*.err*
+*.out*
+fmri_analysis/fsl/tmp_batch/*
+fmri_data_prep/scitran/

README.md

@@ -1,21 +1,30 @@
-# Self_Regulation_Ontology - fMRI analysis
+# Navigating and Using the Repo
 
-### Setting up the docker image
-This is the recommended way to use the repo
+The following is a list of directories and their contents, in order of importance
 
-Run: 
-```
-docker build --rm -t fmri_env . 
-```
-That's it!
+## `fmri_analysis`: Aim1 fMRI Analysis (TODO: include aim2, aim4)  
 
-In docker\_files/run_docker.txt you can find example docker commands.
-If you start the notebook version, 
-you can access it at the following url:
-http://127.0.0.1:8888/lab?
+`fmri_analysis` contains the main scripts of the repo for running standard contrast analyses.
+The main files are all in `scripts` and the `utils` dir within.  
+To run these scripts using Sherlock or other computing clusters, view the README located in `Self_Regulation_Ontology_fMRI/fmri_analysis/batch_files/aim1`.
 
-### Setting up python environment
+1. `1stlevel_analysis.py` runs 1stlevels with the help of` utils/firstlevel_utils.py`  
+2. `2ndlevel_analysis.py` runs 2ndlevels with the help of `utils/firstlevel_utils.py`, `utils.secondlevel_utils.py` and `utils/utils.py`  
+3. `Visualizations.py` can be used to run 1st and 2nd level visualizations based on flags passed to it.  
 
-conda create -n SRO python=3.5.3
-source activate SRO
-pip install -r requirements.txt
+4. Once these analyses are complete, navigate to `Self_Regulation_Onotology_fMRI/fmri_analysis/scripts/notebooks/` and run 2 notebooks (currently run locally with data mounted; see the first cells): 1) `0_2ndlevel_EFA.ipynb` performs exploratory factor analysis on the 2ndlevel contrasts and examines how parcels fall in factor space, and 2) `1_label_and_functional_distances.ipynb` compares the distances between 2ndlevel contrasts in functional and theory-driven spaces against null models.  
+
+## `behavioral_data_prep`
+Contains code for generating events files from task data and transfering them to the BIDS directory containing the scan data.
+
+## `docker_files` and `singularity_images`
+The former contains requirement files which help create the docker image. The latter contains the singularity image(s) built out of the docker image, which can be used to run the environment on Sherlock, Stanford HPCC.
+
+## `fmri_experiments`
+Contains the code to run the experiments used in aim1 and aim2 of the project.
+
+5. `fmri_data_prep`
+Contains scripts and atlases to parcellate the data, used with collaborator Mac Shine.
+
+6. `fmri_prepoc`
+Legacy code.