Repository: bids-standard/bids-starter-kit Branch: main Commit: 409a857932d3 Files: 91 Total size: 251.4 KB Directory structure: gitextract_ajxyoq0h/ ├── .all-contributorsrc ├── .github/ │ └── workflows/ │ └── deploy_book.yml ├── .gitignore ├── LICENSE ├── Makefile ├── README.md ├── interactiveTreeVisualization/ │ └── epilepsyClassification2017/ │ ├── tree.html │ ├── treeData.js │ ├── treeFunctions.js │ └── treeStyle.css ├── matlabCode/ │ ├── anat/ │ │ ├── createBIDS_T1w_json_full.m │ │ ├── createBIDS_T1w_json_full_schma_based.m │ │ └── createBIDS_T1w_json_short.m │ ├── eeg-meg/ │ │ ├── createBIDS_meg_json_full.m │ │ ├── createBIDS_meg_json_short.m │ │ └── rename_brainvision_files.m │ ├── fmap/ │ │ └── createBIDS_fmap_json.m │ ├── func/ │ │ ├── createBIDS_bold_json_full.m │ │ └── createBIDS_bold_json_short.m │ ├── general/ │ │ ├── README.md │ │ ├── bids_spreadsheet2participants.m │ │ ├── createBIDS_dataset_description_json.m │ │ ├── createBIDS_events_tsv_json_full.m │ │ ├── createBIDS_participants_tsv.m │ │ ├── createBIDS_samples_tsv.m │ │ ├── input/ │ │ │ └── spreadsheet_to_convert.xlsx │ │ └── tests/ │ │ ├── data/ │ │ │ ├── participants.json │ │ │ └── participants.tsv │ │ └── test_bids_spreadsheet2participants.m │ ├── ieeg/ │ │ ├── createBIDS_channels_tsv.m │ │ ├── createBIDS_coordsystem_json.m │ │ ├── createBIDS_data_WriteBrainVisionWithFieldtrip.m │ │ ├── createBIDS_electrodes_tsv.m │ │ └── createBIDS_ieeg_json.m │ ├── micr/ │ │ ├── createBIDS_micr_json_full.m │ │ └── createBIDS_micr_json_short.m │ ├── miss_hit.cfg │ └── pet/ │ ├── createBIDS_blood_auto_tsv_and_json_short.m │ ├── createBIDS_blood_manual_tsv_and_json_full.m │ ├── createBIDS_blood_manual_tsv_and_json_short.m │ ├── createBIDS_pet_json_full.m │ └── createBIDS_pet_json_short.m ├── pythonCode/ │ ├── createBIDS_MP2RAGE_json.py │ └── createBIDS_dataset_description_json.py ├── reports/ │ └── Google-2018-report.md ├── src/ │ ├── CONTRIBUTING.md │ ├── _config.yml │ ├── _toc.yml │ ├── epilepsy_phenotype.rst │ ├── index.md │ ├── references.bib │ └── tree.html └── templates/ ├── participants.json ├── participants.tsv ├── phenotype/ │ ├── EpilepsyClassification.tsv │ └── EpilepsyClassification2017.json ├── samples.json ├── samples.tsv ├── sub-01/ │ └── ses-01/ │ ├── anat/ │ │ ├── sub-01_ses-01_acq-FullExample_run-01_T1w.json │ │ └── sub-01_ses-01_acq-ShortExample_run-01_T1w.json │ ├── eeg/ │ │ ├── sub-01_ses-01_task-FilterExample_eeg.json │ │ ├── sub-01_ses-01_task-FullExample_eeg.json │ │ ├── sub-01_ses-01_task-MinimalExample_eeg.json │ │ └── sub-01_ses-01_task-ReferenceExample_eeg.json │ ├── fmap/ │ │ ├── sub-01_ses-01_acq-Case1_run-01_phasediff.json │ │ ├── sub-01_ses-01_acq-Case2_run-01_phase1.json │ │ ├── sub-01_ses-01_acq-Case2_run-01_phase2.json │ │ ├── sub-01_ses-01_acq-Case3_run-01_fieldmap.json │ │ └── sub-01_ses-01_acq-Case4_dir-LR_run-01_epi.json │ ├── func/ │ │ ├── sub-01_ses-01_task-FullExample_run-01_bold.json │ │ ├── sub-01_ses-01_task-FullExample_run-01_events.json │ │ ├── sub-01_ses-01_task-FullExample_run-01_events.tsv │ │ └── sub-01_ses-01_task-ShortExample_run-01_bold.json │ ├── ieeg/ │ │ ├── sub-01_ses-01_coordsystem.json │ │ ├── sub-01_ses-01_electrodes.tsv │ │ ├── sub-01_ses-01_task-LongExample_run-01_channels.tsv │ │ └── sub-01_ses-01_task-LongExample_run-01_ieeg.json │ ├── meg/ │ │ ├── sub-01_ses-01_task-FullExample_acq-CTF_run-1_proc-sss_meg.json │ │ └── sub-01_ses-01_task-ShortExample_acq-CTF_run-1_proc-sss_meg.json │ ├── micr/ │ │ ├── sub-01_ses-01_sample-01_acq-Full_stain-03_chunk-01_SEM.json │ │ └── sub-01_ses-01_sample-01_acq-Short_stain-03_chunk-01_SEM.json │ └── pet/ │ ├── sub-01_ses-01_recording-AutosamplerShortExample_blood.json │ ├── sub-01_ses-01_recording-AutosamplerShortExample_blood.tsv │ ├── sub-01_ses-01_recording-ManualFullExample_blood.json │ ├── sub-01_ses-01_recording-ManualFullExample_blood.tsv │ ├── sub-01_ses-01_recording-ManualShortExample_blood.json │ ├── sub-01_ses-01_recording-ManualShortExample_blood.tsv │ ├── sub-01_ses-01_task-FullExample_pet.json │ └── sub-01_ses-01_task-ShortExample_pet.json └── sub-epilepsy01/ └── ses-01/ └── ieeg/ ├── sub-epilepsy01_ses-01_electrodes.json └── sub-epilepsy01_ses-01_electrodes.tsv ================================================ FILE CONTENTS ================================================ ================================================ FILE: .all-contributorsrc ================================================ { "files": [ "README.md" ], "imageSize": 100, "commit": false, "contributors": [ { "login": "dorahermes", "name": "Dora Hermes", "avatar_url": "https://avatars1.githubusercontent.com/u/4977351?v=4", "profile": "https://github.com/dorahermes", "contributions": [ "code", "content", "ideas", "review", "maintenance", "doc" ] }, { "login": "chrisgorgo", "name": "Chris Gorgolewski", "avatar_url": "https://avatars2.githubusercontent.com/u/238759?v=4", "profile": "http://chrisgorgolewski.org", 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Creative Commons may be contacted at creativecommons.org. ================================================ FILE: Makefile ================================================ .PHONY: all clean define BROWSER_PYSCRIPT import os, webbrowser, sys from urllib.request import pathname2url webbrowser.open("file://" + pathname2url(os.path.abspath(sys.argv[1]))) endef export BROWSER_PYSCRIPT define PRINT_HELP_PYSCRIPT import re, sys for line in sys.stdin: match = re.match(r'^([a-zA-Z_-]+):.*?## (.*)$$', line) if match: target, help = match.groups() print("%-20s %s" % (target, help)) endef export PRINT_HELP_PYSCRIPT BROWSER := python -c "$$BROWSER_PYSCRIPT" # Put it first so that "make" without argument is like "make help". help: @python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST) clean: rm -fr src/_build/ book: clean ## build the book jupyter-book build src view: book ## view the book $(BROWSER) $$PWD/src/_build/html/index.html test: ## build the book and tests the links jupyter-book build src --builder linkcheck ================================================ FILE: README.md ================================================ [![All Contributors](https://img.shields.io/badge/all_contributors-43-orange.svg?style=flat-square)](#contributors-) # The Starter-kit has moved to the new BIDS website. ## Contributors ✨ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):

