def run(args=None, config=None):
parser = AnalysisParser('config')
args = parser.parse_analysis_args(args)
config = args.config
subs = ['CoRe_011', 'CoRe_023', 'CoRe_054', 'CoRe_079', 'CoRe_082', 'CoRe_087', 'CoRe_094', 'CoRe_100',
'CoRe_107', 'CoRe_155', 'CoRe_192', 'CoRe_195', 'CoRe_220', 'CoRe_235', 'CoRe_267', 'CoRe_268']
base_path = '/media/sf_hcp/sleepdata/'
for sb_i in np.arange(0,len(subs)):
sb_i=1
sb = subs[sb_i]
day1_fmri = glob.glob(base_path + sb + '/proc/*nii')
day1_vmrk = glob.glob(base_path + sb + '/proc/*Day*1*_N*vmrk')
print(day1_fmri)
fmri = nib.load(day1_fmri[0])
canica = CanICA(n_components=40, smoothing_fwhm=6.,
threshold=None, verbose=10, random_state=0)
fmri_info = helpers.fmri_info(day1_fmri[0])
canica.fit(fmri)
cimg = canica.components_img_.get_data()
TR = fmri_info[0]
tr_times = np.arange(0, 30, TR)
hrf = helpers.get_hrf(tr_times)
# %matplotlib auto
for i in np.arange(0,40):
plt.subplot(4,10,i+1)
plt.imshow(np.max(cimg[:,:,:,i],axis=2))
plt.title(str(i))
# in order: DMN, auditory, visual, lingual, parietal, striatal, thalamic
comps = [35,28,30,39,8,9,32]
allcomp_ts = canica.transform([fmri])[0].transpose()
comps_ts = allcomp_ts[comps,:]
network_labs = ['DMN','auditory','visual','lingual',
'parietal','striatal','thalamic']
for i in np.arange(0,len(comps)):
plt.subplot(2,5,i+1)
plt.imshow(np.max(cimg[:,:,:,comps[i]],axis=2))
plt.title(network_labs[i])
np.save(str.replace(day1_fmri[0],'.nii','_comps'), comps_ts)
detrend=True,
high_pass=0.008,
t_r=0.72)
## Run ICA
start = time.time()
print("RUNNING ICA")
canica.fit(nifti_list)
end = time.time()
print('Elapsed time %f' % (end - start))
# Save-stuff
canica.components_img_.to_filename('wm_ica_components_d%i.nii.gz' %
(n_components))
canica.mask_img_.to_filename('wm_ica_mask.nii.gz')
## Project all data into ICA space
print('Transforming data...')
start = time.time()
X = canica.transform(nifti_list)
end = time.time()
print('Elapsed time %f' % (end - start))
# Save
result_dict = dict()
result_dict['X'] = X
result_dict['data_list'] = nifti_list
sio.savemat('wm_ica_ts_d%i' % (n_components), result_dict)
def run(args=None, config=None):
parser = AnalysisParser('config')
args = parser.parse_analysis_args(args)
config = args.config
eeg_path = '/media/sf_shared/graddata/ica_denoised_raw.fif'
fmri_path = '/media/sf_shared/CoRe_011/rfMRI/d2/11-BOLD_Sleep_BOLD_Sleep_20150824220820_11.nii'
vmrk_path = '/media/sf_shared/CoRe_011/eeg/CoRe_011_Day2_Night_01.vmrk'
event_ids, event_lats = helpers.read_vmrk(vmrk_path)
event_lats = np.array(event_lats)
grad_inds = [
index for index, value in enumerate(event_ids) if value == 'R1'
]
grad_inds = np.array(grad_inds)
grad_lats = event_lats[grad_inds]
grad_lats = grad_lats / 20 # resample from 5000Hz to 250Hz
start_ind = int(grad_lats[0])
end_ind = int(grad_lats[-1])
canica = CanICA(n_components=40,
smoothing_fwhm=6.,
threshold=None,
verbose=10,
random_state=0)
fmri = nib.load(fmri_path)
# get TR, n_slices, and n_TRs
fmri_info = helpers.fmri_info(fmri_path)
canica.fit(fmri)
cimg = canica.components_img_.get_data()
TR = fmri_info[0]
tr_times = np.arange(0, 30, TR)
hrf = get_hrf(tr_times)
# plot components
for i in np.arange(0, 40):
plt.subplot(4, 10, i + 1)
plt.imshow(np.max(cimg[:, :, :, i], axis=2))
# get the EEG
raw = mne.io.read_raw_fif(eeg_path, preload=True)
raw_data = raw.get_data()
# get power spectrum for different sleep stages (BOLD)
comps = canica.transform([fmri])[0].transpose()
bold_srate = 1 / fmri_info[0]
bold_epochl = int(7500 / (250 / bold_srate))
#bold_pxx,bold_f = pxx_bold_component_epoch(comps, bold_srate, 250, bold_epochl, sleep_stages)
#eeg_pxx,eeg_f = pxx_eeg_epochs(raw_data, sleep_stages, 7500)
# concatenate the epochs, then compute the psd
# 1) get triggers, 2) concatenate data, 3) compute psd
def get_trigger_inds(trigger_name, event_ids):
trig_inds = [
index for index, value in enumerate(event_ids)
if value == trigger_names[trig]
]
return trig_inds
def epoch_triggers(raw_data, lats, pre_samples, post_samples):
