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Merge pull request #513 from effigies/fix/custom-columns
fix: Align column values and definitions for custom columns
2 parents 8cb9d67 + 1bbc94e commit bd8a951

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‎eeg_ds003645s_hed_demo/sub-004/ses-1/eeg/sub-004_ses-1_task-FacePerception_run-1_events.tsv‎

Lines changed: 1 addition & 1 deletion
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@@ -1,5 +1,5 @@
11
onset duration event_type face_type rep_status rep_lag trial value stim_file
2-
24.26672727 n/a show_face_initial scrambled_face first_show n/a 1 4 s107.bmp
2+
24.26672727 n/a show_face_initial scrambled_face first_show n/a 1 17 s107.bmp
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25.11309091 n/a show_circle n/a n/a n/a 1 0 circle.bmp
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25.28036364 n/a right_press n/a n/a n/a 1 4096 n/a
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26.81309091 n/a show_cross n/a n/a n/a 2 1 cross.bmp

‎eeg_ds003645s_hed_demo/task-FacePerception_events.json‎

Lines changed: 16 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -95,22 +95,22 @@
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"value": {
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"Description": "Numerical event marker",
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"Levels": {
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"x0": "Disappearance of face image and display of the inter-stimulus circle simultaneously",
99-
"x1": "Disappearance of face image and display of the inter-stimulus circle simultaneously",
100-
"x2": "Initial setup with left finger key press indicating above average symmetry",
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"x3": "Initial setup with right finger key press indicating above average symmetry",
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"x5": "Initial presentation of famous face",
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"x6": "Immediate repeated presentation of famous face",
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"x7": "Delayed repeated presentation of famous face",
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"x13": "Initial presentation of unfamiliar face",
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"x14": "Immediate repeated presentation of unfamiliar face",
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"x15": "Delayed repeated presentation of unfamiliar face",
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"x17": "Initial presentation of scrambled face",
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"x18": "Immediate repeated presentation of scrambled face",
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"x19": "Delayed repeated presentation of scrambled face",
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"x256": "Left finger key press",
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"x4096": "Right finger key press",
113-
"x4352": "Left and right finger key presses"
98+
"0": "Disappearance of face image and display of the inter-stimulus circle simultaneously",
99+
"1": "Disappearance of face image and display of the inter-stimulus circle simultaneously",
100+
"2": "Initial setup with left finger key press indicating above average symmetry",
101+
"3": "Initial setup with right finger key press indicating above average symmetry",
102+
"5": "Initial presentation of famous face",
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"6": "Immediate repeated presentation of famous face",
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"7": "Delayed repeated presentation of famous face",
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"13": "Initial presentation of unfamiliar face",
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"14": "Immediate repeated presentation of unfamiliar face",
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"15": "Delayed repeated presentation of unfamiliar face",
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"17": "Initial presentation of scrambled face",
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"18": "Immediate repeated presentation of scrambled face",
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"19": "Delayed repeated presentation of scrambled face",
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"256": "Left finger key press",
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"4096": "Right finger key press",
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"4352": "Left and right finger key presses"
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}
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}
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}

‎eeg_ds003645s_hed_library/task-FacePerception_events.json‎

Lines changed: 20 additions & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -107,31 +107,30 @@
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}
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},
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"hed_def_setup": {
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"Description": "Metadata dictionary for gathering setup definitions",
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"HED": {
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"setup_def": "(Definition/Initialize-recording, (Recording))"
113-
}
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110+
"Description": "Metadata dictionary for gathering setup definitions",
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"HED": {
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"setup_def": "(Definition/Initialize-recording, (Recording))"
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}
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},
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"value": {
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"Description": "Numerical event marker",
118117
"Levels": {
119-
"x0": "Disappearance of face image and display of the inter-stimulus circle simultaneously",
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"x1": "Disappearance of face image and display of the inter-stimulus circle simultaneously",
121-
"x2": "Initial setup with left finger key press indicating above average symmetry",
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"x3": "Initial setup with right finger key press indicating above average symmetry",
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"x5": "Initial presentation of famous face",
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"x6": "Immediate repeated presentation of famous face",
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"x7": "Delayed repeated presentation of famous face",
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"x13": "Initial presentation of unfamiliar face",
127-
"x14": "Immediate repeated presentation of unfamiliar face",
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"x15": "Delayed repeated presentation of unfamiliar face",
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"x17": "Initial presentation of scrambled face",
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"x18": "Immediate repeated presentation of scrambled face",
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"x19": "Delayed repeated presentation of scrambled face",
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"x256": "Left finger key press",
133-
"x4096": "Right finger key press",
134-
"x4352": "Left and right finger key presses"
118+
"0": "Disappearance of face image and display of the inter-stimulus circle simultaneously",
119+
"1": "Disappearance of face image and display of the inter-stimulus circle simultaneously",
120+
"2": "Initial setup with left finger key press indicating above average symmetry",
121+
"3": "Initial setup with right finger key press indicating above average symmetry",
122+
"5": "Initial presentation of famous face",
123+
"6": "Immediate repeated presentation of famous face",
124+
"7": "Delayed repeated presentation of famous face",
125+
"13": "Initial presentation of unfamiliar face",
126+
"14": "Immediate repeated presentation of unfamiliar face",
127+
"15": "Delayed repeated presentation of unfamiliar face",
128+
"17": "Initial presentation of scrambled face",
129+
"18": "Immediate repeated presentation of scrambled face",
130+
"19": "Delayed repeated presentation of scrambled face",
131+
"256": "Left finger key press",
132+
"4096": "Right finger key press",
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"4352": "Left and right finger key presses"
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}
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}
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}