Dora Hermes
💻 🖋 🤔 👀 🚧 📖
Chris Gorgolewski
👀 🚧 🐛
Chris Holdgraf
👀 🖋 🚧
Chris Gahnström
💻 🖋 🤔
Elizabeth DuPre
👀 🚧 🤔 🖋 📖
Utmost Happiness
💻 🖋 🤔
Kirstie Whitaker
👀 🤔 🚧 🖋 📖 🐛

Patrick Park
🤔 🖋 👀
Peer Herholz
💻
Cyril Pernet
💻
Stefan Appelhoff
👀 💻 🖋 🤔
Ilkay Isik
🐛
Teon L Brooks
🐛
ayab
🖋

Remi Gau
🖋
Jaap van der Aar
💻 🖋 🤔
Giulio Castegnaro
💻 🖋 🤔
Franklin Feingold
🐛 👀
Thomas Nichols
👀
Pieter Vandemaele
🐛
Guillaume Flandin
👀 🤔

Robert Oostenveld
🐛 👀 🤔
Happy
🖋
Tal Pal Attia
💻
Kay Robbins
🤔 🖋
Eduard Klapwijk
🤔
Dorien Huijser
🤔
Arshitha Basavaraj
🤔

Lennart Wittkuhn
🤔
Anthony Galassi
🤔 💻
Athanasia Monika Mowinckel
🤔 💻
Yoni Ashar
🤔
dkp
🐛
James Kent
🤔
Chris Benjamin
📖

Isla
📖
Chris Markiewicz
📖
Ankit Gupta
📖
Alex von Lautz
📖
Alexandre Hutton
📖
Abrren Chen
🚧
Gabriel Silveira
🐛 💻

nathan liang
🐛
This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome! ================================================ FILE: interactiveTreeVisualization/epilepsyClassification2017/tree.html ================================================ ILAE classification of the epilepsies Tree

ILAE classification of the epilepsies Tree

Scheffer, I. E., Berkovic, S., Capovilla, G., Connolly, M. B., French, J., Guilhoto, L., ... & Nordli, D. R. (2017). ILAE classification of the epilepsies: position paper of the ILAE Commission for Classification and Terminology. Epilepsia, 58(4), 512-521.

    

