def test_multi_roi_timeseries(): import matplotlib.pyplot as plt from os import path from samri.plotting import summary, timeseries from samri.utilities import bids_substitution_iterator from samri.fetch.local import roi_from_atlaslabel substitutions = bids_substitution_iterator( sessions=[ 'ofM', 'ofMaF', ], subjects=[ '4007', ], runs=[ '0', '1', ], modalities=[ 'bold', 'cbv', ], data_dir='/usr/share/samri_bidsdata', # BOLD scans are not recognized, since the current (=sci-biology/samri_bidsdata-0.2) filt file suffix also contains `_maths_` for CBV, but not for BOLD. validate_for_template="{data_dir}/l1/sub-{subject}/ses-{session}/sub-{subject}_ses-{session}_task-JogB_acq-EPIlowcov_run-{run}_{modality}.nii.gz", ) mapping='/usr/share/mouse-brain-atlases/dsurqe_labels.csv' atlas='/usr/share/mouse-brain-atlases/dsurqec_40micron_labels.nii' my_roi = roi_from_atlaslabel(atlas, mapping=mapping, label_names=['cortex'], ) timecourses, designs, _, events_dfs, subplot_titles = summary.ts_overviews(substitutions, my_roi, ts_file_template="{data_dir}/l1/sub-{subject}/ses-{session}/sub-{subject}_ses-{session}_task-JogB_acq-EPIlowcov_run-{run}_{modality}.nii.gz", betas_file_template="{data_dir}/l1/sub-{subject}/ses-{session}/sub-{subject}_ses-{session}_task-JogB_acq-EPIlowcov_run-{run}_{modality}_betas.nii.gz", design_file_template="{data_dir}/l1/sub-{subject}/ses-{session}/sub-{subject}_ses-{session}_task-JogB_acq-EPIlowcov_run-{run}_{modality}_design.mat", event_file_template='{data_dir}/preprocessing/sub-{subject}/ses-{session}/func/sub-{subject}_ses-{session}_task-JogB_acq-EPIlowcov_run-{run}_events.tsv', n_jobs_percentage=0.5, ) style_file = path.join(path.dirname(path.realpath(__file__)),'../samri_multiple-ts.conf') plt.style.use(style_file) timeseries.multi(timecourses, designs, events_dfs, subplot_titles, quantitative=False, save_as='_multi_roi_timeseries.pdf', )
def qc_regressor(sessions, subjects, scans, workflow_name, mask, data_dir="~/ni_data/ofM.dr", save_as="", ): from samri.plotting import summary, timeseries plt.style.use('samri_multiple-ts.conf') substitutions = bids_substitution_iterator(sessions,subjects,scans,data_dir,workflow_name) timecourses, designs, stat_maps, events_dfs, subplot_titles = summary.ts_overviews(substitutions, mask, ts_file_template="{data_dir}/preprocessing/{preprocessing_dir}/sub-{subject}/ses-{session}/func/sub-{subject}_ses-{session}_trial-{scan}.nii.gz", beta_file_template="{data_dir}/l1/{l1_dir}/sub-{subject}/ses-{session}/sub-{subject}_ses-{session}_trial-{scan}_cope.nii.gz", design_file_template="{data_dir}/l1/{l1_workdir}/_subject_session_scan_{subject}.{session}.{scan}/modelgen/run0.mat", event_file_template="{data_dir}/preprocessing/{preprocessing_dir}/sub-{subject}/ses-{session}/func/sub-{subject}_ses-{session}_trial-{scan}_events.tsv", ) timeseries.multi(timecourses, designs, stat_maps, events_dfs, subplot_titles, figure="timecourses", quantitative=False, save_as=save_as, )
def qc_regressor(sessions, subjects, scans, workflow_name, mask, data_dir="~/ni_data/ofM.dr", save_as="", ): from samri.plotting import summary, timeseries plt.style.use('samri_multiple-ts.conf') substitutions = bids_substitution_iterator(sessions,subjects,scans,data_dir,workflow_name) timecourses, designs, stat_maps, events_dfs, subplot_titles = summary.ts_overviews(substitutions, mask, ts_file_template="{data_dir}/preprocessing/{preprocessing_dir}/sub-{subject}/ses-{session}/func/sub-{subject}_ses-{session}_task-{scan}.nii.gz", beta_file_template="{data_dir}/l1/{l1_dir}/sub-{subject}/ses-{session}/sub-{subject}_ses-{session}_task-{scan}_cope.nii.gz", design_file_template="{data_dir}/l1/{l1_workdir}/_subject_session_scan_{subject}.{session}.{scan}/modelgen/run0.mat", event_file_template="{data_dir}/preprocessing/{preprocessing_dir}/sub-{subject}/ses-{session}/func/sub-{subject}_ses-{session}_task-{scan}_events.tsv", ) timeseries.multi(timecourses, designs, stat_maps, events_dfs, subplot_titles, figure="timecourses", quantitative=False, save_as=save_as, )
def test_multi_roi_timeseries(): import matplotlib.pyplot as plt from os import path from samri.plotting import summary, timeseries from samri.utilities import bids_substitution_iterator from samri.fetch.local import roi_from_atlaslabel substitutions = bids_substitution_iterator( sessions=[ 'ofM', 'ofMaF', ], subjects=[ '4007', ], runs=[ '0', '1', ], modalities=[ 'bold', 'cbv', ], data_dir='/usr/share/samri_bidsdata', # BOLD scans are not recognized, since the current (=sci-biology/samri_bidsdata-0.2) filt file suffix also contains `_maths_` for CBV, but not for BOLD. validate_for_template= "{data_dir}/l1/sub-{subject}/ses-{session}/sub-{subject}_ses-{session}_task-JogB_acq-EPIlowcov_run-{run}_{modality}.nii.gz", ) mapping = '/usr/share/mouse-brain-atlases/dsurqe_labels.csv' atlas = '/usr/share/mouse-brain-atlases/dsurqec_40micron_labels.nii' my_roi = roi_from_atlaslabel( atlas, mapping=mapping, label_names=['cortex'], ) timecourses, designs, _, events_dfs, subplot_titles = summary.ts_overviews( substitutions, my_roi, ts_file_template= "{data_dir}/l1/sub-{subject}/ses-{session}/sub-{subject}_ses-{session}_task-JogB_acq-EPIlowcov_run-{run}_{modality}.nii.gz", betas_file_template= "{data_dir}/l1/sub-{subject}/ses-{session}/sub-{subject}_ses-{session}_task-JogB_acq-EPIlowcov_run-{run}_{modality}_betas.nii.gz", design_file_template= "{data_dir}/l1/sub-{subject}/ses-{session}/sub-{subject}_ses-{session}_task-JogB_acq-EPIlowcov_run-{run}_{modality}_design.mat", event_file_template= '{data_dir}/preprocessing/sub-{subject}/ses-{session}/func/sub-{subject}_ses-{session}_task-JogB_acq-EPIlowcov_run-{run}_events.tsv', n_jobs_percentage=0.5, ) style_file = path.join(path.dirname(path.realpath(__file__)), '../samri_multiple-ts.conf') plt.style.use(style_file) timeseries.multi( timecourses, designs, events_dfs, subplot_titles, quantitative=False, save_as='_multi_roi_timeseries.pdf', )