‎fnirs_automaticity/events.json‎

Lines changed: 2 additions & 6 deletions
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@@ -31,11 +31,7 @@
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},
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"shown_stimulus": {
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"Description": "visual stimulus shown on the presentation screen",
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"Levels": {
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"white X": "small white fixation cross on the middle of the screen, indicating that the participant should relax and focus on the cross. At the beginning of a trial, a metronome sound of 1.5 Hz was played during the first 8 seconds of the white fixation cross.",
36-
"red X": "small red fixation cross in the middle of the screen, indicating that the participant should start tapping/stepping the sequence (once) during the single-task conditions",
37-
"QGCQOGCG": "random sequence of 8 letters (C, G, Q, or O) shown at random intervals (0.5-1.5 s) on the middle of the screen during the dual-task conditions. Participants needed to tap/step the sequence once, while simultaneously counting the letter G."
38-
}
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"Format": "string"
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},
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"reported_gs": {
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"Description": "Reported number of G's, as counted by the particpant during the dual-task conditions."
@@ -57,4 +53,4 @@
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"erroneous trial": "trial with more than 1 error in the performed sequence"
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}
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}
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}
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}

‎fnirs_automaticity/participants.tsv‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
participant_id sex age haircolor skincolor handedness footedness musicality comfortlevel_begin comfortlevel_end included reasonforexclusion comfortlevel_before comfortlevel_after headcircumference distance_NzIz distance_LPARPA reason_for_exclusion
22
sub-06 M 29 blond light 10 10 31 5.5 2.5 1 n/a 5.5 2.5 59 41 39.5 n/a
3-
sub-10 F 22 dark brown light intermidiate 10 13 27 n/a n/a 0 n/a 5 2 57 39 37 more than half of the channels with SCI < 0.7
3+
sub-10 F 22 dark brown light intermediate 10 13 27 n/a n/a 0 n/a 5 2 57 39 37 more than half of the channels with SCI < 0.7
44
sub-19 F 22 light brown very light 10 6 41 n/a n/a 1 n/a 7.5 3 56 36 38 n/a
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sub-21 F 21 dark brown light 10 10 9 n/a n/a 1 n/a 7 4 55 37 35 n/a
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sub-27 F 25 light brown light 10 3 7 n/a n/a 1 n/a 7 2 54 37.5 36 n/a
@@ -11,7 +11,7 @@ sub-38 M 24 light brown light 10 16 31 n/a n/a 1 n/a NA NA 61 40 41 n/a
1111
sub-43 F 21 light brown light 10 15 18 n/a n/a 1 n/a 7 NA 58 39 38 n/a
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sub-44 M 24 blond light 9 15 10 n/a n/a 1 n/a 7.5 6.5 59 40 39 n/a
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sub-52 F 26 dark brown light 10 16 33 n/a n/a 1 n/a 7 4 57 39 35 n/a
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sub-53 M 27 completely black light intermidiate 10 6 10 n/a n/a 1 n/a 8 2 61 40 39 n/a
14+
sub-53 M 27 black light intermediate 10 6 10 n/a n/a 1 n/a 8 2 61 40 39 n/a
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sub-63 M 23 blond light 10 13 32 n/a n/a 1 n/a 4 3 57 39 39.5 n/a
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sub-67 F 22 light brown light 10 5 32 n/a n/a 1 n/a 8 NA 60 40 37 n/a
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sub-69 F 26 blond light 9 12 26 n/a n/a 1 n/a 7.5 4 58 40 39 n/a

