Updated oxford examples.

OHBA-analysis · Mar 14, 2024 · c651ba6 · c651ba6
1 parent c89699a
commit c651ba6
Show file tree

Hide file tree

Showing 18 changed files with 64 additions and 66 deletions.
diff --git a/examples/oxford/automated_ica_pipeline/1_maxfilter.py b/examples/oxford/automated_ica_pipeline/1_maxfilter.py
@@ -9,12 +9,12 @@
 
 # Setup paths to raw (pre-maxfiltered) fif files
 input_files = [
-    "path/to/file1.fif",
-    "path/to/file2.fif",
+    "data/raw/file1.fif",
+    "data/raw/file2.fif",
 ]
 
 # Directory to save the maxfiltered data to
-output_directory = "output/maxfilter"
+output_directory = "data/maxfilter"
 
 # Run MaxFiltering
 #

diff --git a/examples/oxford/automated_ica_pipeline/2_preprocess.py b/examples/oxford/automated_ica_pipeline/2_preprocess.py
@@ -10,8 +10,8 @@
 from osl import preprocessing, utils
 
 # Files and directories
-raw_file = "output/maxfilter/{subject}_tsss.fif"  # {subject} will be replace by the name for the subject
-preproc_dir = "output/preproc"  # output directory containing the preprocess files
+raw_file = "data/maxfilter/{subject}_tsss.fif"  # {subject} will be replace by the name for the subject
+preproc_dir = "data/preproc"  # output directory containing the preprocess files
 
 subjects = ["sub-001", "sub-002"]
 
@@ -21,13 +21,13 @@
     - filter: {l_freq: 0.5, h_freq: 125, method: iir, iir_params: {order: 5, ftype: butter}}
     - notch_filter: {freqs: 50 100}
     - resample: {sfreq: 250}
-    - bad_segments: {segment_len: 500, picks: mag, significance_level: 0.1}
-    - bad_segments: {segment_len: 500, picks: grad, significance_level: 0.1}
-    - bad_segments: {segment_len: 500, picks: mag, mode: diff, significance_level: 0.1}
-    - bad_segments: {segment_len: 500, picks: grad, mode: diff, significance_level: 0.1}
-    - bad_channels: {picks: mag, significance_level: 0.1}
-    - bad_channels: {picks: grad, significance_level: 0.1}
-    - ica_raw: {picks: meg, n_components: 64}
+    - bad_segments: {segment_len: 500, picks: mag}
+    - bad_segments: {segment_len: 500, picks: grad}
+    - bad_segments: {segment_len: 500, picks: mag, mode: diff}
+    - bad_segments: {segment_len: 500, picks: grad, mode: diff}
+    - bad_channels: {picks: mag}
+    - bad_channels: {picks: grad}
+    - ica_raw: {picks: meg, n_components: 40}
     - ica_autoreject: {picks: meg, ecgmethod: correlation, eogthreshold: auto}
     - interpolate_bads: {}
 """

diff --git a/examples/oxford/automated_ica_pipeline/3_coregister.py b/examples/oxford/automated_ica_pipeline/3_coregister.py
@@ -17,9 +17,9 @@
 from osl import source_recon, utils
 
 # Directories
-preproc_dir = "/output/preproc"
+preproc_dir = "data/preproc"
 anat_dir = "path/to/smri/dir"
-coreg_dir = "output/coreg"
+coreg_dir = "data/coreg"
 fsl_dir = "/opt/ohba/fsl/6.0.5"  # this is where FSL is installed on hbaws
 
 # Files ({subject} will be replaced by the name for the subject)

diff --git a/examples/oxford/automated_ica_pipeline/4_source_reconstruct.py b/examples/oxford/automated_ica_pipeline/4_source_reconstruct.py
@@ -13,9 +13,9 @@
 from osl import source_recon, utils
 
 # Directories
-preproc_dir = "output/preproc"
-coreg_dir = "output/coreg"
-src_dir = "output/src"
+preproc_dir = "data/preproc"
+coreg_dir = "data/coreg"
+src_dir = "data/src"
 fsl_dir = "/opt/ohba/fsl/6.0.5"  # this is where FSL is installed on hbaws
 
