diff --git a/examples/oxford/automated_ica_pipeline/1_maxfilter.py b/examples/oxford/automated_ica_pipeline/1_maxfilter.py index 3835ea75..1744776d 100644 --- 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 index 5f26639d..1f77f339 100644 --- 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 index 71dd47be..3a39992d 100644 --- 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 index 515238bc..b88003c4 100644 --- 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 index 8fe22342..2ae176a5 100644 --- 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 index 3835ea75..1744776d 100644 --- 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 index 2c13442a..b3708d17 100644 --- 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 index fc172cca..e04ece48 100644 --- 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 index eb85d328..23839bf4 100644 --- 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 index 863034ee..1531dbd6 100644 --- 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 index 8fe22342..2ae176a5 100644 --- 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 index dffa26f7..b58de7c4 100644 --- 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 index 3835ea75..1744776d 100644 --- 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 index 2c13442a..1713f6f7 100644 --- 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 index 14111657..8421a6c4 100644 --- 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 index 02a11c34..7def40c9 100644 --- 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 index bc4a2c1f..49d24bb6 100644 --- 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 index 8fe22342..2ae176a5 100644 --- 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__":