Add derivatives

.datalad/.gitattributes

@@ -0,0 +1 @@
+config annex.largefiles=nothing

.datalad/config

@@ -0,0 +1,2 @@
+[datalad "dataset"]
+	id = 437f863f-48e4-49a0-934c-8d90748a9fc4

.gitattributes

@@ -3,6 +3,7 @@
 *.json annex.largefiles=nothing
 *.txt annex.largefiles=nothing
 *.tsv annex.largefiles=nothing
+*.tsv.gz annex.largefiles=anything
 *.nii.gz annex.largefiles=anything
 *.tgz annex.largefiles=anything
 *_scans.tsv annex.largefiles=anything
@@ -12,3 +13,5 @@ sub-*/**/*_events.tsv annex.largefiles=anything
 .bidsignore annex.largefiles=nothing
 *.html annex.largefiles=anything
 *.svg annex.largefiles=anything
+* annex.backend=MD5E
+**/.git* annex.largefiles=nothing

README

@@ -1,13 +1,14 @@
 <!-- vim: syntax=Markdown -->
-# Courtois-NeuroMod: [xxxx subdataset, fmriprep derivatives](https://github.com/courtois-neuromod/xxxxx.fmriprep) 
+# Courtois-NeuroMod: [Friends subdataset, physprep derivatives](https://github.com/courtois-neuromod/friends.physprep) 
 
 The [Courtois project on Neural Modelling (Courtois NeuroMod)](https://www.cneuromod.ca/) aims at training artificial neural networks using extensive experimental data on individual human brain activity and behaviour.
 
-Participants performed task xxx while functional data being acquired in the MRI scanner . A extensive description can be found [here](https://docs.cneuromod.ca/en/latest/DATASETS.html#xxxx).
+Participants performed task Friends while functional data being acquired in the MRI scanner. A extensive description can be found [here](https://docs.cneuromod.ca/en/latest/DATASETS.html#friends).
 
-This subdataset is organized following the [brain imaging data structure (BIDS)](https://bids.neuroimaging.io/) (including extensions in development) and contains:
-- [x] [preprocessed neuroimaging data](https://docs.cneuromod.ca/en/latest/DERIVATIVES.html#fmriprep)
+This subdataset is organized following a [brain imaging data structure (BIDS)](https://bids.neuroimaging.io/) like structure (including extensions in development) and contains:
+- [ ] preprocessed neuroimaging data
 - [ ] behavioral variables in event files
+- [x] preprocessed physiological data
 
 *(unchecked are collected data which have not yet been integrated in the dataset)*
 

dataset_description.json

@@ -1,30 +1,23 @@
 {
-    "Name": "<xxxxx> sub-dataset of the Courtois-Neuromod project processed with fMRIPrep - fMRI PREProcessing workflow",
-    "BIDSVersion": "1.4.0",
+    "Name": "friends.physprep sub-dataset of the Courtois-Neuromod project processed with physprep - custom python scripts",
+    "BIDSVersion": "1.9.0",
     "DatasetType": "derivative",
     "GeneratedBy": [
         {
-            "Name": "fMRIPrep",
-            "Version": "20.2.5",
-            "CodeURL": "https://github.com/nipreps/fmriprep/archive/20.2.5.tar.gz"
+            "Name": "physprep",
+            "CodeURL": "https://github.com/courtois-neuromod/physprep"
         }
     ],
     "HowToAcknowledge": "Please cite our paper (), and include the generated citation boilerplate within the Methods section of the text.",
     "SourceDatasets": [
         {
-	    "name": "cneuromod xxxxx dataset",
-            "URL": "https://github.com/courtois-neuromod/xxxxx"
-        },
-        {
-	    "name": "cneuromod anatomical smriprep derivatives",
-            "URL": "https://github.com/courtois-neuromod/anat.smriprep"
+	    "name": "cneuromod friends dataset",
+            "URL": "https://github.com/courtois-neuromod/friends"
         }
-
     ],
     "License": "https://docs.cneuromod.ca/en/latest/ACCESS.html#data-transfer-agreement-(dta)",
     "ReferencesAndLinks": [
-        "https://docs.cneuromod.ca/",
-	"https://doi.org/10.1038/s41592-018-0235-4"
+        "https://docs.cneuromod.ca/"
     ],
     "Authors": [
         "Pierre Bellec",

