n_fft = int(raw.info["sfreq"])
n_per_seg = n_fft
n_overlap = n_fft // 2
assert n_overlap < n_per_seg  # Obviously true
spectrum = raw.compute_psd(method="welch", n_fft=n_fft, n_overlap=n_overlap, n_per_seg=n_per_seg)

>>ValueError: noverlap must be less than nperseg.

import mne
from mne.time_frequency import psd_array_welch
import os

sample_data_folder = mne.datasets.sample.data_path()
sample_data_raw_file = os.path.join(sample_data_folder, 'MEG', 'sample', 'sample_audvis_raw.fif')
raw = mne.io.read_raw_fif(sample_data_raw_file)

annotations = mne.Annotations(onset=[5, 6.5], duration=[1, 1], description=['bad', 'bad'])
raw.set_annotations(annotations)

n_fft = int(raw.info["sfreq"])
n_overlap = n_fft // 2

# psd_array_welch fails
psds, freqs = psd_array_welch(raw.get_data(reject_by_annotation='NaN'), n_fft, n_fft=n_fft, n_overlap=n_overlap)
>> ValueError: noverlap must be less than nperseg.

# raw.compute_psd fails
spectrum = raw.compute_psd(method="welch", n_fft=n_fft, n_overlap=n_overlap)
>> ValueError: noverlap must be less than nperseg.

# specifying n_per_seg explicitly does not help
n_per_seg = n_fft
assert n_overlap < n_per_seg  # True
spectrum = raw.compute_psd(method="welch", n_fft=n_fft, n_overlap=n_overlap, n_per_seg=n_per_seg)
>> ValueError: noverlap must be less than nperseg.

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[11], line 1
----> 1 spectrum = raw.compute_psd(method="welch", **kwargs)

File <decorator-gen-336>:12, in compute_psd(self, method, fmin, fmax, tmin, tmax, picks, exclude, proj, remove_dc, reject_by_annotation, n_jobs, verbose, **method_kw)

File ~/anaconda3/envs/local_sns013/lib/python3.12/site-packages/mne/io/base.py:2232, in BaseRaw.compute_psd(self, method, fmin, fmax, tmin, tmax, picks, exclude, proj, remove_dc, reject_by_annotation, n_jobs, verbose, **method_kw)
   2229 method = _validate_method(method, type(self).__name__)
   2230 self._set_legacy_nfft_default(tmin, tmax, method, method_kw)
-> 2232 return Spectrum(
   2233     self,
   2234     method=method,
   2235     fmin=fmin,
   2236     fmax=fmax,
   2237     tmin=tmin,
   2238     tmax=tmax,
   2239     picks=picks,
   2240     exclude=exclude,
   2241     proj=proj,
   2242     remove_dc=remove_dc,
   2243     reject_by_annotation=reject_by_annotation,
   2244     n_jobs=n_jobs,
   2245     verbose=verbose,
   2246     **method_kw,
   2247 )

File ~/anaconda3/envs/local_sns013/lib/python3.12/site-packages/mne/time_frequency/spectrum.py:1146, in Spectrum.__init__(self, inst, method, fmin, fmax, tmin, tmax, picks, exclude, proj, remove_dc, reject_by_annotation, n_jobs, verbose, **method_kw)
   1144 self._nave = getattr(inst, "nave", None)
   1145 # compute the spectra
-> 1146 self._compute_spectra(data, fmin, fmax, n_jobs, method_kw, verbose)
   1147 # check for correct shape and bad values
   1148 self._check_values()

File ~/anaconda3/envs/local_sns013/lib/python3.12/site-packages/mne/time_frequency/spectrum.py:445, in BaseSpectrum._compute_spectra(self, data, fmin, fmax, n_jobs, method_kw, verbose)
    443 def _compute_spectra(self, data, fmin, fmax, n_jobs, method_kw, verbose):
    444     # make the spectra
--> 445     result = self._psd_func(
    446         data, self.sfreq, fmin=fmin, fmax=fmax, n_jobs=n_jobs, verbose=verbose
    447     )
    448     # assign ._data ._freqs, ._shape
    449     psds, freqs = result

