D0100, 0102, and 0103 line noise filtering fails
jimzhang629 opened this issue · comments
I ran the line noise filtering for everyone again, but D0100, 0102, and 0103 failed. This is the error message for D0100, but it’s similar for the other two. There seem to be channels missing..?
Extracting EDF parameters from C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_acq-01_run-02_ieeg.edf...
EDF file detected
Setting channel info structure...
Creating raw.info structure...
Output is truncated. View as a scrollable element or open in a text editor. Adjust cell output settings...
C:\Users\jz421\Desktop\GlobalLocal\IEEG_Pipelines\ieeg\io.py:113: RuntimeWarning: The number of channels in the channels.tsv sidecar file (231) does not match the number of channels in the raw data file (244). Will not try to set channel names.
new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)
C:\Users\jz421\Desktop\GlobalLocal\IEEG_Pipelines\ieeg\io.py:113: RuntimeWarning: The unit for channel(s) Trigger has changed from NA to V.
new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)
C:\Users\jz421\Desktop\GlobalLocal\IEEG_Pipelines\ieeg\io.py:113: RuntimeWarning: DigMontage is only a subset of info. There are 13 channel positions not present in the DigMontage. The channels missing from the montage are:
['P4', 'FP1', 'F7', 'F3', 'C3', 'T5', 'P3', 'O1', 'T3', 'C4', 'T4', 'T6', 'O2'].
Consider using inst.rename_channels to match the montage nomenclature, or inst.set_channel_types if these are not EEG channels, or use the on_missing parameter if the channel positions are allowed to be unknown in your analyses.
new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)
C:\Users\jz421\Desktop\GlobalLocal\IEEG_Pipelines\ieeg\io.py:113: RuntimeWarning: participants.tsv file not found for C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_acq-01_run-01_ieeg.edf
new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)
Reading events from C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_acq-01_run-02_events.tsv.
Reading channel info from C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_channels.tsv.
Reading electrode coords from C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\sub-D0100\ieeg\sub-D0100_space-ACPC_electrodes.tsv.
Extracting EDF parameters from C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_acq-01_run-03_ieeg.edf...
EDF file detected
Setting channel info structure...
Creating raw.info structure...
C:\Users\jz421\Desktop\GlobalLocal\IEEG_Pipelines\ieeg\io.py:113: RuntimeWarning: The number of channels in the channels.tsv sidecar file (231) does not match the number of channels in the raw data file (244). Will not try to set channel names.
new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)
C:\Users\jz421\Desktop\GlobalLocal\IEEG_Pipelines\ieeg\io.py:113: RuntimeWarning: The unit for channel(s) Trigger has changed from NA to V.
new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)
C:\Users\jz421\Desktop\GlobalLocal\IEEG_Pipelines\ieeg\io.py:113: RuntimeWarning: DigMontage is only a subset of info. There are 13 channel positions not present in the DigMontage. The channels missing from the montage are:
['P4', 'FP1', 'F7', 'F3', 'C3', 'T5', 'P3', 'O1', 'T3', 'C4', 'T4', 'T6', 'O2'].
Consider using inst.rename_channels to match the montage nomenclature, or inst.set_channel_types if these are not EEG channels, or use the on_missing parameter if the channel positions are allowed to be unknown in your analyses.
new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)
C:\Users\jz421\Desktop\GlobalLocal\IEEG_Pipelines\ieeg\io.py:113: RuntimeWarning: participants.tsv file not found for C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_acq-01_run-02_ieeg.edf
new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)
Reading events from C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_acq-01_run-03_events.tsv.
Reading channel info from C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_channels.tsv.
Reading electrode coords from C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\sub-D0100\ieeg\sub-D0100_space-ACPC_electrodes.tsv.
Extracting EDF parameters from C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_acq-01_run-04_ieeg.edf...
EDF file detected
Setting channel info structure...
Creating raw.info structure...