physio_events.json

@@ -0,0 +1,26 @@
+{
+    "trial_type": {
+        "LongName": "Physiological events category",
+        "Description": "Indicator of the physiological event extracted from the preprocessed timeseries",
+        "Levels": {
+            "r_peak": "R peak extracted from preprocessed ecg signal using ecg_peaks promac method from neurokit2",
+            "r_peak_corrected": "Corrected R peak using signal_fixpeaks neurokit method from neurokit2 on r_peak",
+            "systolic_peak": "Systolic peak extracted from preprocessed ppg signal using ppg_findpeaks elgendi method from neurokit2",
+            "systolic_peak_corrected": "Corrected systolic peak using signal_fixpeaks neurokit method form neurokit2 on systolic_peak",
+            "scr_onset": "Skin conductance response onset extracted from the phasic component of the EDA signal using eda_process neurokit method from neurokit2",
+            "scr_peak": "Skin conductance response peak extracted from the phasic component of the EDA signal using eda_process neurokit method from neurokit2",
+            "scr_recovery": "Skin conductance response recovery (half amplitude of the SCR decline) extracted from the phasic component of the EDA signal using eda_process neurokit method from neurokit2",
+            "inhale_max": "Respiratory peak extracted from preprocessed respiratory signal using rsp_process khodadad2018 method from neurokit2",
+            "exhale_max": "Respiratory trough extracted from preprocessed respiratory signal using rsp_process khodadad2018 method from neurokit2"
+        }
+    },
+    "channel": {
+        "Description": "Physiological modality associated with the event",
+        "Levels": {
+            "ECG": "Continuous preprocessed electrocardiogram measurement",
+            "PPG": "Continuous preprocessed pulse measurement",
+            "RSP": "Continuous preprocessed respiratory measurements",
+            "EDAPhasic": "Continuous phasic component of the preprocessed electrodermal measurement"
+        }
+    }
+}

preproc_physio.json

@@ -0,0 +1,30 @@
+{
+    "StartTime": 0,
+    "SamplingFrequency": 1000,
+    "Columns": [
+        "PPG",
+        "ECG",
+        "RSP",
+        "EDA",
+        "EDATonic",
+        "EDAPhasic"
+    ],
+    "PPG": {
+        "Description": "Preprocessed PPG signal"
+    },
+    "ECG": {
+        "Description": "Preprocessed ECG signal"
+    },
+    "RSP": {
+        "Description": "Preprocessed respiratory signal"
+    },
+    "EDA": {
+        "Description": "Preprocessed EDA signal"
+    },
+    "EDATonic": {
+        "Description": "Tonic component from the preprocessed EDA signal"
+    },
+    "EDAPhasic": {
+        "Description": "Phasic component from the preprocessed EDA signal"
+    }
+}

sub-01/ses-001/func/sub-01_ses-001_task-s01e02a_desc-physio_events.tsv

@@ -0,0 +1 @@
+../../../.git/annex/objects/1g/5G/MD5E-s108222--0285935e9cb93d1e4073aec08380430b.tsv/MD5E-s108222--0285935e9cb93d1e4073aec08380430b.tsv

sub-01/ses-001/func/sub-01_ses-001_task-s01e02a_desc-preproc_physio.tsv.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/5M/k6/MD5E-s34349930--d4c1bcc28e0edee17ee9fed0f414a98e.tsv.gz/MD5E-s34349930--d4c1bcc28e0edee17ee9fed0f414a98e.tsv.gz