 # Files
@@ -33,7 +33,7 @@
         freq_range: [1, 45]
         chantypes: [mag, grad]
         rank: {meg: 60}
-        parcellation_file: fmri_d100_parcellation_with_PCC_reduced_2mm_ss5mm_ds8mm.nii.gz
+        parcellation_file: Glasser52_binary_space-MNI152NLin6_res-8x8x8.nii.gz
         method: spatial_basis
         orthogonalisation: symmetric
 """

diff --git a/examples/oxford/automated_ica_pipeline/5_sign_flip.py b/examples/oxford/automated_ica_pipeline/5_sign_flip.py
@@ -11,7 +11,7 @@
 from osl.source_recon import find_template_subject, run_src_batch, setup_fsl
 
 # Directories
-src_dir = "output/src"
+src_dir = "data/src"
 fsl_dir = "/opt/ohba/fsl/6.0.5"  # this is where FSL is installed on hbaws
 
 if __name__ == "__main__":

diff --git a/examples/oxford/manual_ica_pipeline/1_maxfilter.py b/examples/oxford/manual_ica_pipeline/1_maxfilter.py
@@ -9,12 +9,12 @@
 
 # Setup paths to raw (pre-maxfiltered) fif files
 input_files = [
-    "path/to/file1.fif",
-    "path/to/file2.fif",
+    "data/raw/file1.fif",
+    "data/raw/file2.fif",
 ]
 
 # Directory to save the maxfiltered data to
-output_directory = "output/maxfilter"
+output_directory = "data/maxfilter"
 
 # Run MaxFiltering
 #

diff --git a/examples/oxford/manual_ica_pipeline/2_preprocess.py b/examples/oxford/manual_ica_pipeline/2_preprocess.py
@@ -10,8 +10,8 @@
 from osl import preprocessing, utils
 
 # Files and directories
-raw_file = "output/maxfilter/{subject}_tsss.fif"  # {subject} will be replace by the name for the subject
-preproc_dir = "output/preproc"  # output directory containing the preprocess files
+raw_file = "data/maxfilter/{subject}_tsss.fif"  # {subject} will be replace by the name for the subject
+preproc_dir = "data/preproc"  # output directory containing the preprocess files
 
 subjects = ["sub-001", "sub-002"]
 
@@ -21,13 +21,13 @@
     - filter: {l_freq: 0.5, h_freq: 125, method: iir, iir_params: {order: 5, ftype: butter}}
     - notch_filter: {freqs: 50 100}
     - resample: {sfreq: 250}
-    - bad_segments: {segment_len: 500, picks: mag, significance_level: 0.1}
-    - bad_segments: {segment_len: 500, picks: grad, significance_level: 0.1}
-    - bad_segments: {segment_len: 500, picks: mag, mode: diff, significance_level: 0.1}
-    - bad_segments: {segment_len: 500, picks: grad, mode: diff, significance_level: 0.1}
-    - bad_channels: {picks: mag, significance_level: 0.1}
-    - bad_channels: {picks: grad, significance_level: 0.1}
-    - ica_raw: {picks: meg, n_components: 64}
+    - bad_segments: {segment_len: 500, picks: mag}
+    - bad_segments: {segment_len: 500, picks: grad}
+    - bad_segments: {segment_len: 500, picks: mag, mode: diff}
+    - bad_segments: {segment_len: 500, picks: grad, mode: diff}
+    - bad_channels: {picks: mag}
+    - bad_channels: {picks: grad}
+    - ica_raw: {picks: meg, n_components: 40}
     - ica_autoreject: {apply: False}
     - interpolate_bads: {}
 """

diff --git a/examples/oxford/manual_ica_pipeline/3_manual_ica.py b/examples/oxford/manual_ica_pipeline/3_manual_ica.py
@@ -39,8 +39,8 @@ def plot_psd(raw, save_dir):
 #%% Setup paths
 
 # Directories
-preproc_dir = "output/preproc"
-output_dir = "output/preproc_ica"
+preproc_dir = "data/preproc"
+output_dir = "data/preproc_ica"
 
