skeletal running and installation instruction

docs/README.md

@@ -1,6 +1,43 @@
 ![](pnl-bwh-hms.png)
 
-Outlier detection tool utilizing FreeSurfer segmentation statistics, built using https://plotly.com/dash/
+
+
+Outlier detection tool utilizing FreeSurfer segmentation statistics, built using https://plotly.com/dash .
+However, it can be used for any table that has properties on the first row and subject ids on the first column.
+Potential applications include [TBSS](https://github.com/pnlbwh/TBSS/blob/master/docs/TUTORIAL.md#step-6-roivoxelwise-analysis) roi statistics, and group-level statistics generated by [mriqc](https://github.com/poldracklab/mriqc). 
+
+# Installation
+
+Clone the repository:
+
+    git clone https://github.com/pnlbwh/freesurfer-analysis.git
+
+On Python 3, installation of dependencies can be as simple as:
+
+    pip install -r requirements.txt
+
+# Running
+
+* Visualize summary on web browser (http://localhost:8050/):
+
+```bash
+# comma separted (default)
+python scripts\generate-summary.py -i path\to\asegstats_lh.csv -o \tmp\fs-stats\
+# tab separated
+python scripts\generate-summary.py -i path\to\asegstats_lh.csv -t tab -o \tmp\fs-stats\
+```
+
+* Enable roi rendering (for FreeSurfer only) with visualization:
+
+
+    python scripts\generate-summary.py -i path\to\asegstats_lh.csv -o \tmp\fs-stats\ -t path\to\sub-$\anat\freesurfer
+
+
+* Generate input table from FreeSurfer statistics:
+
+
+    python scripts\stats2table.py -c path\to\caselist.txt -t path\to\sub-$\anat\freesurfer -o \tmp\fs-stats
+
 
 
 # Troubleshooting