sub-01/ses-001/func/sub-01_ses-001_task-s01e02a_desc-quality.json

@@ -0,0 +1,26 @@
+{
+    "PPG": {
+        "Description": "continuous pulse measurement",
+        "PercentageValid": 1.0,
+        "QualityAssessment": "Pass"
+    },
+    "ECG": {
+        "Description": "continuous electrocardiogram measurement",
+        "PercentageValid": 1.0,
+        "QualityAssessment": "Pass"
+    },
+    "EDA": {
+        "Description": "continuous electrodermal measurement",
+        "PercentageValid": 1.0,
+        "QualityAssessment": "Pass"
+    },
+    "RSP": {
+        "Description": "continuous breathing measurement",
+        "PercentageValid": 1.0,
+        "QualityAssessment": "Pass"
+    },
+    "Description": {
+        "PercentageValid": "Percentage of acceptable 1.0min windows within a run based on modality specific criterion",
+        "QualityAssessment": "Quality assessment of the run. Pass if more than 80% of the run is classified as Acceptable, otherwise Fail"
+    }
+}

sub-01/ses-001/func/sub-01_ses-001_task-s01e02b_desc-physio_events.tsv

@@ -0,0 +1 @@
+../../../.git/annex/objects/2G/F7/MD5E-s105834--a1ff1944dc7fd73a952a0f90ee05589b.tsv/MD5E-s105834--a1ff1944dc7fd73a952a0f90ee05589b.tsv

sub-01/ses-001/func/sub-01_ses-001_task-s01e02b_desc-preproc_physio.tsv.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/p5/p0/MD5E-s34431233--510831e6f0f04efab8c7d4e54e1fc026.tsv.gz/MD5E-s34431233--510831e6f0f04efab8c7d4e54e1fc026.tsv.gz

sub-01/ses-001/func/sub-01_ses-001_task-s01e02b_desc-quality.json

@@ -0,0 +1,26 @@
+{
+    "PPG": {
+        "Description": "continuous pulse measurement",
+        "PercentageValid": 1.0,
+        "QualityAssessment": "Pass"
+    },
+    "ECG": {
+        "Description": "continuous electrocardiogram measurement",
+        "PercentageValid": 1.0,
+        "QualityAssessment": "Pass"
+    },
+    "EDA": {
+        "Description": "continuous electrodermal measurement",
+        "PercentageValid": 1.0,
+        "QualityAssessment": "Pass"
+    },
+    "RSP": {
+        "Description": "continuous breathing measurement",
+        "PercentageValid": 1.0,
+        "QualityAssessment": "Pass"
+    },
+    "Description": {
+        "PercentageValid": "Percentage of acceptable 1.0min windows within a run based on modality specific criterion",
+        "QualityAssessment": "Quality assessment of the run. Pass if more than 80% of the run is classified as Acceptable, otherwise Fail"
+    }
+}

sub-01/ses-001/func/sub-01_ses-001_task-s01e03a_desc-physio_events.tsv

@@ -0,0 +1 @@
+../../../.git/annex/objects/9m/KV/MD5E-s97933--d1c0258008601e7e7b8d5b9d97e9cf89.tsv/MD5E-s97933--d1c0258008601e7e7b8d5b9d97e9cf89.tsv

sub-01/ses-001/func/sub-01_ses-001_task-s01e03a_desc-preproc_physio.tsv.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/9Q/Jj/MD5E-s33599728--76d69716e7a537b97636f46c144b61fd.tsv.gz/MD5E-s33599728--76d69716e7a537b97636f46c144b61fd.tsv.gz

sub-01/ses-001/func/sub-01_ses-001_task-s01e03a_desc-quality.json

@@ -0,0 +1,26 @@
+{
+    "PPG": {
+        "Description": "continuous pulse measurement",
+        "PercentageValid": 1.0,
+        "QualityAssessment": "Pass"
+    },
+    "ECG": {
+        "Description": "continuous electrocardiogram measurement",
+        "PercentageValid": 1.0,
+        "QualityAssessment": "Pass"
+    },
+    "EDA": {
+        "Description": "continuous electrodermal measurement",
+        "PercentageValid": 0.82,
+        "QualityAssessment": "Pass"
+    },
+    "RSP": {
+        "Description": "continuous breathing measurement",
+        "PercentageValid": 1.0,
+        "QualityAssessment": "Pass"
+    },
+    "Description": {
+        "PercentageValid": "Percentage of acceptable 1.0min windows within a run based on modality specific criterion",
+        "QualityAssessment": "Quality assessment of the run. Pass if more than 80% of the run is classified as Acceptable, otherwise Fail"
+    }
+}