 # Subjects
 subjects = ["sub-001", "sub-002"]

diff --git a/examples/oxford/manual_ica_pipeline/4_coregister.py b/examples/oxford/manual_ica_pipeline/4_coregister.py
@@ -17,9 +17,9 @@
 from osl import source_recon, utils
 
 # Directories
-preproc_dir = "/output/preproc_ica"
-anat_dir = "path/to/smri/dir"
-coreg_dir = "output/coreg"
+preproc_dir = "data/preproc_ica"
+anat_dir = "data/smri"
+coreg_dir = "data/coreg"
 fsl_dir = "/opt/ohba/fsl/6.0.5"  # this is where FSL is installed on hbaws
 
 # Files ({subject} will be replaced by the name for the subject)

diff --git a/examples/oxford/manual_ica_pipeline/5_source_reconstruct.py b/examples/oxford/manual_ica_pipeline/5_source_reconstruct.py
@@ -11,9 +11,9 @@
 from osl import source_recon, utils
 
 # Directories
-preproc_dir = "output/preproc_ica"
-coreg_dir = "output/coreg"
-src_dir = "output/src"
+preproc_dir = "data/preproc_ica"
+coreg_dir = "data/coreg"
+src_dir = "data/src"
 fsl_dir = "/opt/ohba/fsl/6.0.5"  # this is where FSL is installed on hbaws
 
 # Files
@@ -31,7 +31,7 @@
         freq_range: [1, 45]
         chantypes: [mag, grad]
         rank: {meg: 60}
-        parcellation_file: fmri_d100_parcellation_with_PCC_reduced_2mm_ss5mm_ds8mm.nii.gz
+        parcellation_file: Glasser52_binary_space-MNI152NLin6_res-8x8x8.nii.gz
         method: spatial_basis
         orthogonalisation: symmetric
 """

diff --git a/examples/oxford/manual_ica_pipeline/6_sign_flip.py b/examples/oxford/manual_ica_pipeline/6_sign_flip.py
@@ -11,7 +11,7 @@
 from osl.source_recon import find_template_subject, run_src_batch, setup_fsl
 
 # Directories
-src_dir = "output/src"
+src_dir = "data/src"
 fsl_dir = "/opt/ohba/fsl/6.0.5"  # this is where FSL is installed on hbaws
 
 if __name__ == "__main__":

diff --git a/examples/oxford/maxfilter/maxfilter.py b/examples/oxford/maxfilter/maxfilter.py
@@ -9,11 +9,11 @@
 
 # Setup paths to raw (pre-maxfiltered) fif files
 input_files = [
-    "/ohba/pi/knobre/datasets/covid/rawbids/sub-004/meg/sub-004_task-restEO.fif",
+    "data/raw/file1.fif",
 ]
 
 # Directory to save the maxfiltered data to
-output_directory = "/ohba/pi/knobre/cgohil/covid/maxfilter"
+output_directory = "data/maxfilter"
 
 # Run MaxFiltering
 run_maxfilter_batch(

diff --git a/examples/oxford/ssp_pipeline/1_maxfilter.py b/examples/oxford/ssp_pipeline/1_maxfilter.py
@@ -9,12 +9,12 @@
 
 # Setup paths to raw (pre-maxfiltered) fif files
 input_files = [
-    "path/to/file1.fif",
-    "path/to/file2.fif",
+    "data/raw/file1.fif",
+    "data/raw/file2.fif",
 ]
 
 # Directory to save the maxfiltered data to
-output_directory = "output/maxfilter"
+output_directory = "data/maxfilter"
 
 # Run MaxFiltering
 #

diff --git a/examples/oxford/ssp_pipeline/2_preprocess.py b/examples/oxford/ssp_pipeline/2_preprocess.py
@@ -10,8 +10,8 @@
 from osl import preprocessing, utils
 
 # Files and directories
-raw_file = "output/maxfilter/{subject}_tsss.fif"  # {subject} will be replace by the name for the subject
-preproc_dir = "output/preproc"  # output directory containing the preprocess files
+raw_file = "data/maxfilter/{subject}_tsss.fif"  # {subject} will be replace by the name for the subject
+preproc_dir = "data/preproc"  # output directory containing the preprocess files
 
 subjects = ["sub-001", "sub-002"]
 
