RHINO example without visualisations + AAL parcellation. (#240)

examples/oxford/no_viz_pipeline/README.md

@@ -0,0 +1,4 @@
+Pipeline without any visualisations
+-----------------------------------
+
+Sometimes there are errors when generating plots. In this pipeline we use OSL without any visualisations.

examples/oxford/no_viz_pipeline/do_rhino.py

@@ -0,0 +1,100 @@
+"""RHINO without any visualisations.
+
+"""
+
+# Authors: Chetan Gohil <chetan.gohil@psych.ox.ac.uk>
+
+import numpy as np
+
+from osl.source_recon import setup_fsl, rhino
+
+setup_fsl("/opt/ohba/fsl/6.0.5")  # this is where FSL is installed on hbaws
+
+# Directories
+preproc_dir = "output/preproc"
+anat_dir = "path/to/smri/dir"
+coreg_dir = "output/coreg"
+
+# Files ({subject} will be replaced by the name for the subject)
+preproc_file = preproc_dir + "/{subject}_tsss_preproc_raw.fif"
+smri_file = anat_dir + "/{subject}/anat/{subject}_T1w.nii"
+
+# Subjects to coregister
+subjects = ["sub-001", "sub-002"]
+
+def fix_headshape_points(src_dir, subject, preproc_file, smri_file):
+    filenames = rhino.get_coreg_filenames(src_dir, subject)
+
+    # Load saved headshape and nasion files
+    hs = np.loadtxt(filenames["polhemus_headshape_file"])
+    nas = np.loadtxt(filenames["polhemus_nasion_file"])
+    lpa = np.loadtxt(filenames["polhemus_lpa_file"])
+    rpa = np.loadtxt(filenames["polhemus_rpa_file"])
+
+    # Remove headshape points on the nose
+    remove = np.logical_and(hs[1] > max(lpa[1], rpa[1]), hs[2] < nas[2])
+    hs = hs[:, ~remove]
+
+    # Remove headshape points on the neck
+    remove = hs[2] < min(lpa[2], rpa[2]) - 4
+    hs = hs[:, ~remove]
+
+    # Remove headshape points far from the head in any direction
+    remove = np.logical_or(
+        hs[0] < lpa[0] - 5,
+        np.logical_or(
+            hs[0] > rpa[0] + 5,
+            hs[1] > nas[1] + 5,
+        ),
+    )
+    hs = hs[:, ~remove]
+
+    # Overwrite headshape file
+    np.savetxt(filenames["polhemus_headshape_file"], hs)
+
+
+# Main RHINO code
+
+for subject in subjects:
+
+    # Input files
+    preproc_file_ = preproc_file.format(subject=subject)
+    smri_file_ = smri_file.format(subject=subject)
+
+    # Extract fiducials and headshape points
+    filenames = rhino.get_coreg_filenames(src_dir, subject)
+    rhino.extract_polhemus_from_info(
+        fif_file=preproc_file_,
+        headshape_outfile=filenames["polhemus_headshape_file"],
+        nasion_outfile=filenames["polhemus_nasion_file"],
+        rpa_outfile=filenames["polhemus_rpa_file"],
+        lpa_outfile=filenames["polhemus_lpa_file"],
+    )
+
+    # Clean up headshape points
+    fix_headshape_points(src_dir, subject, preproc_file_, smri_file_)
+
+    # Extract surfaces from the structural
+    rhino.compute_surfaces(
+        smri_file=smri_file_,
+        subjects_dir=src_dir,
+        subject=subject,
+        include_nose=False,
+    )
+
+    # Coregistration
+    rhino.coreg(
+        fif_file=preproc_file_,
+        subjects_dir=src_dir,
+        subject=subject,
+        use_headshape=True,
+        use_nose=False,
+    )
+
+    # Forward model
+    rhino.forward_model(
+        subjects_dir=src_dir,
+        subject=subject,
+        model="Single Layer"
+        gridstep=8,
+    )

examples/oxford/ssp_pipeline/4_coregister.py

@@ -17,7 +17,7 @@
 from osl import source_recon, utils
 
 # Directories
-preproc_dir = "/output/preproc_ssp"
+preproc_dir = "output/preproc_ssp"
 anat_dir = "path/to/smri/dir"
 coreg_dir = "output/coreg"
 fsl_dir = "/opt/ohba/fsl/6.0.5"  # this is where FSL is installed on hbaws