================================================ FILE: interactiveTreeVisualization/epilepsyClassification2017/treeData.js ================================================ var treeData = [{ "name": "Epilepsy Classification", "parent": "null", "_children": [ // ****** Seizure Type ****** { "name": "Seizure Type", "parent": "Epilepsy Classification", "_children": [ // *** Generalised *** { "name": "Generalised", "parent": "Seizure Type", "_children": [{ "name": "Motor", "parent": "Generalised", "_children": [{ "name": "Generalized tonic-clonic and variants", "parent": "Motor" }, { "name": "Generalized tonic", "parent": "Motor" }, { "name": "Generalized atonic", "parent": "Motor" }, { "name": "Myoclonic", "parent": "Motor" }, { "name": "Myoclonic-atonic", "parent": "Motor" }, { "name": "Epileptic spasms", "parent": "Motor" } ] }, { "name": "Non-motor", "parent": "Generalised", "_children": [{ "name": "Typical Absence", "parent": "Non-motor" }, { "name": "Atypical Absence", "parent": "Non-motor" }, { "name": "Myoclonic absence", "parent": "Non-motor" }, { "name": "Absence with eyelid myoclonia", "parent": "Non-motor" }] } ] }, // *** Focal *** { "name": "Focal", "parent": "Seizure Type", "_children": [{ "name": "Awareness", "parent": "Focal", "_children": [{ "name": "Aware", "parent": "Awareness", }, { "name": "Impaired Awareness", "parent": "Awareness", }] }, { "name": "Motor", "parent": "Focal", "_children": [{ "name": "Focal clonic seizure", "parent": "Motor" }, { "name": "Focal tonic seizure", "parent": "Motor" }, { "name": "Focal motor seizure with dystonia", "parent": "Motor" }, { "name": "Focal myoclonic seizure", "parent": "Motor" }, { "name": "Focal atonic seizure", "parent": "Motor" }, { "name": "Focal motor seizure with paresis/paralysis", "parent": "Motor" }, { "name": "Focal epileptic spasms", "parent": "Motor" }, { "name": "Focal hyperkinetic seizure", "parent": "Motor" }, { "name": "Focal automatism seizure", "parent": "Motor" }, { "name": "Focal motor seizure with dysarthria / anarthria", "parent": "Motor" }, { "name": "Focal motor seizure with negative myoclonus", "parent": "Motor" }, { "name": "Focal motor seizure with version", "parent": "Motor" }, { "name": "Focal bilateral motor seizure", "parent": "Motor" } ] }, { "name": "Non-motor", "parent": "Focal", "_children": [{ "name": "Focal sensory seizure", "parent": "Non-motor", "_children": [{ "name": "Focal somatosensory seizure", "parent": "Focal sensory seizure" }, { "name": "Focal sensory visual seizure", "parent": "Focal sensory seizure" }, { "name": "Focal sensory auditory seizure", "parent": "Focal sensory seizure" }, { "name": "Focal sensory olfactory seizure", "parent": "Focal sensory seizure" }, { "name": "Focal sensory gustatory seizure", "parent": "Focal sensory seizure" }, { "name": "Focal sensory vestibular seizure", "parent": "Focal sensory seizure" }, { "name": "Focal sensory seizure with hot-cold sensations", "parent": "Focal sensory seizure" }, { "name": "Focal sensory seizure with cephalic sensation", "parent": "Focal sensory seizure" }] }, { "name": "Focal cognitive seizure", "parent": "Non-motor", "_children": [{ "name": "Focal cognitive seizure with expressive dysphasia / aphasia", "parent": "Focal cognitive seizure" }, { "name": "Focal cognitive seizure with anomia", "parent": "Focal cognitive seizure" }, { "name": "Focal cognitive seizure with receptive dysphasia / aphasia", "parent": "Focal cognitive seizure" }, { "name": "Focal cognitive seizure with auditory agnosia", "parent": "Focal cognitive seizure" }, { "name": "Focal cognitive seizure with conduction dysphasia / aphasia", "parent": "Focal cognitive seizure" }, { "name": "Focal cognitive seizure with dyslexia / alexia", "parent": "Focal cognitive seizure" }, { "name": "Focal cognitive seizure with memory impairment", "parent": "Focal cognitive seizure" }, { "name": "Focal cognitive seizure with deja vu / jamais vu", "parent": "Focal cognitive seizure" }, { "name": "Focal cognitive seizure with hallucination", "parent": "Focal cognitive seizure" }, { "name": "Focal cognitive seizure with illusion", "parent": "Focal cognitive seizure" }, { "name": "Focal cognitive seizure with dissociation", "parent": "Focal cognitive seizure" }, { "name": "Focal cognitive seizure with forced thinking", "parent": "Focal cognitive seizure" }, { "name": "Focal cognitive seizure with dyscalculia / acalculia", "parent": "Focal cognitive seizure" }, { "name": "Focal cognitive seizure with dysgraphia/agraphia", "parent": "Focal cognitive seizure" }, { "name": "Focal cognitive seizure with left-right confusion", "parent": "Focal cognitive seizure" }, { "name": "Focal cognitive seizure with neglect", "parent": "Focal cognitive seizure" }] }, { "name": "Focal emotional seizure", "parent": "Non-motor", "_children": [{ "name": "Focal emotional seizure with fear/anxiety/panic", "parent": "Focal emotional seizure" }, { "name": "Focal emotional seizure with laughing (gelastic)", "parent": "Focal emotional seizure" }, { "name": "Focal emotional seizure with crying (dacrystic)", "parent": "Focal emotional seizure" }, { "name": "Focal emotional seizure with pleasure", "parent": "Focal emotional seizure" }, { "name": "Focal emotional seizure with anger", "parent": "Focal emotional seizure" }] }, { "name": "Focal autonomic