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* Examples: Added examples for mrc_meguk notts and cambridge sites. * Update CamCAN example scripts. * Added recommended setting example scripts for Oxford. * Updated Wakeman-Henson example scripts. --------- Co-authored-by: Rukuang Huang <rukuang.huang@jesus.ox.ac.uk>
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,108 @@ | ||
| """Coregisteration. | ||
| The scripts was first run for all subjects (with n_init=1). Then for subjects | ||
| whose coregistration looked a bit off we re-run this script just for that | ||
| particular subject with a higher n_init. | ||
| """ | ||
|
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| # Authors: Chetan Gohil <chetan.gohil@psych.ox.ac.uk> | ||
|
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| import numpy as np | ||
| import pathlib | ||
| from glob import glob | ||
| from dask.distributed import Client | ||
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| from osl import source_recon, utils | ||
|
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| # Directories | ||
| BASE_DIR = "/well/woolrich/projects/camcan" | ||
| PREPROC_DIR = BASE_DIR + "/summer23/preproc" | ||
| COREG_DIR = BASE_DIR + "/summer23/coreg" | ||
| ANAT_DIR = BASE_DIR + "/cc700/mri/pipeline/release004/BIDS_20190411/anat" | ||
| FSL_DIR = "/well/woolrich/projects/software/fsl" | ||
|
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||
| # Files | ||
| PREPROC_FILE = ( | ||
| PREPROC_DIR | ||
| + "/mf2pt2_{0}_ses-rest_task-rest_meg" | ||
| + "/mf2pt2_{0}_ses-rest_task-rest_meg_preproc_raw.fif" | ||
| ) | ||
| SMRI_FILE = ANAT_DIR + "/{0}/anat/{0}_T1w.nii" | ||
|
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| # Settings | ||
| config = """ | ||
| source_recon: | ||
| - extract_fiducials_from_fif: {} | ||
| - fix_headshape_points: {} | ||
| - compute_surfaces: | ||
| include_nose: False | ||
| - coregister: | ||
| use_nose: False | ||
| use_headshape: True | ||
| #n_init: 50 | ||
| """ | ||
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| def fix_headshape_points(src_dir, subject, preproc_file, smri_file, epoch_file): | ||
| filenames = source_recon.rhino.get_coreg_filenames(src_dir, subject) | ||
|
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| # 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"]) | ||
|
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| # Drop nasion by 4cm and remove headshape points more than 7 cm away | ||
| nas[2] -= 40 | ||
| distances = np.sqrt( | ||
| (nas[0] - hs[0]) ** 2 + (nas[1] - hs[1]) ** 2 + (nas[2] - hs[2]) ** 2 | ||
| ) | ||
| keep = distances > 70 | ||
| hs = hs[:, keep] | ||
|
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| # Remove anything outside of rpa | ||
| keep = hs[0] < rpa[0] | ||
| hs = hs[:, keep] | ||
|
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| # Remove anything outside of lpa | ||
| keep = hs[0] > lpa[0] | ||
| hs = hs[:, keep] | ||
|
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| # Remove headshape points on the neck | ||
| remove = hs[2] < min(lpa[2], rpa[2]) - 4 | ||
| hs = hs[:, ~remove] | ||
|
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| # Overwrite headshape file | ||
| utils.logger.log_or_print(f"overwritting {filenames['polhemus_headshape_file']}") | ||
| np.savetxt(filenames["polhemus_headshape_file"], hs) | ||
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| if __name__ == "__main__": | ||
| utils.logger.set_up(level="INFO") | ||
| source_recon.setup_fsl(FSL_DIR) | ||
|
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| # Get subjects | ||
| subjects = [] | ||
| for subject in sorted(glob(PREPROC_FILE.replace("{0}", "*"))): | ||
| subjects.append(pathlib.Path(subject).stem.split("_")[1]) | ||
|
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||
| # Setup files | ||
| smri_files = [] | ||
| preproc_files = [] | ||
| for subject in subjects: | ||
| smri_files.append(SMRI_FILE.format(subject)) | ||
| preproc_files.append(PREPROC_FILE.format(subject)) | ||
|
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| # Setup parallel processing | ||
| # client = Client(n_workers=8, threads_per_worker=1) | ||
|
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| # Run coregistration | ||
| source_recon.run_src_batch( | ||
| config, | ||
| src_dir=COREG_DIR, | ||
| subjects=subjects, | ||
| preproc_files=preproc_files, | ||
| smri_files=smri_files, | ||
| extra_funcs=[fix_headshape_points], | ||
| # dask_client=True, | ||
| ) |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,19 @@ | ||
| """Data preparation: time-delay embedding and principal component analysis. | ||
| """ | ||
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| # Authors: Chetan Gohil <chetan.gohil@psych.ox.ac.uk> | ||
|
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| from glob import glob | ||
|
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| from osl_dynamics.data import Data | ||
|
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| files = sorted(glob("/well/woolrich/projects/camcan/summer23/src/*/sflip_parc-raw.fif")) | ||
| data = Data(files, picks="misc", reject_by_annotation="omit", n_jobs=16) | ||
| methods = { | ||
| "tde_pca": {"n_embeddings": 15, "n_pca_components": 100}, | ||
| "standardize": {}, | ||
| } | ||
| data.prepare(methods) | ||
| data.save("/well/woolrich/projects/camcan/summer23/prepared") | ||
| data.delete_dir() |
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