SNIRF HbM GLM Analysis

Importage

# KF Tools and related imports
from kftools.data import fetch_file
from kftools.snirf import snirf_task_ana,kf_plot_glm_contrast_topo

Grab the data

data_dir='.'

fetch_file(data_dir=data_dir, filetype='kp-snf-hbm',
            site='pitch', task='ft', subid='sub010', sesid='ses01')

Out:

Downloading pitch_sub010_ft_ses01_1017-1706_kp-snf-hbm.snirf

Downloading...
From: https://drive.google.com/uc?id=1BcZHsmDWgxhppg_j4yqBLj2MBM20kzM_
To: /home/runner/work/kernel-flow-tools/kernel-flow-tools/examples/pitch_sub010_ft_ses01_1017-1706_kp-snf-hbm.snirf

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Specify and run the GLM model

f = 'pitch_sub010_ft_ses01_1017-1706_kp-snf-hbm.snirf'

res_hbo = snirf_task_ana(f,chromo='hbo')
res_hbr = snirf_task_ana(f, chromo='hbr')

res_hbo.keys()

Out:

Loading /home/runner/work/kernel-flow-tools/kernel-flow-tools/examples/pitch_sub010_ft_ses01_1017-1706_kp-snf-hbm.snirf
Reading 0 ... 6435  =      0.000 ...   779.279 secs...
Used Annotations descriptions: ['Rest', 'Tapping/L', 'Tapping/R']
Multiple event values for single event times found. Creating new event value to reflect simultaneous events.
Not setting metadata
280 matching events found
Applying baseline correction (mode: mean)
Using data from preloaded Raw for 280 events and 26 original time points ...
3 bad epochs dropped
Used Annotations descriptions: ['Rest', 'Tapping/L', 'Tapping/R']
/home/runner/work/kernel-flow-tools/kernel-flow-tools/kftools/snirf/mne.py:106: RuntimeWarning: (X, Y) fit (-0.0, -20.4) more than 20 mm from head frame origin
  sphere_params =  _check_sphere('auto', info=hbm.info, sphere_units='m')
Loading /home/runner/work/kernel-flow-tools/kernel-flow-tools/examples/pitch_sub010_ft_ses01_1017-1706_kp-snf-hbm.snirf
Reading 0 ... 6435  =      0.000 ...   779.279 secs...
Used Annotations descriptions: ['Rest', 'Tapping/L', 'Tapping/R']
Multiple event values for single event times found. Creating new event value to reflect simultaneous events.
Not setting metadata
280 matching events found
Applying baseline correction (mode: mean)
Using data from preloaded Raw for 280 events and 26 original time points ...
3 bad epochs dropped
Used Annotations descriptions: ['Rest', 'Tapping/L', 'Tapping/R']
/home/runner/work/kernel-flow-tools/kernel-flow-tools/kftools/snirf/mne.py:106: RuntimeWarning: (X, Y) fit (-0.0, -20.4) more than 20 mm from head frame origin
  sphere_params =  _check_sphere('auto', info=hbm.info, sphere_units='m')

dict_keys(['df_evs', 'ev', 'ev_d', 'hbm', 'hbm_ep', 'hbm_ev_LgtR', 'hbm_ev_RgtL', 's', 'design_matrix', 'data_subset', 'sphere_params', 'glm_est', 'contrast_LgtR', 'contrast_vec_LgtR', 'contrast_RgtL', 'estmrg_LgtR', 'estmrg_RgtL', 'contrast_LgtRest', 'contrast_vec_LgtRest', 'contrast_RgtRest', 'estmrg_LgtRest', 'estmrg_RgtRest', 'pos_LgtR', 'pos_RgtL', 'chs_LgtR', 'chs_RgtL', 'sphere_LgtR', 'sphere_RgtL', 'chromo'])

Look at GLM results

HbO, Left > Right contrast

glmest = res_hbo['glm_est']
con = res_hbo['contrast_LgtR'].data
disp = kf_plot_glm_contrast_topo(glmest, con, chromo='hbo',
                                 vmin=0,vmax=0.5,sig_thr=0.00001)
disp.show()

Out:

/home/runner/work/kernel-flow-tools/kernel-flow-tools/kftools/snirf/mne.py:245: RuntimeWarning: (X, Y) fit (-0.0, -20.4) more than 20 mm from head frame origin
  estmrg, pos, chs, sphere = _handle_overlaps(info, t, sphere, estimates)

HbO, Right > Left contrast

glmest = res_hbo['glm_est']
con = res_hbo['contrast_RgtL'].data
disp = kf_plot_glm_contrast_topo(glmest, con, chromo='hbo',
                                 vmin=0,vmax=0.5,sig_thr=0.00001)
disp.show()

Out:

/home/runner/work/kernel-flow-tools/kernel-flow-tools/kftools/snirf/mne.py:245: RuntimeWarning: (X, Y) fit (-0.0, -20.4) more than 20 mm from head frame origin
  estmrg, pos, chs, sphere = _handle_overlaps(info, t, sphere, estimates)

HbR, Left > Right contrast

glmest = res_hbr['glm_est']
con = res_hbr['contrast_LgtR'].data
disp = kf_plot_glm_contrast_topo(glmest, con, chromo='hbr',
                                 vmin=0,vmax=0.3,sig_thr=0.0001)
disp.show()

Out:

/home/runner/work/kernel-flow-tools/kernel-flow-tools/kftools/snirf/mne.py:245: RuntimeWarning: (X, Y) fit (-0.0, -20.4) more than 20 mm from head frame origin
  estmrg, pos, chs, sphere = _handle_overlaps(info, t, sphere, estimates)

HbR, Right > Left contrast

glmest = res_hbr['glm_est']
con = res_hbr['contrast_RgtL'].data
disp = kf_plot_glm_contrast_topo(glmest, con, chromo='hbr',
                                 vmin=0,vmax=0.5,sig_thr=0.0001)
disp.show()

Out:

/home/runner/work/kernel-flow-tools/kernel-flow-tools/kftools/snirf/mne.py:245: RuntimeWarning: (X, Y) fit (-0.0, -20.4) more than 20 mm from head frame origin
  estmrg, pos, chs, sphere = _handle_overlaps(info, t, sphere, estimates)