Documentation update with T2 example

README.md

@@ -102,6 +102,28 @@ python3 -m crashs fit \
 
 You should find the output from running CRASHS in folder `/my/crashs/folder/sample_data/ashs_pmc_t1/subj01/crashs`.
 
+### T2 Example
+
+Another example in the `sample_data` folder can be used to test CRASHS for T2-weighted MRI processed with the ASHS-PMC atlas. It is better to run this example on a machine with an NVidia GPU because a nnU-Net is used by CRASHS to generate the white matter label; otherwise expect it to take 30-60 minutes to complete. If using Docker, include the flag `--gpus all` when calling the `docker run` command to make the GPU available to the container.
+
+You can run the example in the Docker container like this:
+
+```sh
+python3 -m crashs fit -C /package -s left -c heur \
+    /data/ashs_pmc_alveus/subj02/ashs \
+    ashs_pmc_alveus \
+    /data/ashs_pmc_alveus/subj02/crashs
+```
+
+Or using CRASHS pip install like this:
+
+```sh
+python3 -m crashs fit -s left -c heur \
+    /my/crashs/folder/sample_data/ashs_pmc_alveus/subj02/ashs \
+    ashs_pmc_alveus \
+    /my/crashs/folder/sample_data/ashs_pmc_alveus/subj02/crashs
+```
+
 ## Outputs from CRASHS
 The program generates many outputs, but the most useful ones are:
 * `fitting/[ID]_fitted_omt_hw_target.vtk`: the grey/white and grey/csf boundaries estimated by the `cruise_cortex_extraction` module of NighRes. These meshes are in physical (RAS) coordinate space, not in voxel (IJK) space output by Nighres. *If you extract meshes from the T1-ASHS segmentation in ITK-SNAP, those should line up with these meshes.*