File <decorator-gen-5>:12, in psd_array_welch(x, sfreq, fmin, fmax, n_fft, n_overlap, n_per_seg, n_jobs, average, window, remove_dc, output, verbose)

File ~/anaconda3/envs/local_sns013/lib/python3.12/site-packages/mne/time_frequency/psd.py:272, in psd_array_welch(x, sfreq, fmin, fmax, n_fft, n_overlap, n_per_seg, n_jobs, average, window, remove_dc, output, verbose)
    270     agg_func = np.concatenate
    271     func = _func
--> 272 f_spect = parallel(
    273     my_spect_func(d, func=func, freq_sl=freq_sl, average=average, output=output)
    274     for d in x_splits
    275 )
    276 psds = agg_func(f_spect, axis=0)
    277 shape = dshape + (len(freqs),)

File ~/anaconda3/envs/local_sns013/lib/python3.12/site-packages/mne/time_frequency/psd.py:273, in <genexpr>(.0)
    270     agg_func = np.concatenate
    271     func = _func
    272 f_spect = parallel(
--> 273     my_spect_func(d, func=func, freq_sl=freq_sl, average=average, output=output)
    274     for d in x_splits
    275 )
    276 psds = agg_func(f_spect, axis=0)
    277 shape = dshape + (len(freqs),)

File ~/anaconda3/envs/local_sns013/lib/python3.12/site-packages/mne/time_frequency/psd.py:75, in _spect_func(epoch, func, freq_sl, average, output)
     73     spect = np.apply_along_axis(_decomp_aggregate_mask, -1, epoch, **kwargs)
     74 else:
---> 75     spect = _decomp_aggregate_mask(epoch, **kwargs)
     76 return spect

File ~/anaconda3/envs/local_sns013/lib/python3.12/site-packages/mne/time_frequency/psd.py:52, in _decomp_aggregate_mask(epoch, func, average, freq_sl)
     51 def _decomp_aggregate_mask(epoch, func, average, freq_sl):
---> 52     _, _, spect = func(epoch)
     53     spect = spect[..., freq_sl, :]
     54     # Do the averaging here (per epoch) to save memory

File ~/anaconda3/envs/local_sns013/lib/python3.12/site-packages/mne/time_frequency/psd.py:266, in psd_array_welch.<locals>.func(*args, **kwargs)
    259 with warnings.catch_warnings():
    260     warnings.filterwarnings(
    261         action="ignore",
    262         module="scipy",
    263         category=UserWarning,
    264         message=r"nperseg = \d+ is greater than input length",
    265     )
--> 266     return _func(*args, **kwargs)

File ~/anaconda3/envs/local_sns013/lib/python3.12/site-packages/scipy/signal/_spectral_py.py:783, in spectrogram(x, fs, window, nperseg, noverlap, nfft, detrend, return_onesided, scaling, axis, mode)
    780     noverlap = nperseg // 8
    782 if mode == 'psd':
--> 783     freqs, time, Sxx = _spectral_helper(x, x, fs, window, nperseg,
    784                                         noverlap, nfft, detrend,
    785                                         return_onesided, scaling, axis,
    786                                         mode='psd')
    788 else:
    789     freqs, time, Sxx = _spectral_helper(x, x, fs, window, nperseg,
    790                                         noverlap, nfft, detrend,
    791                                         return_onesided, scaling, axis,
    792                                         mode='stft')

File ~/anaconda3/envs/local_sns013/lib/python3.12/site-packages/scipy/signal/_spectral_py.py:1851, in _spectral_helper(x, y, fs, window, nperseg, noverlap, nfft, detrend, return_onesided, scaling, axis, mode, boundary, padded)
   1849     noverlap = int(noverlap)
   1850 if noverlap >= nperseg:
-> 1851     raise ValueError('noverlap must be less than nperseg.')
   1852 nstep = nperseg - noverlap
   1854 # Padding occurs after boundary extension, so that the extended signal ends
   1855 # in zeros, instead of introducing an impulse at the end.
   1856 # I.e. if x = [..., 3, 2]
   1857 # extend then pad -> [..., 3, 2, 2, 3, 0, 0, 0]
   1858 # pad then extend -> [..., 3, 2, 0, 0, 0, 2, 3]

ValueError: noverlap must be less than nperseg.