sub-01/ses-001/func/sub-01_ses-001_task-s01e03b_desc-physio_events.tsv

@@ -0,0 +1 @@
+../../../.git/annex/objects/3F/4q/MD5E-s100473--5ed24d8f11cc6c50a9e93fd8c72743c4.tsv/MD5E-s100473--5ed24d8f11cc6c50a9e93fd8c72743c4.tsv

sub-01/ses-001/func/sub-01_ses-001_task-s01e03b_desc-preproc_physio.tsv.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/QX/FG/MD5E-s33476053--40290d909901be0b6f3136a1cdf3671f.tsv.gz/MD5E-s33476053--40290d909901be0b6f3136a1cdf3671f.tsv.gz

sub-01/ses-001/func/sub-01_ses-001_task-s01e03b_desc-quality.json

@@ -0,0 +1,26 @@
+{
+    "PPG": {
+        "Description": "continuous pulse measurement",
+        "PercentageValid": 1.0,
+        "QualityAssessment": "Pass"
+    },
+    "ECG": {
+        "Description": "continuous electrocardiogram measurement",
+        "PercentageValid": 1.0,
+        "QualityAssessment": "Pass"
+    },
+    "EDA": {
+        "Description": "continuous electrodermal measurement",
+        "PercentageValid": 1.0,
+        "QualityAssessment": "Pass"
+    },
+    "RSP": {
+        "Description": "continuous breathing measurement",
+        "PercentageValid": 1.0,
+        "QualityAssessment": "Pass"
+    },
+    "Description": {
+        "PercentageValid": "Percentage of acceptable 1.0min windows within a run based on modality specific criterion",
+        "QualityAssessment": "Quality assessment of the run. Pass if more than 80% of the run is classified as Acceptable, otherwise Fail"
+    }
+}

sub-01/ses-002/func/sub-01_ses-002_task-s01e04a_desc-physio_events.tsv

@@ -0,0 +1 @@
+../../../.git/annex/objects/Vv/fJ/MD5E-s106224--24946e1ddfc0f28494a05645571403a9.tsv/MD5E-s106224--24946e1ddfc0f28494a05645571403a9.tsv

sub-01/ses-002/func/sub-01_ses-002_task-s01e04a_desc-preproc_physio.tsv.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/P3/3Q/MD5E-s35862890--9356a61403b9022fff9dfa2060aaa678.tsv.gz/MD5E-s35862890--9356a61403b9022fff9dfa2060aaa678.tsv.gz

sub-01/ses-002/func/sub-01_ses-002_task-s01e04a_desc-quality.json

@@ -0,0 +1,26 @@
+{
+    "PPG": {
+        "Description": "continuous pulse measurement",
+        "PercentageValid": 1.0,
+        "QualityAssessment": "Pass"
+    },
+    "ECG": {
+        "Description": "continuous electrocardiogram measurement",
+        "PercentageValid": 1.0,
+        "QualityAssessment": "Pass"
+    },
+    "EDA": {
+        "Description": "continuous electrodermal measurement",
+        "PercentageValid": 1.0,
+        "QualityAssessment": "Pass"
+    },
+    "RSP": {
+        "Description": "continuous breathing measurement",
+        "PercentageValid": 1.0,
+        "QualityAssessment": "Pass"
+    },
+    "Description": {
+        "PercentageValid": "Percentage of acceptable 1.0min windows within a run based on modality specific criterion",
+        "QualityAssessment": "Quality assessment of the run. Pass if more than 80% of the run is classified as Acceptable, otherwise Fail"
+    }
+}

sub-01/ses-002/func/sub-01_ses-002_task-s01e04b_desc-physio_events.tsv

@@ -0,0 +1 @@
+../../../.git/annex/objects/43/69/MD5E-s105132--7630370df73c603c896e0bf3897be390.tsv/MD5E-s105132--7630370df73c603c896e0bf3897be390.tsv