‎genetics_ukbb/participants.json‎

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{
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"age": {
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"LongName": "age",
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"Description": "age of the participant",
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"Units": "month"
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},
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"sex": {
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"LongName": "sex",
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"Description": "sex of the participant",
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"Levels": {
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"M": "male",
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"F": "female"
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}
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},
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"group": {
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"LongName": "group",
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"Description": "classification of participant based on study desease status",
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"Levels": {
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"patient": "patient",
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"control": "control"
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}
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},
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"genetic_id": {
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"LongName": "genetic_id",
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"Description": "Uniq sample ID per genotyped sample in genetic database"
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},
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"IDH": {
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"LongName": "isocitrate dehydrogenase gene",
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"Description": "mutation present or abscent",
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"Levels": {
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"yes": "present",
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"no": "abscent"
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} },
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"BatchID": {
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"LongName": "BatchID",
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"Description": "SNP array genotyping uniq batch ID per group of subjects",
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"Levels": {
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"b001": "Batch sequence number 1",
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"b002": "Batch sequence number 2"
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}
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},
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"VariationSetType": {
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"LongName": "VariationSetType",
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"Description": "Availability of SNV and/or CNV information",
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"Levels": {
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"SNV": "Single-nucleotide variants",
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"CNV": "Copy-Number Variants",
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"SNV/CNV": "Single-nucleotide variants/Copy-Number Variants"
49-
}
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},
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"Assembly": {
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"LongName": "Assembly",
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"Description": "Reference genome from which the sample variations were computed",
54-
"Levels": {
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"hg19": "Human genome version 19 equivalent to GRCh37 (Genome Reference consorcium of human build 37)",
56-
"hg38": "Human genome version 38 equivalent to GRCh38 (Genome Reference consorcium of human build 38)",
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"hg19/hg38": "Genome used to compute respectively the variations"
58-
}
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},
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"GeneticDataType": {
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"LongName": "GeneticDataType",
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"Description": "Raw genetic data type submited for the dataset",
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"Levels": {
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"WES": "Whole Exome Sequencing data (compressed FastQ or binary data format such as BAM or CRAM )",
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"SNP_intensity": "SNP array intensity data (text formated data type known as Illumina Final Report data)",
66-
"WES/SNP_intensity": "Both WES or SNP array data are available"
67-
}
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}
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}
1+
{
2+
"age": {
3+
"LongName": "age",
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"Description": "age of the participant",
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"Units": "month"
6+
},
7+
"sex": {
8+
"LongName": "sex",
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"Description": "sex of the participant",
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"Levels": {
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"M": "male",
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"F": "female"
13+
}
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},
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"group": {
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"LongName": "group",
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"Description": "classification of participant based on study desease status",
18+
"Levels": {
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"patient": "patient",
20+
"control": "control"
21+
}
22+
},
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"genetic_id": {
24+
"LongName": "genetic_id",
25+
"Description": "Uniq sample ID per genotyped sample in genetic database"
26+
},
27+
"IDH": {
28+
"LongName": "isocitrate dehydrogenase gene",
29+
"Description": "mutation present or abscent",
30+
"Levels": {
31+
"yes": "present",
32+
"no": "abscent"
33+
}
34+
},
35+
"BatchID": {
36+
"LongName": "BatchID",
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"Description": "SNP array genotyping uniq batch ID per group of subjects",
38+
"Levels": {
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"b001": "Batch sequence number 1",
40+
"b002": "Batch sequence number 2",
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"b003": "Batch sequence number 3",
42+
"b004": "Batch sequence number 4",
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"b005": "Batch sequence number 5"
44+
}
45+
},
46+
"VariationSetType": {
47+
"LongName": "VariationSetType",
48+
"Description": "Availability of SNV and/or CNV information",
49+
"Levels": {
50+
"SNV": "Single-nucleotide variants",
51+
"CNV": "Copy-Number Variants",
52+
"SNV/CNV": "Single-nucleotide variants/Copy-Number Variants"
53+
}
54+
},
55+
"Assembly": {
56+
"LongName": "Assembly",
57+
"Description": "Reference genome from which the sample variations were computed",
58+
"Levels": {
59+
"hg19": "Human genome version 19 equivalent to GRCh37 (Genome Reference consorcium of human build 37)",
60+
"hg38": "Human genome version 38 equivalent to GRCh38 (Genome Reference consorcium of human build 38)",
61+
"hg19/hg38": "Genome used to compute respectively the variations"
62+
}
63+
},
64+
"GeneticDataType": {
65+
"LongName": "GeneticDataType",
66+
"Description": "Raw genetic data type submited for the dataset",
67+
"Levels": {
68+
"WES": "Whole Exome Sequencing data (compressed FastQ or binary data format such as BAM or CRAM )",
69+
"SNP_intensity": "SNP array intensity data (text formated data type known as Illumina Final Report data)",
70+
"WES/SNP_intensity": "Both WES or SNP array data are available"
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}
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}
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}

