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',
)