@@ -21,14 +21,12 @@
     - filter: {l_freq: 0.5, h_freq: 125, method: iir, iir_params: {order: 5, ftype: butter}}
     - notch_filter: {freqs: 50 100}
     - resample: {sfreq: 250}
-    - bad_segments: {segment_len: 500, picks: mag, significance_level: 0.1}
-    - bad_segments: {segment_len: 500, picks: grad, significance_level: 0.1}
-    - bad_segments: {segment_len: 500, picks: mag, mode: diff, significance_level: 0.1}
-    - bad_segments: {segment_len: 500, picks: grad, mode: diff, significance_level: 0.1}
-    - bad_channels: {picks: mag, significance_level: 0.1}
-    - bad_channels: {picks: grad, significance_level: 0.1}
-    - ica_raw: {picks: meg, n_components: 64}
-    - ica_autoreject: {apply: False}
+    - bad_segments: {segment_len: 500, picks: mag}
+    - bad_segments: {segment_len: 500, picks: grad}
+    - bad_segments: {segment_len: 500, picks: mag, mode: diff}
+    - bad_segments: {segment_len: 500, picks: grad, mode: diff}
+    - bad_channels: {picks: mag}
+    - bad_channels: {picks: grad}
     - interpolate_bads: {}
 """
 

diff --git a/examples/oxford/ssp_pipeline/3_ssp_denoise.py b/examples/oxford/ssp_pipeline/3_ssp_denoise.py
@@ -16,9 +16,9 @@
 
 
 # Directories
-preproc_dir = "output/preproc"
-ssp_preproc_dir = "output/preproc_ssp"
-report_dir = "output/preproc_ssp/report"
+preproc_dir = "data/preproc"
+ssp_preproc_dir = "data/preproc_ssp"
+report_dir = "data/preproc_ssp/report"
 
 os.makedirs(ssp_preproc_dir, exist_ok=True)
 os.makedirs(report_dir, exist_ok=True)

diff --git a/examples/oxford/ssp_pipeline/4_coregister.py b/examples/oxford/ssp_pipeline/4_coregister.py
@@ -17,9 +17,9 @@
 from osl import source_recon, utils
 
 # Directories
-preproc_dir = "output/preproc_ssp"
+preproc_dir = "data/preproc_ssp"
 anat_dir = "path/to/smri/dir"
-coreg_dir = "output/coreg"
+coreg_dir = "data/coreg"
 fsl_dir = "/opt/ohba/fsl/6.0.5"  # this is where FSL is installed on hbaws
 
 # Files ({subject} will be replaced by the name for the subject)

diff --git a/examples/oxford/ssp_pipeline/5_source_reconstruct.py b/examples/oxford/ssp_pipeline/5_source_reconstruct.py
@@ -11,9 +11,9 @@
 from osl import source_recon, utils
 
 # Directories
-preproc_dir = "output/preproc_ssp"
-coreg_dir = "output/coreg"
-src_dir = "output/src"
+preproc_dir = "data/preproc_ssp"
+coreg_dir = "data/coreg"
+src_dir = "data/src"
 fsl_dir = "/opt/ohba/fsl/6.0.5"  # this is where FSL is installed on hbaws
 
 # Files
@@ -31,7 +31,7 @@
         freq_range: [1, 45]
         chantypes: [mag, grad]
         rank: {meg: 60}
-        parcellation_file: fmri_d100_parcellation_with_PCC_reduced_2mm_ss5mm_ds8mm.nii.gz
+        parcellation_file: Glasser52_binary_space-MNI152NLin6_res-8x8x8.nii.gz
         method: spatial_basis
         orthogonalisation: symmetric
 """

diff --git a/examples/oxford/ssp_pipeline/6_sign_flip.py b/examples/oxford/ssp_pipeline/6_sign_flip.py
@@ -11,7 +11,7 @@
 from osl.source_recon import find_template_subject, run_src_batch, setup_fsl
 
 # Directories
-src_dir = "output/src"
+src_dir = "data/src"
 fsl_dir = "/opt/ohba/fsl/6.0.5"  # this is where FSL is installed on hbaws
 
 if __name__ == "__main__":