‎pet002/participants.tsv‎

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participant_id height weight age gender
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sub-01 163.5 51 21.5086 female
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sub-02 170 51.2 20.7255 female
1+
participant_id height weight age gender
2+
sub-01 163.5 51 21.5086 F
3+
sub-02 170 51.2 20.7255 F

‎xeeg_hed_score/sub-ieegModulator/ses-ieeg01/ieeg/sub-ieegModulator_ses-ieeg01_electrodes.json‎

Lines changed: 43 additions & 40 deletions
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{
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"name": {
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"Description": "REQUIRED. Name of the electrode"
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},
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"x": {
6-
"Description": "REQUIRED. Recorded position along the x-axis"
7-
},
8-
"y": {
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"Description": "REQUIRED. Recorded position along the y-axis"
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},
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"z": {
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"Description": "REQUIRED. Recorded position along the z-axis"
13-
},
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"size": {
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"Description": "Surface area of the electrode in mm^2"
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},
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"hemisphere": {
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"Description": "Hemisphere in which the electrode is placed",
19-
"Levels": {
20-
"L": "Left hemisphere",
21-
"R": "Right hemisphere"
22-
}
23-
},
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"seizure_zone": {
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"LongName": "Seizure onset zone",
26-
"Description": "Conclusion drawn by an epileptologist on electrode involvement in the seizures",
27-
"Levels": {
28-
"SOZ": "Seizure Onset Zone, the region where the recorded clinical seizures started during the recording period",
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"IrritativeZone": "Region of cortex that generates interictal epileptiform discharges, but not seizures",
30-
"EarlyPropagationZone": "Seizures propagate into this region within first 3 seconds after seizure onset. Not seizure onset",
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"Resected": "Region of cortex that was resected",
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"ResectedEdge": "Region of cortex that is within 1 cm of the edge of the resected area"
33-
}
34-
},
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"Destrieux_label": {
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"Description": "Label number according to the Destrieux Brain Atlas obtained from Freesurfer"
37-
},
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"Destrieux_label_text": {
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"Description": "Label name of the brain region according to the Destrieux Brain Atlas obtained from Freesurfer"
40-
}
41-
}
2+
"name": {
3+
"Description": "REQUIRED. Name of the electrode"
4+
},
5+
"x": {
6+
"Description": "REQUIRED. Recorded position along the x-axis"
7+
},
8+
"y": {
9+
"Description": "REQUIRED. Recorded position along the y-axis"
10+
},
11+
"z": {
12+
"Description": "REQUIRED. Recorded position along the z-axis"
13+
},
14+
"size": {
15+
"Description": "Surface area of the electrode in mm^2"
16+
},
17+
"hemisphere": {
18+
"Description": "Hemisphere in which the electrode is placed",
19+
"Levels": {
20+
"L": "Left hemisphere",
21+
"R": "Right hemisphere"
22+
}
23+
},
24+
"seizure_zone": {
25+
"LongName": "Seizure onset zone",
26+
"Description": "Conclusion drawn by an epileptologist on electrode involvement in the seizures",
27+
"Levels": {
28+
"SOZ": "Seizure Onset Zone, the region where the recorded clinical seizures started during the recording period",
29+
"IrritativeZone": "Region of cortex that generates interictal epileptiform discharges, but not seizures",
30+
"EarlyPropagationZone": "Seizures propagate into this region within first 3 seconds after seizure onset. Not seizure onset",
31+
"Resected": "Region of cortex that was resected",
32+
"ResectedEdge": "Region of cortex that is within 1 cm of the edge of the resected area",
33+
"IrritativeZone, EarlyPropagationZone": "Combined region"
34+
}
35+
},
36+
"Destrieux_label": {
37+
"Description": "Label number according to the Destrieux Brain Atlas obtained from Freesurfer",
38+
"Format": "integer"
39+
},
40+
"Destrieux_label_text": {
41+
"Description": "Label name of the brain region according to the Destrieux Brain Atlas obtained from Freesurfer",
42+
"Format": "string"
43+
}
44+
}

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