C:\Users\jz421\Desktop\GlobalLocal\IEEG_Pipelines\ieeg\io.py:113: RuntimeWarning: The number of channels in the channels.tsv sidecar file (231) does not match the number of channels in the raw data file (244). Will not try to set channel names.
new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)
C:\Users\jz421\Desktop\GlobalLocal\IEEG_Pipelines\ieeg\io.py:113: RuntimeWarning: The unit for channel(s) Trigger has changed from NA to V.
new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)
C:\Users\jz421\Desktop\GlobalLocal\IEEG_Pipelines\ieeg\io.py:113: RuntimeWarning: DigMontage is only a subset of info. There are 13 channel positions not present in the DigMontage. The channels missing from the montage are:
['P4', 'FP1', 'F7', 'F3', 'C3', 'T5', 'P3', 'O1', 'T3', 'C4', 'T4', 'T6', 'O2'].
Consider using inst.rename_channels to match the montage nomenclature, or inst.set_channel_types if these are not EEG channels, or use the on_missing parameter if the channel positions are allowed to be unknown in your analyses.
new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)
C:\Users\jz421\Desktop\GlobalLocal\IEEG_Pipelines\ieeg\io.py:113: RuntimeWarning: participants.tsv file not found for C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_acq-01_run-03_ieeg.edf
new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)
Reading events from C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_acq-01_run-04_events.tsv.
Reading channel info from C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_channels.tsv.
Reading electrode coords from C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\sub-D0100\ieeg\sub-D0100_space-ACPC_electrodes.tsv.
Reading 0 ... 6496255 = 0.000 ... 3172.000 secs...
C:\Users\jz421\Desktop\GlobalLocal\IEEG_Pipelines\ieeg\io.py:113: RuntimeWarning: The number of channels in the channels.tsv sidecar file (231) does not match the number of channels in the raw data file (244). Will not try to set channel names.
new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)
C:\Users\jz421\Desktop\GlobalLocal\IEEG_Pipelines\ieeg\io.py:113: RuntimeWarning: The unit for channel(s) Trigger has changed from NA to V.
new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)
C:\Users\jz421\Desktop\GlobalLocal\IEEG_Pipelines\ieeg\io.py:113: RuntimeWarning: DigMontage is only a subset of info. There are 13 channel positions not present in the DigMontage. The channels missing from the montage are:
['P4', 'FP1', 'F7', 'F3', 'C3', 'T5', 'P3', 'O1', 'T3', 'C4', 'T4', 'T6', 'O2'].
Consider using inst.rename_channels to match the montage nomenclature, or inst.set_channel_types if these are not EEG channels, or use the on_missing parameter if the channel positions are allowed to be unknown in your analyses.
new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)
C:\Users\jz421\Desktop\GlobalLocal\IEEG_Pipelines\ieeg\io.py:113: RuntimeWarning: participants.tsv file not found for C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_acq-01_run-04_ieeg.edf
new_raw = read_raw_bids(bids_path=BIDS_path, verbose=verbose)
[Parallel(n_jobs=6)]: Using backend LokyBackend with 6 concurrent workers.
[Parallel(n_jobs=6)]: Done 1 tasks | elapsed: 32.8s
[Parallel(n_jobs=6)]: Done 2 tasks | elapsed: 32.9s
[Parallel(n_jobs=6)]: Done 3 tasks | elapsed: 33.1s
[Parallel(n_jobs=6)]: Done 4 tasks | elapsed: 33.3s
[Parallel(n_jobs=6)]: Done 5 tasks | elapsed: 33.4s
[Parallel(n_jobs=6)]: Done 6 tasks | elapsed: 33.5s
[Parallel(n_jobs=6)]: Done 7 tasks | elapsed: 47.9s
[Parallel(n_jobs=6)]: Done 8 tasks | elapsed: 48.3s
[Parallel(n_jobs=6)]: Done 9 tasks | elapsed: 48.4s
[Parallel(n_jobs=6)]: Done 10 tasks | elapsed: 48.5s
[Parallel(n_jobs=6)]: Done 11 tasks | elapsed: 48.6s
[Parallel(n_jobs=6)]: Done 12 tasks | elapsed: 48.7s
...
