py-neuromodulation 0.0.2__py3-none-any.whl → 0.0.3__py3-none-any.whl

py_neuromodulation/data/derivatives/sub-testsub_ses-EphysMedOff_task-gripforce_run-0/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_SETTINGS.json

@@ -1,273 +0,0 @@
-{
-    "sampling_rate_features_hz": 10,
-    "segment_length_features_ms": 1000,
-    "preprocessing": [
-        "raw_resampling",
-        "notch_filter",
-        "re_referencing"
-    ],
-    "documentation_preprocessing_options": [
-        "raw_resampling",
-        "notch_filter",
-        "re_referencing",
-        "raw_normalization"
-    ],
-    "features": {
-        "raw_hjorth": false,
-        "return_raw": false,
-        "bandpass_filter": false,
-        "stft": false,
-        "fft": true,
-        "sharpwave_analysis": false,
-        "fooof": false,
-        "bursts": false,
-        "linelength": false,
-        "coherence": false,
-        "nolds": false,
-        "mne_connectivity": false
-    },
-    "postprocessing": {
-        "feature_normalization": true,
-        "project_cortex": false,
-        "project_subcortex": false
-    },
-    "raw_resampling_settings": {
-        "resample_freq_hz": 1000
-    },
-    "documentation_normalization_options": [
-        "mean",
-        "median",
-        "zscore",
-        "zscore-median",
-        "quantile",
-        "power",
-        "robust",
-        "minmax"
-    ],
-    "raw_normalization_settings": {
-        "normalization_time_s": 30,
-        "normalization_method": "zscore",
-        "clip": 3
-    },
-    "feature_normalization_settings": {
-        "normalization_time_s": 30,
-        "normalization_method": "zscore",
-        "clip": 3
-    },
-    "frequency_ranges_hz": {
-        "theta": [
-            4,
-            8
-        ],
-        "alpha": [
-            8,
-            12
-        ],
-        "low beta": [
-            13,
-            20
-        ],
-        "high beta": [
-            20,
-            35
-        ],
-        "low gamma": [
-            60,
-            80
-        ],
-        "high gamma": [
-            90,
-            200
-        ],
-        "HFA": [
-            200,
-            400
-        ]
-    },
-    "fft_settings": {
-        "windowlength_ms": 1000,
-        "log_transform": true,
-        "kalman_filter": false
-    },
-    "stft_settings": {
-        "windowlength_ms": 500,
-        "log_transform": true,
-        "kalman_filter": false
-    },
-    "bandpass_filter_settings": {
-        "segment_lengths_ms": {
-            "theta": 1000,
-            "alpha": 500,
-            "low beta": 333,
-            "high beta": 333,
-            "low gamma": 100,
-            "high gamma": 100,
-            "HFA": 100
-        },
-        "bandpower_features": {
-            "activity": true,
-            "mobility": false,
-            "complexity": false
-        },
-        "log_transform": true,
-        "kalman_filter": false
-    },
-    "kalman_filter_settings": {
-        "Tp": 0.1,
-        "sigma_w": 0.7,
-        "sigma_v": 1,
-        "frequency_bands": [
-            "theta",
-            "alpha",
-            "low beta",
-            "high beta",
-            "low gamma",
-            "high gamma",
-            "HFA"
-        ]
-    },
-    "burst_settings": {
-        "threshold": 75,
-        "time_duration_s": 30,
-        "frequency_bands": [
-            "low beta",
-            "high beta",
-            "low gamma"
-        ],
-        "burst_features": {
-            "duration": true,
-            "amplitude": true,
-            "burst_rate_per_s": true,
-            "in_burst": true
-        }
-    },
-    "sharpwave_analysis_settings": {
-        "sharpwave_features": {
-            "peak_left": true,
-            "peak_right": true,
-            "trough": true,
-            "width": true,
-            "prominence": true,
-            "interval": true,
-            "decay_time": true,
-            "rise_time": true,
-            "sharpness": true,
-            "rise_steepness": true,
-            "decay_steepness": true,
-            "slope_ratio": true
-        },
-        "filter_ranges_hz": [
-            [
-                5,
-                80
-            ],
-            [
-                5,
-                30
-            ]
-        ],
-        "detect_troughs": {
-            "estimate": true,
-            "distance_troughs_ms": 10,
-            "distance_peaks_ms": 5
-        },
-        "detect_peaks": {
-            "estimate": true,
-            "distance_troughs_ms": 5,
-            "distance_peaks_ms": 10
-        },
-        "estimator": {
-            "mean": [
-                "peak_left",
-                "peak_right",
-                "trough",
-                "width",
-                "prominence",
-                "interval",
-                "decay_time",
-                "rise_time",
-                "sharpness",
-                "rise_steepness",
-                "decay_steepness",
-                "slope_ratio"
-            ],
-            "median": null,
-            "max": [
-                "prominence",
-                "sharpness"
-            ],
-            "min": null,
-            "var": null
-        },
-        "apply_estimator_between_peaks_and_troughs": true
-    },
-    "project_cortex_settings": {
-        "max_dist_mm": 20
-    },
-    "project_subcortex_settings": {
-        "max_dist_mm": 5
-    },
-    "coherence": {
-        "channels": [
-            [
-                "LFP_RIGHT_0",
-                "ECOG_RIGHT_0"
-            ]
-        ],
-        "frequency_bands": [
-            "high beta",
-            "low gamma"
-        ],
-        "features": {
-            "mean_fband": true,
-            "max_fband": true,
-            "max_allfbands": true
-        },
-        "method": {
-            "coh": true,
-            "icoh": true
-        }
-    },
-    "fooof": {
-        "aperiodic": {
-            "exponent": true,
-            "offset": true,
-            "knee": true
-        },
-        "periodic": {
-            "center_frequency": false,
-            "band_width": false,
-            "height_over_ap": false
-        },
-        "windowlength_ms": 800,
-        "peak_width_limits": [
-            0.5,
-            12
-        ],
-        "max_n_peaks": 3,
-        "min_peak_height": 0,
-        "peak_threshold": 2,
-        "freq_range_hz": [
-            2,
-            40
-        ],
-        "knee": true
-    },
-    "nolds_features": {
-        "sample_entropy": false,
-        "correlation_dimension": false,
-        "lyapunov_exponent": true,
-        "hurst_exponent": false,
-        "detrended_fluctutaion_analysis": false,
-        "data": {
-            "raw": true,
-            "frequency_bands": [
-                "low beta"
-            ]
-        }
-    },
-    "mne_connectiviy": {
-        "method": "plv",
-        "mode": "multitaper"
-    }
-}

