Document running instructions for WMA

docs/TUTORIAL.md

@@ -540,6 +540,29 @@ for performing whole-brain tractography parcellation. The outputs of that script
 * a parcellation of the entire white matter into 800 fiber clusters
 * a parcellation of anatomical fiber tracts organized according to the brain lobes they connect
 
+Here is an abridged snapshot of the output directory (you should examine the `*csv` files):
+
+```python
+wma800/
+└── sub-1122_ses-1_dir-416
+    ├── AnatomicalTracts
+    │   └── diffusion_measurements_anatomical_tracts.csv
+    ├── FiberClustering
+    │   ├── InitialClusters
+    │   ├── OutlierRemovedClusters
+    │   ├── SeparatedClusters
+    │   │   ├── diffusion_measurements_commissural.csv
+    │   │   ├── diffusion_measurements_left_hemisphere.csv
+    │   │   ├── diffusion_measurements_right_hemisphere.csv
+    │   │   ├── tracts_commissural
+    │   │   ├── tracts_left_hemisphere
+    │   │   └── tracts_right_hemisphere
+    │   └── TransformedClusters
+    └── TractRegistration
+        └── sub-1122_ses-1_dir-416
+            └── output_tractography
+```
+
 
 Configuration:
 
@@ -560,13 +583,52 @@ Consult `wm_apply_ORG_atlas_to_subject.sh --help` to know the details of these p
 
 Run it:
 
+##### Through Luigi pipeline
+
 ```bash
 export LUIGI_CONFIG_PATH=/path/to/dwi_pipe_params.cfg
 
 exec/ExecuteTask --task Wma800 \
 --bids-data-dir /data/pnl/DIAGNOSE_CTE_U01/rawdata -c 1001 --dwi-template sub-*/ses-01/dwi/*_dwi.nii.gz
 ```
 
+##### On a PNL workstation physically or through NoMachine
+
+```
+NEW_SOFT_DIR=/rfanfs/pnl-zorro/software/pnlpipe3/
+source ${NEW_SOFT_DIR}/bashrc3
+
+wm_apply_ORG_atlas_to_subject.sh \
+-i /path/to/your.vtk \
+-o /path/to/output/dir/ \
+-a ${NEW_SOFT_DIR}/ORG-Atlases-1.2 \
+-s ${NEW_SOFT_DIR}/Slicer-4.10.2-linux-amd64/SlicerWithExtensions.sh \
+-m "${NEW_SOFT_DIR}/Slicer-4.10.2-linux-amd64/SlicerWithExtensions.sh --launch FiberTractMeasurements" \
+-n 8 -c 2 -d 1
+```
+
+The same command applies for running it on PNL's GRX node: `dna007.partners.org` except a change in the software directory:
+
+> NEW_SOFT_DIR=/data/pnl/soft/pnlpipe3/
+
+You should consult [SlicerDMRI/whitematteranalysis](https://github.com/SlicerDMRI/whitematteranalysis) repository
+for meaning of the above arguments.
+
+##### Through SSH
+
+Just append the `-x 1` flag to the above command to enable virtual X server:
+
+```
+wm_apply_ORG_atlas_to_subject.sh \
+...
+-n 8 -c 2 -d 1 -x 1
+```
+
+However, running it through SSH requires availability of `xvfb-run` on that server--may it be a PNL workstation or a GRX node.
+The good news is that we have already installed `xorg-x11-server-Xvfb` in most servers. So you should be all set. 
+But if you find `xvfb-run`'s absence, reach out to PNL engineers for help.
+Lastly, you can use the same `-x 1` flag to run it through `bsub` on `pri_pnl` queue in ERIS cluster.
+
 
 
 # Fs2Dwi pipeline