Updated examples.

OHBA-analysis · Aug 2, 2024 · 9839268 · 9839268
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Showing 10 changed files with 16 additions and 16 deletions.
diff --git a/examples/ctf/ctf_with_headshape_pos/2_coregister.py b/examples/ctf/ctf_with_headshape_pos/2_coregister.py
@@ -9,7 +9,7 @@
 
 from osl import source_recon, utils
 
-def save_polhemus_from_pos(outdir, subject, preproc_file, smri_file, epoch_file):
+def save_polhemus_from_pos(outdir, subject):
     """Saves fiducials/headshape from a pos file."""
 
     # Get path to pos file
@@ -107,8 +107,8 @@ def fix_headshape_points(outdir, subject, preproc_file, smri_file, epoch_file):
 
 # Fif files containing the sensor-level preprocessed data for each subject
 preproc_files = [
-    "data/sub-not001_task-resteyesopen/sub-not001_task-resteyesopen_preproc_raw.fif",
-    "data/sub-not002_task-resteyesopen/sub-not002_task-resteyesopen_preproc_raw.fif",
+    "data/sub-not001_task-resteyesopen/sub-not001_task-resteyesopen_preproc-raw.fif",
+    "data/sub-not002_task-resteyesopen/sub-not002_task-resteyesopen_preproc-raw.fif",
 ]
 
 # The corresponding structurals for each subject

diff --git a/examples/ctf/ctf_with_headshape_pos/3_source_reconstruct.py b/examples/ctf/ctf_with_headshape_pos/3_source_reconstruct.py
@@ -26,8 +26,8 @@
 
 # Fif files containing the sensor-level preprocessed data for each subject
 preproc_files = [
-    "data/sub-not001_task-resteyesopen/sub-not001_task-resteyesopen_preproc_raw.fif",
-    "data/sub-not002_task-resteyesopen/sub-not002_task-resteyesopen_preproc_raw.fif",
+    "data/sub-not001_task-resteyesopen/sub-not001_task-resteyesopen_preproc-raw.fif",
+    "data/sub-not002_task-resteyesopen/sub-not002_task-resteyesopen_preproc-raw.fif",
 ]
 
 # Directory to save output to

diff --git a/examples/ctf/ctf_with_smri_fid/2_coregister.py b/examples/ctf/ctf_with_smri_fid/2_coregister.py
@@ -25,7 +25,7 @@
 subjects = ["LN_VTA2"]
 
 # Lists for input files
-preproc_files = ["data/LN_VTA2/mg04938_BrainampDBS_20170504_01_preproc_raw.fif"]
+preproc_files = ["data/LN_VTA2/mg04938_BrainampDBS_20170504_01_preproc-raw.fif"]
 smri_files = ["smri/LN_VTA2.nii"]
 
 # Output directory

diff --git a/examples/ctf/ctf_with_smri_fid/3_source_reconstruct.py b/examples/ctf/ctf_with_smri_fid/3_source_reconstruct.py
@@ -24,7 +24,7 @@
 subjects = ["LN_VTA2"]
 
 # Fif files containing the sensor-level preprocessed data for each subject
-preproc_files = ["data/LN_VTA2/mg04938_BrainampDBS_20170504_01_preproc_raw.fif"]
+preproc_files = ["data/LN_VTA2/mg04938_BrainampDBS_20170504_01_preproc-raw.fif"]
 
 # Directories
 outdir = "data"

diff --git a/examples/elekta/3_coregister.py b/examples/elekta/3_coregister.py
@@ -21,7 +21,7 @@
 anatdir = "smri"
 
 # Files ({subject} will be replaced by the name for the subject)
-preproc_file = outdir + "{subject}/{subject}_tsss_preproc_raw.fif"
+preproc_file = outdir + "{subject}/{subject}_tsss_preproc-raw.fif"
 smri_file = anatdir + "/{subject}/anat/{subject}_T1w.nii"
 
 # Subjects to coregister

diff --git a/examples/elekta/4_source_reconstruct.py b/examples/elekta/4_source_reconstruct.py
@@ -16,7 +16,7 @@
 outdir = "data"
 
 # Files
-preproc_file = outdir + "/{subject}_tsss_preproc_raw.fif"  # {subject} will be replaced by the subject name
+preproc_file = outdir + "/{subject}_tsss_preproc-raw.fif"  # {subject} will be replaced by the subject name
 
 # Subjects to do
 subjects = ["sub-001", "sub-002"]

diff --git a/examples/opm/2_coregister.py b/examples/opm/2_coregister.py
@@ -8,7 +8,7 @@
 
 from osl import source_recon, utils
 
-def coregister(outdir, subject, preproc_file, smri_file, epoch_file):
+def coregister(outdir, subject, preproc_file):
     """Coregister OPM data."""
 
     # Create dummy coregistration files
@@ -44,7 +44,7 @@ def coregister(outdir, subject, preproc_file, smri_file, epoch_file):
 
 # Fif files containing the sensor-level preprocessed data for each subject
 preproc_files = [
-    "data/13703/13703-braille_test-meg_preproc_raw.fif",
+    "data/13703/13703-braille_test-meg_preproc-raw.fif",
 ]
 
 # The corresponding structurals for each subject

diff --git a/examples/opm/3_source_reconstruct.py b/examples/opm/3_source_reconstruct.py
@@ -29,7 +29,7 @@
 
 # Fif files containing the sensor-level preprocessed data for each subject
 preproc_files = [
-    "data/13703/13703-braille_test-meg_preproc_raw.fif",
+    "data/13703/13703-braille_test-meg_preproc-raw.fif",
 ]
 
 # Do source reconstruction

diff --git a/examples/parallelisation/parallel_source_reconstruct.py b/examples/parallelisation/parallel_source_reconstruct.py
@@ -28,7 +28,7 @@
 
     # Files
     smri_file = anatdir + "/{0}/anat/{0}_T1w.nii"
-    preproc_file = outdir + "{0}_ses-rest_task-rest_meg/{0}_ses-rest_task-rest_meg_preproc_raw.fif"
+    preproc_file = outdir + "{0}_ses-rest_task-rest_meg/{0}_ses-rest_task-rest_meg_preproc-raw.fif"
 
     # Settings
     config = """
@@ -51,7 +51,7 @@
             orthogonalisation: symmetric
     """
 
-    def remove_headshape_points(outdir, subject, preproc_file, smri_file, epoch_file):
+    def remove_headshape_points(outdir, subject):
         """Removes headshape points near the nose."""
 
         # Get coreg filenames

diff --git a/examples/parallelisation/serial_source_reconstruct.py b/examples/parallelisation/serial_source_reconstruct.py
@@ -24,7 +24,7 @@
 
 # Files
 smri_file = anatdir + "/{0}/anat/{0}_T1w.nii"
-preproc_file = outdir + "{0}_ses-rest_task-rest_meg/{0}_ses-rest_task-rest_meg_preproc_raw.fif"
+preproc_file = outdir + "{0}_ses-rest_task-rest_meg/{0}_ses-rest_task-rest_meg_preproc-raw.fif"
 
 # Settings
 config = """
@@ -47,7 +47,7 @@
         orthogonalisation: symmetric
 """
 
-def remove_headshape_points(outdir, subject, preproc_file, smri_file, epoch_file):
+def remove_headshape_points(outdir, subject):
     """Removes headshape points near the nose."""
 
     # Get coreg filenames