py_neuromodulation/data/derivatives/sub-testsub_ses-EphysMedOff_task-gripforce_run-0/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_SIDECAR.json

@@ -1,6 +0,0 @@
-{
-    "original_fs": 1000.0,
-    "final_fs": 1000,
-    "sfreq": 10,
-    "sess_right": null
-}

py_neuromodulation/data/derivatives/sub-testsub_ses-EphysMedOff_task-gripforce_run-0/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_nm_channels.csv

@@ -1,11 +0,0 @@
-,name,rereference,used,target,type,status,new_name
-0,LFP_RIGHT_0,LFP_RIGHT_2,1,0,dbs,good,LFP_RIGHT_0-LFP_RIGHT_2
-1,LFP_RIGHT_1,LFP_RIGHT_0,1,0,dbs,good,LFP_RIGHT_1-LFP_RIGHT_0
-2,LFP_RIGHT_2,LFP_RIGHT_1,1,0,dbs,good,LFP_RIGHT_2-LFP_RIGHT_1
-3,ECOG_RIGHT_0,average,1,0,ecog,good,ECOG_RIGHT_0-avgref
-4,ECOG_RIGHT_1,average,1,0,ecog,good,ECOG_RIGHT_1-avgref
-5,ECOG_RIGHT_2,average,1,0,ecog,good,ECOG_RIGHT_2-avgref
-6,ECOG_RIGHT_3,average,1,0,ecog,good,ECOG_RIGHT_3-avgref
-7,ECOG_RIGHT_4,average,1,0,ecog,good,ECOG_RIGHT_4-avgref
-8,ECOG_RIGHT_5,average,1,0,ecog,good,ECOG_RIGHT_5-avgref
-9,MOV_RIGHT,None,0,1,misc,good,MOV_RIGHT