epochs = np.zeros(
(raw_data.shape[0], lats.shape[0], pre_samples + post_samples))
for lat in np.arange(0, lats.shape[0]):
epochs[:, lat, :] = raw_data[:, lats[lat] - pre_samples:lats[lat] +
post_samples]
return epochs
trigger_names = ['wake', 'NREM1', 'NREM2', 'NREM3']
"""
epoch BOLD and get power for different trigger types
what you actually want is single trial EEG and BOLD psd
first get all the indices that are contained within the BOLD timeseries
then, get the EEG power spectrum values within those same indices
"""
eeg_srate = 250
bold_pre_samples = 15
bold_post_samples = 25
eeg_pre_samples = int(bold_pre_samples * fmri_info[0] * eeg_srate)
eeg_post_samples = int(bold_post_samples * fmri_info[0] * eeg_srate)
bold_conversion = eeg_srate / (1 / fmri_info[0])
all_bold_epochs = []
all_eeg_epochs = []
for trig in np.arange(0, len(trigger_names)):
trig_inds = get_trigger_inds(trigger_names[trig], event_ids)
trig_lats = event_lats[trig_inds]
bold_lats = ((trig_lats - start_ind) / bold_conversion).astype(int)
bads = np.where((bold_lats - bold_pre_samples < 0)
| (bold_lats + bold_post_samples >= comps.shape[1]))
bold_lats = np.delete(bold_lats, bads, axis=0)
eeg_lats = np.delete(trig_lats, bads, axis=0)
bold_epochs = epoch_triggers(comps, bold_lats, bold_pre_samples,
bold_post_samples)
eeg_epochs = epoch_triggers(raw_data, eeg_lats, eeg_pre_samples,
eeg_post_samples)
all_bold_epochs.append(bold_epochs)
all_eeg_epochs.append(eeg_epochs)
# comput power
for i in np.arange(0, len(all_eeg_epochs)):
eeg_epochs = all_eeg_epochs[i]
bold_epochs = all_bold_epochs[i]
bold_f, bold_pxx = signal.welch(bold_epochs)
eeg_f, eeg_pxx = signal.welch(eeg_epochs)
gauss = signal.gaussian(eeg_srate, 20)
gauss = gauss / np.sum(gauss)
freqs = np.zeros((5, 2))
freqs[0, 0] = 1
freqs[0, 1] = 3
freqs[1, 0] = 4
freqs[1, 1] = 7
freqs[2, 0] = 8
freqs[2, 1] = 15
freqs[3, 0] = 17
freqs[3, 1] = 30
freqs[4, 0] = 30
freqs[4, 1] = 80
chan_freqs = filter_and_downsample(raw_data, comps, freqs, start_ind,
end_ind)
conved = convolve_chanfreqs(np.log(chan_freqs), hrf)
# epoch all the hrf-convolved filtered EEG power
all_conved_epochs = []
for trig in np.arange(0, len(trigger_names)):
trig_inds = get_trigger_inds(trigger_names[trig], event_ids)
trig_lats = event_lats[trig_inds]
bold_lats = ((trig_lats - start_ind) / bold_conversion).astype(int)
bads = np.where((bold_lats - bold_pre_samples < 0)
| (bold_lats + bold_post_samples >= comps.shape[1]))
bold_lats = np.delete(bold_lats, bads, axis=0)
conved_epochs = np.zeros(
(conved.shape[0], conved.shape[1], bold_lats.shape[0],
bold_pre_samples + bold_post_samples))
for i in np.arange(0, conved.shape[1]):
conved_epochs[:, i, :] = epoch_triggers(conved[:, i, :], bold_lats,
bold_pre_samples,
bold_post_samples)
all_conved_epochs.append(conved_epochs)
sig1 = chan_freqs[3, 2, :]
sig2 = comps[0, :]
sig2 = butter_bandpass_filter(sig2, 0.005, 0.1, 1 / fmri_info[0])
nlags = 50
def xcorr(sig1, sig2, nlags):
vec_l = sig1.shape[0] - nlags
xcorrs = np.zeros(nlags)
vec1 = sig1[int(sig1.shape[0] / 2 - vec_l / 2):int(sig1.shape[0] / 2 +
vec_l / 2)]
start_p = 0
for i in np.arange(0, nlags):
vec2 = sig2[(start_p + i):(start_p + vec_l + i)]
xcorrs[i] = np.corrcoef(vec1, vec2)[0, 1]
return xcorrs
all_xcorrs = []
for i in np.arange(0, len(all_conved_epochs)):
xc_i = np.zeros(
(1, all_conved_epochs[i].shape[1], all_conved_epochs[i].shape[2],
all_bold_epochs[i].shape[0], 20))
for j in np.arange(0, 1):
print(j)
for k in np.arange(0, all_conved_epochs[i].shape[1]):
for el in np.arange(0, all_conved_epochs[i].shape[2]):
for m in np.arange(0, all_bold_epochs[i].shape[0]):
xc_i[j, k, el,
m, :] = xcorr(all_conved_epochs[i][5, k, el, :],
all_bold_epochs[i][m, el, :], 20)
all_xcorrs.append(xc_i)
plt.plot(np.mean(all_xcorrs[1][0, 1, :, 0, :], axis=0))
plt.plot(np.mean(all_xcorrs[2][0, 1, :, 0, :], axis=0))
plt.plot(np.mean(all_xcorrs[3][0, 1, :, 0, :], axis=0))
# correlate power across different epochs
"""