sub-01/ses-002/func/sub-01_ses-002_task-s01e04b_desc-preproc_physio.tsv.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/Z5/Z5/MD5E-s35949200--f5546fbcf6174c02b604ac240aa68dc7.tsv.gz/MD5E-s35949200--f5546fbcf6174c02b604ac240aa68dc7.tsv.gz

sub-01/ses-002/func/sub-01_ses-002_task-s01e04b_desc-quality.json

@@ -0,0 +1,26 @@
+{
+    "PPG": {
+        "Description": "continuous pulse measurement",
+        "PercentageValid": 1.0,
+        "QualityAssessment": "Pass"
+    },
+    "ECG": {
+        "Description": "continuous electrocardiogram measurement",
+        "PercentageValid": 1.0,
+        "QualityAssessment": "Pass"
+    },
+    "EDA": {
+        "Description": "continuous electrodermal measurement",
+        "PercentageValid": 0.92,
+        "QualityAssessment": "Pass"
+    },
+    "RSP": {
+        "Description": "continuous breathing measurement",
+        "PercentageValid": 1.0,
+        "QualityAssessment": "Pass"
+    },
+    "Description": {
+        "PercentageValid": "Percentage of acceptable 1.0min windows within a run based on modality specific criterion",
+        "QualityAssessment": "Quality assessment of the run. Pass if more than 80% of the run is classified as Acceptable, otherwise Fail"
+    }
+}

sub-01/ses-002/func/sub-01_ses-002_task-s01e05a_desc-physio_events.tsv

@@ -0,0 +1 @@
+../../../.git/annex/objects/Zg/1X/MD5E-s99364--0db3da7ac108840a1b2275cc81ed4698.tsv/MD5E-s99364--0db3da7ac108840a1b2275cc81ed4698.tsv

sub-01/ses-002/func/sub-01_ses-002_task-s01e05a_desc-preproc_physio.tsv.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/KQ/W6/MD5E-s33232481--9bde3d9e34332f3d4abdfd9519477ce9.tsv.gz/MD5E-s33232481--9bde3d9e34332f3d4abdfd9519477ce9.tsv.gz

sub-01/ses-002/func/sub-01_ses-002_task-s01e05a_desc-quality.json

@@ -0,0 +1,26 @@
+{
+    "PPG": {
+        "Description": "continuous pulse measurement",
+        "PercentageValid": 1.0,
+        "QualityAssessment": "Pass"
+    },
+    "ECG": {
+        "Description": "continuous electrocardiogram measurement",
+        "PercentageValid": 1.0,
+        "QualityAssessment": "Pass"
+    },
+    "EDA": {
+        "Description": "continuous electrodermal measurement",
+        "PercentageValid": 0.91,
+        "QualityAssessment": "Pass"
+    },
+    "RSP": {
+        "Description": "continuous breathing measurement",
+        "PercentageValid": 1.0,
+        "QualityAssessment": "Pass"
+    },
+    "Description": {
+        "PercentageValid": "Percentage of acceptable 1.0min windows within a run based on modality specific criterion",
+        "QualityAssessment": "Quality assessment of the run. Pass if more than 80% of the run is classified as Acceptable, otherwise Fail"
+    }
+}

sub-01/ses-002/func/sub-01_ses-002_task-s01e05b_desc-physio_events.tsv

@@ -0,0 +1 @@
+../../../.git/annex/objects/71/wF/MD5E-s99965--ed4afaafe2877ca4413c00953dc432eb.tsv/MD5E-s99965--ed4afaafe2877ca4413c00953dc432eb.tsv

sub-01/ses-002/func/sub-01_ses-002_task-s01e05b_desc-preproc_physio.tsv.gz

@@ -0,0 +1 @@
+../../../.git/annex/objects/f9/pW/MD5E-s34064349--887b28155fbe6244b3e9f81a1b450209.tsv.gz/MD5E-s34064349--887b28155fbe6244b3e9f81a1b450209.tsv.gz