py_neuromodulation/data/participants.json

@@ -1,32 +0,0 @@
-{
-    "participant_id": {
-        "Description": "Unique participant identifier"
-    },
-    "age": {
-        "Description": "Age of the participant at time of testing",
-        "Units": "years"
-    },
-    "sex": {
-        "Description": "Biological sex of the participant",
-        "Levels": {
-            "F": "female",
-            "M": "male"
-        }
-    },
-    "hand": {
-        "Description": "Handedness of the participant",
-        "Levels": {
-            "R": "right",
-            "L": "left",
-            "A": "ambidextrous"
-        }
-    },
-    "weight": {
-        "Description": "Body weight of the participant",
-        "Units": "kg"
-    },
-    "height": {
-        "Description": "Body height of the participant",
-        "Units": "m"
-    }
-}

py_neuromodulation/data/participants.tsv

@@ -1,2 +0,0 @@
-participant_id	age	sex	hand	weight	height
-sub-testsub	n/a	n/a	n/a	n/a	n/a

py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_space-mni_coordsystem.json

@@ -1,5 +0,0 @@
-{
-    "iEEGCoordinateSystem": "Other",
-    "iEEGCoordinateSystemDescription": "n/a",
-    "iEEGCoordinateUnits": "m"
-}

py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_space-mni_electrodes.tsv

@@ -1,11 +0,0 @@
-name	x	y	z	size	impedance
-LFP_RIGHT_0	0.0118280802308701	-0.0151597482742092	-0.00776909845640809	n/a	n/a
-LFP_RIGHT_1	0.0123908351968705	-0.0142925082817827	-0.0059367986990887	n/a	n/a
-LFP_RIGHT_2	0.012930849148285701	-0.0134128499400548	-0.00409165661961333	n/a	n/a
-ECOG_RIGHT_0	0.037318173999999996	-0.048610126639999994	0.06179765474	n/a	n/a
-ECOG_RIGHT_1	0.0401598943	-0.037315929830000004	0.06431171618	n/a	n/a
-ECOG_RIGHT_2	0.040943035780000005	-0.02721778456	0.06409518407999999	n/a	n/a
-ECOG_RIGHT_3	0.03978395522	-0.01700523081	0.06386618136	n/a	n/a
-ECOG_RIGHT_4	0.03968813641	-0.005528024572	0.06168254254	n/a	n/a
-ECOG_RIGHT_5	0.03751915924	0.004304913414	0.060541263549999995	n/a	n/a
-MOV_RIGHT	n/a	n/a	n/a	n/a	n/a

py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_channels.tsv

@@ -1,11 +0,0 @@
-name	type	units	low_cutoff	high_cutoff	description	sampling_frequency	status	status_description
-LFP_RIGHT_0	DBS	µV	0.0	500.0	Deep Brain Stimulation	1000.0	good	n/a
-LFP_RIGHT_1	DBS	µV	0.0	500.0	Deep Brain Stimulation	1000.0	good	n/a
-LFP_RIGHT_2	DBS	µV	0.0	500.0	Deep Brain Stimulation	1000.0	good	n/a
-ECOG_RIGHT_0	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
-ECOG_RIGHT_1	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
-ECOG_RIGHT_2	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
-ECOG_RIGHT_3	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
-ECOG_RIGHT_4	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
-ECOG_RIGHT_5	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
-MOV_RIGHT	MISC	µV	0.0	500.0	Miscellaneous	1000.0	good	n/a

py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.json

@@ -1,18 +0,0 @@
-{
-    "TaskName": "gripforce",
-    "Manufacturer": "Brain Products",
-    "PowerLineFrequency": 60.0,
-    "SamplingFrequency": 1000.0,
-    "SoftwareFilters": "n/a",
-    "RecordingDuration": 19.0,
-    "RecordingType": "continuous",
-    "iEEGReference": "n/a",
-    "ECOGChannelCount": 6,
-    "SEEGChannelCount": 3,
-    "EEGChannelCount": 0,
-    "EOGChannelCount": 0,
-    "ECGChannelCount": 0,
-    "EMGChannelCount": 0,
-    "MiscChannelCount": 1,
-    "TriggerChannelCount": 0
-}