[Parallel(n_jobs=6)]: Done 231 tasks | elapsed: 10.4min
[Parallel(n_jobs=6)]: Done 232 tasks | elapsed: 10.5min
[Parallel(n_jobs=6)]: Done 239 out of 243 | elapsed: 10.7min remaining: 10.7s
[Parallel(n_jobs=6)]: Done 243 out of 243 | elapsed: 10.9min finished
Output is truncated. View as a scrollable element or open in a text editor. Adjust cell output settings...
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\participants.tsv'...
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\participants.json'...
Writing 'C:/Users/jz421/Box/CoganLab/BIDS-1.1_GlobalLocal/BIDS/derivatives/clean/sub-D0100/ieeg/sub-D0100_acq-01_space-ACPC_electrodes.tsv'...
Writing 'C:/Users/jz421/Box/CoganLab/BIDS-1.1_GlobalLocal/BIDS/derivatives/clean/sub-D0100/ieeg/sub-D0100_acq-01_space-ACPC_coordsystem.json'...
The provided raw data contains annotations, but you did not pass an "event_id" mapping from annotation descriptions to event codes. We will generate arbitrary event codes. To specify custom event codes, please pass "event_id".
Used Annotations descriptions: ['BAD boundary', 'EDGE boundary', 'Response/c75/r75', 'Response/c75/s75', 'Response/i75/n75', 'Response/i75/r75', 'Response/i75/s75', 'Stimulus/c75/r75', 'Stimulus/c75/s75', 'Stimulus/i75/n75', 'Stimulus/i75/r75', 'Stimulus/i75/s75']
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_acq-01_run-01_desc-clean_events.tsv'...
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_acq-01_run-01_desc-clean_events.json'...
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\dataset_description.json'...
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_acq-01_run-01_desc-clean_ieeg.json'...
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_acq-01_run-01_desc-clean_channels.tsv'...
Copying data files to sub-D0100_task-GlobalLocal_acq-01_run-01_desc-clean_ieeg.edf
C:\Users\jz421\Desktop\GlobalLocal\IEEG_Pipelines\ieeg\io.py:242: RuntimeWarning: Converting data files to EDF format
write_raw_bids(run, bids_path, allow_preload=True, format=format,
C:\Users\jz421\Desktop\GlobalLocal\IEEG_Pipelines\ieeg\io.py:242: RuntimeWarning: EDF format requires equal-length data blocks, so 0.99951171875 seconds of zeros were appended to all channels when writing the final block.
write_raw_bids(run, bids_path, allow_preload=True, format=format,
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\sub-D0100\sub-D0100_scans.tsv'...
Wrote C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\sub-D0100\sub-D0100_scans.tsv entry with ieeg\sub-D0100_task-GlobalLocal_acq-01_run-01_desc-clean_ieeg.edf.
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\participants.tsv'...
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\participants.json'...
Writing 'C:/Users/jz421/Box/CoganLab/BIDS-1.1_GlobalLocal/BIDS/derivatives/clean/sub-D0100/ieeg/sub-D0100_acq-01_space-ACPC_electrodes.tsv'...
Writing 'C:/Users/jz421/Box/CoganLab/BIDS-1.1_GlobalLocal/BIDS/derivatives/clean/sub-D0100/ieeg/sub-D0100_acq-01_space-ACPC_coordsystem.json'...
The provided raw data contains annotations, but you did not pass an "event_id" mapping from annotation descriptions to event codes. We will generate arbitrary event codes. To specify custom event codes, please pass "event_id".
Used Annotations descriptions: ['BAD boundary', 'EDGE boundary', 'Response/c25/r25', 'Response/c25/s25', 'Response/i25/n25', 'Response/i25/r25', 'Response/i25/s25', 'Stimulus/c25/r25', 'Stimulus/c25/s25', 'Stimulus/i25/n25', 'Stimulus/i25/r25', 'Stimulus/i25/s25']
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_acq-01_run-02_desc-clean_events.tsv'...
