diff --git a/source/index.rst b/source/index.rst index de91c63..9182972 100644 --- a/source/index.rst +++ b/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:: diff --git a/source/tools/SET.rst b/source/tools/SET.rst new file mode 100644 index 0000000..b860caf --- /dev/null +++ b/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. \ No newline at end of file