py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.vhdr

@@ -1,35 +0,0 @@
-Brain Vision Data Exchange Header File Version 1.0
-; Written using pybv 0.7.5
-
-[Common Infos]
-Codepage=UTF-8
-DataFile=sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.eeg
-MarkerFile=sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.vmrk
-DataFormat=BINARY
-; Data orientation: MULTIPLEXED=ch1,pt1, ch2,pt1 ...
-DataOrientation=MULTIPLEXED
-NumberOfChannels=10
-; Sampling interval in microseconds
-SamplingInterval=1000.0
-
-[Binary Infos]
-BinaryFormat=IEEE_FLOAT_32
-
-[Channel Infos]
-; Each entry: Ch<Channel number>=<Name>,<Reference channel name>,
-; <Resolution in "Unit">,<Unit>, Future extensions..
-; Fields are delimited by commas, some fields might be omitted (empty).
-; Commas in channel names are coded as "\1".
-Ch1=LFP_RIGHT_0,,0.1,µV
-Ch2=LFP_RIGHT_1,,0.1,µV
-Ch3=LFP_RIGHT_2,,0.1,µV
-Ch4=ECOG_RIGHT_0,,0.1,µV
-Ch5=ECOG_RIGHT_1,,0.1,µV
-Ch6=ECOG_RIGHT_2,,0.1,µV
-Ch7=ECOG_RIGHT_3,,0.1,µV
-Ch8=ECOG_RIGHT_4,,0.1,µV
-Ch9=ECOG_RIGHT_5,,0.1,µV
-Ch10=MOV_RIGHT,,0.1,µV
-
-[Comment]
-

py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.vmrk

@@ -1,13 +0,0 @@
-Brain Vision Data Exchange Marker File, Version 1.0
-; Exported using pybv 0.7.5
-
-[Common Infos]
-Codepage=UTF-8
-DataFile=sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.eeg
-
-[Marker Infos]
-; Each entry: Mk<Marker number>=<Type>,<Description>,<Position in data points>,
-;             <Size in data points>, <Channel number (0 = marker is related to all channels)>
-;             <Date (YYYYMMDDhhmmssuuuuuu)>
-; Fields are delimited by commas, some fields might be omitted (empty).
-; Commas in type or description text are coded as "\1".

py_neuromodulation/data/sub-testsub/ses-EphysMedOff/sub-testsub_ses-EphysMedOff_scans.tsv

@@ -1,2 +0,0 @@
-filename	acq_time
-ieeg/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.vhdr	n/a

py_neuromodulation/grid_cortex.tsv

@@ -1,40 +0,0 @@
-x	y	z
--13.1	-67.7	69.1
--35.5	-60.0	66.0
--48.3	-55.1	58.2
--60.0	-51.8	48.0
--16.9	-51.6	78.0
--34.8	-49.3	71.7
--67.5	-47.1	31.0
--46.1	-43.7	61.1
--59.8	-39.6	53.3
--14.2	-39.1	81.1
--28.3	-31.2	76.0
--42.3	-30.7	70.2
--67.6	-30.1	41.2
--50.5	-24.4	64.4
--14.6	-22.7	80.2
--60.9	-18.7	50.9
--31.6	-16.9	75.2
--5.1	-12.6	77.3
--65.6	-10.8	37.8
--41.8	-10.2	67.0
--55.1	-4.01	53.2
--22.7	1.2	72.0
--5.8	2.8	74.8
--49.2	3.7	54.7
--34.5	3.9	66.5
--61.55	6.2	35.9
--63.6	8.3	25.7
--40.4	11.8	60.7
--48.7	14.5	50.5
--21.8	16.0	68.9
--58.2	18.2	27.3
--7.0	18.4	70.3
--36.3	19.9	59.6
--48.1	24.6	44.0
--56.8	28.52	20.8
--7.3	33.8	61.7
--22.2	35.0	57.2
--36.8	35.4	47.0
--46.8	35.6	36.0