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_acq-01_run-02_desc-clean_events.json'...
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\dataset_description.json'...
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_acq-01_run-02_desc-clean_ieeg.json'...
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_acq-01_run-02_desc-clean_channels.tsv'...
Copying data files to sub-D0100_task-GlobalLocal_acq-01_run-02_desc-clean_ieeg.edf
C:\Users\jz421\Desktop\GlobalLocal\IEEG_Pipelines\ieeg\io.py:242: RuntimeWarning: Converting data files to EDF format
write_raw_bids(run, bids_path, allow_preload=True, format=format,
C:\Users\jz421\Desktop\GlobalLocal\IEEG_Pipelines\ieeg\io.py:242: RuntimeWarning: EDF format requires equal-length data blocks, so 0.99951171875 seconds of zeros were appended to all channels when writing the final block.
write_raw_bids(run, bids_path, allow_preload=True, format=format,
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\sub-D0100\sub-D0100_scans.tsv'...
Wrote C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\sub-D0100\sub-D0100_scans.tsv entry with ieeg\sub-D0100_task-GlobalLocal_acq-01_run-02_desc-clean_ieeg.edf.
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\participants.tsv'...
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\participants.json'...
Writing 'C:/Users/jz421/Box/CoganLab/BIDS-1.1_GlobalLocal/BIDS/derivatives/clean/sub-D0100/ieeg/sub-D0100_acq-01_space-ACPC_electrodes.tsv'...
Writing 'C:/Users/jz421/Box/CoganLab/BIDS-1.1_GlobalLocal/BIDS/derivatives/clean/sub-D0100/ieeg/sub-D0100_acq-01_space-ACPC_coordsystem.json'...
The provided raw data contains annotations, but you did not pass an "event_id" mapping from annotation descriptions to event codes. We will generate arbitrary event codes. To specify custom event codes, please pass "event_id".
Used Annotations descriptions: ['BAD boundary', 'EDGE boundary', 'Response/c75/r25', 'Response/c75/s25', 'Response/i75/n25', 'Response/i75/r25', 'Response/i75/s25', 'Stimulus/c75/r25', 'Stimulus/c75/s25', 'Stimulus/i75/n25', 'Stimulus/i75/r25', 'Stimulus/i75/s25']
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_acq-01_run-03_desc-clean_events.tsv'...
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_acq-01_run-03_desc-clean_events.json'...
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\dataset_description.json'...
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_acq-01_run-03_desc-clean_ieeg.json'...
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_acq-01_run-03_desc-clean_channels.tsv'...
Copying data files to sub-D0100_task-GlobalLocal_acq-01_run-03_desc-clean_ieeg.edf
C:\Users\jz421\Desktop\GlobalLocal\IEEG_Pipelines\ieeg\io.py:242: RuntimeWarning: Converting data files to EDF format
write_raw_bids(run, bids_path, allow_preload=True, format=format,
C:\Users\jz421\Desktop\GlobalLocal\IEEG_Pipelines\ieeg\io.py:242: RuntimeWarning: EDF format requires equal-length data blocks, so 0.99951171875 seconds of zeros were appended to all channels when writing the final block.
write_raw_bids(run, bids_path, allow_preload=True, format=format,
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\sub-D0100\sub-D0100_scans.tsv'...
Wrote C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\sub-D0100\sub-D0100_scans.tsv entry with ieeg\sub-D0100_task-GlobalLocal_acq-01_run-03_desc-clean_ieeg.edf.
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\participants.tsv'...
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\participants.json'...
Writing 'C:/Users/jz421/Box/CoganLab/BIDS-1.1_GlobalLocal/BIDS/derivatives/clean/sub-D0100/ieeg/sub-D0100_acq-01_space-ACPC_electrodes.tsv'...
Writing 'C:/Users/jz421/Box/CoganLab/BIDS-1.1_GlobalLocal/BIDS/derivatives/clean/sub-D0100/ieeg/sub-D0100_acq-01_space-ACPC_coordsystem.json'...
