SET: adding a page.

source/index.rst

@@ -34,6 +34,7 @@ Here, you will find a summary of the tools we develop, and some clues on how we
     tools/recobundles
     tools/other_pipelines
     tools/machine_learning
+    tools/SET
     tools/others
 
 .. toctree::

source/tools/SET.rst

@@ -0,0 +1,42 @@
+
+SET (Surface Enhanced Tractography)
+===================================
+
+
+.. role:: bash(code)
+   :language: bash
+
+1. Run Tractoflow
+
+2. Run civet or freesurfer:
+
+    One possibility is to use CBrain. If you have access to that plateform, that's probably the easiest.
+
+3. QC civet:
+
+    Upcomgin: How to run it and what to expect
+
+4. Download SET:
+
+    1. The singularity (ex: on Beluga: SET/set_1v1/set_1v1.img)
+
+    2. The nextflow (https://github.com/StongeEtienne/set-nf)
+
+5. Run SET:
+
+    .. code-block:: bash
+
+        nextflow run $SET/main.nf \
+            -profile civet2_dkt \
+            --tractoflow $tractoflow_output \
+            --surfaces $civet_output \
+            -with-report report_basic.html \
+            --output_dir $set_output \
+            -with-singularity $singularity \
+            -resume --processes 4
+
+    ** Please note that if you used a recent version of tractoflow, you might need to change line 155 in the main script (https://github.com/StongeEtienne/set-nf/blob/main/main.nf) because PFT_Maps is sometimes called PFT_Tracking_Maps in newer versions.
+
+6. QC results:
+
+    Check the vtk file D_SurfaceFlow/\*_100_1.0.vtk (MI-brain can load this vtk file). It shows the first steps of your streamlines.