Add Docker command to the README.

README.md

@@ -1,12 +1,45 @@
-### How to run this walkthrough
+# XCP-D Walkthrough
 
-1. Open terminal
-2. Navigate to where you want your XCP-D runs, and create a folder called `XCPD_test`
-3. Navigate into this folder: `cd XCPD_test`
-4. Download the singularity image: `singularity build xcp_walkthrough.sif docker://pennlinc/xcp_walkthrough:main`
-5. Run the walkthrough!
-```
+This repository defines a Docker image containing XCP-D and example data.
+When you run the Docker image, it will apply XCP-D to the example data and write out XCP-D derivatives.
+
+The example data are located in `/data/EF/derivatives/fmriprep` within the Docker image.
+
+**NOTE**: You will need to provide your own FreeSurfer license (labeled `<path_to_Freesurfer_license_file>` below).
+
+## How to run this walkthrough
+
+1.  Open terminal
+2.  Navigate to where you want your XCP-D outputs to be generated (labeled `<path_to_test_folder>` below).
+3.  Download the container:
+    -   For Singularity: `singularity build xcp_walkthrough.sif docker://pennlinc/xcp_walkthrough:main`
+    -   For Docker: `docker pull pennlinc/xcp_walkthrough:main`
+4. Run the walkthrough!
+
+### Singularity command
+
+```bash
 #$ -l h_vmem=40G # Allot at least 40G; this is the format for submitting via an SGE cluster
-singularity run --cleanenv -B ~/XCPD_test ~/XCPD_test/xcp_walkthrough.sif /data/EF/derivatives/fmriprep ~/XCPD_test/output --fs-license-file <path_to_Freesurfer_license_file>  participant -vv
+singularity run --cleanenv \
+    -B <path_to_test_folder> \
+    <path_to_test_folder>/xcp_walkthrough.sif \
+    /data/EF/derivatives/fmriprep \
+    <path_to_test_folder>/output \
+    --fs-license-file <path_to_Freesurfer_license_file> \
+    participant \
+    -vv
+```
+
+### Docker command
 
+```bash
+docker run --rm -ti \
+    -v <path_to_test_folder>:/out \
+    -v <path_to_Freesurfer_license_file>:/license.txt \
+    pennlinc/xcp_walkthrough:main \
+    /data/EF/derivatives/fmriprep \
+    /out \
+    --fs-license-file /license.txt \
+    participant \
+    -vv
 ```