The provided raw data contains annotations, but you did not pass an "event_id" mapping from annotation descriptions to event codes. We will generate arbitrary event codes. To specify custom event codes, please pass "event_id".
Used Annotations descriptions: ['BAD boundary', 'EDGE boundary', 'Response/c25/n75', 'Response/c25/r75', 'Response/c25/s75', 'Response/i25/r75', 'Response/i25/s75', 'Stimulus/c25/n75', 'Stimulus/c25/r75', 'Stimulus/c25/s75', 'Stimulus/i25/r75', 'Stimulus/i25/s75']
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_acq-01_run-04_desc-clean_events.tsv'...
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_acq-01_run-04_desc-clean_events.json'...
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\dataset_description.json'...
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_acq-01_run-04_desc-clean_ieeg.json'...
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\sub-D0100\ieeg\sub-D0100_task-GlobalLocal_acq-01_run-04_desc-clean_channels.tsv'...
Copying data files to sub-D0100_task-GlobalLocal_acq-01_run-04_desc-clean_ieeg.edf
C:\Users\jz421\Desktop\GlobalLocal\IEEG_Pipelines\ieeg\io.py:242: RuntimeWarning: Converting data files to EDF format
write_raw_bids(run, bids_path, allow_preload=True, format=format,
Writing 'C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\sub-D0100\sub-D0100_scans.tsv'...
Wrote C:\Users\jz421\Box\CoganLab\BIDS-1.1_GlobalLocal\BIDS\derivatives\clean\sub-D0100\sub-D0100_scans.tsv entry with ieeg\sub-D0100_task-GlobalLocal_acq-01_run-04_desc-clean_ieeg.edf.
outlier round 1 channels: ['LTPS8']
outlier round 1 channels: ['LTPS8', 'FP1']
outlier round 1 channels: ['LTPS8', 'FP1', 'C4']
outlier round 1 channels: ['LTPS8', 'FP1', 'C4', 'T4']
outlier round 1 channels: ['LTPS8', 'FP1', 'C4', 'T4', 'O2']
outlier round 2 channels: ['LTPS8', 'FP1', 'C4', 'T4', 'O2', 'LTMM1']
outlier round 2 channels: ['LTPS8', 'FP1', 'C4', 'T4', 'O2', 'LTMM1', 'F7']
outlier round 2 channels: ['LTPS8', 'FP1', 'C4', 'T4', 'O2', 'LTMM1', 'F7', 'C3']
No "status" column found in input file. Creating.
No "status_description" column found in input file. Creating.
Processing channel LTPS8:
status: bad
description: outlier round 1 more than 3 SDs above mean
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[6], line 91
60 # %%
61 # plot the data before and after filtering
62 # figure_compare([raw, filt],
(...)
87
88 # save the data
89 save_derivative(filt, layout, "clean", True)
---> 91 channel_outlier_marker(filt, 3, 2, save=True) #uhh try this again
93 # filt.info['bads'] += channel_outlier_marker(filt, 3, 2, save=True)
File <decorator-gen-452>:10, in channel_outlier_marker(input_raw, outlier_sd, max_rounds, axis, save, verbose)
File ~\Desktop\GlobalLocal\IEEG_Pipelines\ieeg\navigate.py:155, in channel_outlier_marker(input_raw, outlier_sd, max_rounds, axis, save, verbose)
152 raise ValueError("Raw instance must have filenames attribute to "
153 "save bad channels")
154 for file in tmp.filenames:
--> 155 update(file, bads, desc)
157 return bads
File c:\Users\jz421\AppData\Local\anaconda3\envs\ieeg\Lib\functools.py:909, in singledispatch.<locals>.wrapper(*args, **kw)
905 if not args:
906 raise TypeError(f'{funcname} requires at least '
...
2573 f" status: bad\n"
2574 f" description: {description}"
2575 )
ValueError: Channel FP1 not found in dataset!