seizure", "parent": "Non-motor", "_children": [{ "name": "Focal autonomic seizure with palpitations / tachycardia / bradycardia / asystole", "parent": "Focal autonomic seizure" }, { "name": "Focal autonomic seizure with epigastric sensation", "parent": "Focal autonomic seizure" }, { "name": "Focal autonomic seizure with pallor / flushing", "parent": "Focal autonomic seizure" }, { "name": "Focal autonomic seizure with hypoventilation / hyperventilation / altered respiration", "parent": "Focal autonomic seizure" }, { "name": "Focal autonomic seizure with piloerection", "parent": "Focal autonomic seizure" }, { "name": "Focal autonomic seizure with erection", "parent": "Focal autonomic seizure" }, { "name": "Focal autonomic seizure with urge to urinate / defecate", "parent": "Focal autonomic seizure" }, { "name": "Focal autonomic seizure with lacrimation", "parent": "Focal autonomic seizure" }, { "name": "Focal autonomic seizure with pupillary dilation / constriction", "parent": "Focal autonomic seizure" }] }, { "name": "Focal behavioural arrest seizure", "parent": "Non-motor", "_children": [{ "name": "Focal behavioural arrest seizure", "parent": "Focal behavioural arrest seizure" }] } ] }, { "name": "Focal to bilateral tonic-clonic seizure", "parent": "Focal", "_children": [{ "name": "Focal to bilateral tonic-clonic seizure", "parent": "Focal to bilateral tonic-clonic seizure" }] } ] }, // *** Unknown *** { "name": "Unknown", "parent": "Seizure Type", "_children": [{ "name": "Motor", "parent": "Focal", "_children": [{ "name": "Tonic–clonic", "parent": "Motor" }, { "name": "Epileptic spasms", "parent": "Motor" } ] }, { "name": "Non-motor", "parent": "Focal", "_children": [{ "name": "Behaviour arrest", "parent": "Non-motor" }, { "name": "Unclassified", "parent": "Non-motor" }] } ] } ] }, // ****** Epilepsy Type ****** { "name": "Epilepsy Type", "parent": "Epilepsy Classification", "_children": [{ "name": "Generalised Epilepsy", "parent": "Epilepsy Type" }, { "name": "Focal Epilepsy", "parent": "Epilepsy Type" }, { "name": "Combined generalised and focal Epilepsy", "parent": "Epilepsy Type" }, { "name": "Unknown Epilepsy", "parent": "Epilepsy Type" }] }, // ****** Epilepsy Syndrome ****** { "name": "Epilepsy Syndrome", "parent": "Epilepsy Classification", "_children": [{ "name": "Neonatal/Infantile", "parent": "Epilepsy Syndrome", "_children": [{ "name": "Self-limited neonatal seizures and Self-limited familial neonatal epilepsy", "parent": "Neonatal/Infantile" }, { "name": "Self limited familial and non-familial infantile epilepsy", "parent": "Neonatal/Infantile" }, { "name": "Early myoclonic encephalopathy", "parent": "Neonatal/Infantile" }, { "name": "Ohtahara syndrome", "parent": "Neonatal/Infantile" }, { "name": "West syndrome", "parent": "Neonatal/Infantile" }, { "name": "Dravet syndrome", "parent": "Neonatal/Infantile" }, { "name": "Myoclonic epilepsy in infancy", "parent": "Neonatal/Infantile" }, { "name": "Epilepsy of infancy with migrating focal seizures", "parent": "Neonatal/Infantile" }, { "name": "Myoclonic encephalopathy in non-progressive disorders", "parent": "Neonatal/Infantile" }, { "name": "Febrile seizures plus, genetic epilepsy with febrile seizures plus", "parent": "Neonatal/Infantile" }] }, { "name": "Childhood", "parent": "Epilepsy Syndrome", "_children": [{ "name": "Epilepsy with myoclonic-atonic seizures", "parent": "Childhood" }, { "name": "Epilepsy with eyelid myoclonias", "parent": "Childhood" }, { "name": "Lennox-Gastaut syndrome", "parent": "Childhood" }, { "name": "Childhood absence epilepsy", "parent": "Childhood" }, { "name": "Epilepsy with myoclonic absences", "parent": "Childhood" }, { "name": "Panayiotopoulos syndrome", "parent": "Childhood" }, { "name": "Childhood occipital epilepsy (Gastaut type)", "parent": "Childhood" }, { "name": "Photosensitive occipital lobe epilepsy", "parent": "Childhood" }, { "name": "Childhood epilepsy with centrotemporal spikes", "parent": "Childhood" }, { "name": "Atypical childhood epilepsy with centrotemporal spikes", "parent": "Childhood" }, { "name": "Epileptic encephalopathy with continuous spike-and-wave during sleep", "parent": "Childhood" }, { "name": "Landau-Kleffner syndrome", "parent": "Childhood" }, { "name": "Autosomal dominant nocturnal frontal lobe epilepsy", "parent": "Childhood" }] }, { "name": "Adolescent/Adult", "parent": "Epilepsy Syndrome", "_children": [{ "name": "Juvenile absence epilepsy", "parent": "Adolescent/Adult" }, { "name": "Juvenile myoclonic epilepsy", "parent": "Adolescent/Adult" }, { "name": "Epilepsy with generalized tonic-clonic seizures alone", "parent": "Adolescent/Adult" }, { "name": "Autosomal dominant epilepsy with auditory features", "parent": "Adolescent/Adult" }, { "name": "Other familial temporal lobe epilepsies", "parent": "Adolescent/Adult" }] }, { "name": "Any Age", "parent": "Epilepsy Syndrome", "_children": [{ "name": "Familial focal epilepsy with variable foci", "parent": "Any Age" }, { "name": "Reflex epilepsies", "parent": "Any Age" }, { "name": "Progressive myoclonus epilepsies", "parent": "Any Age" } ] }] }, // ****** Etiology ****** { "name": "Etiology", "parent": "Epilepsy Classification", "_children": [{ "name": "Genetic Etiology", "parent": "Etiology", "_children": [{ "name": "Chromosomal abnormalities", "parent": "Genetic Etiology" }, { "name": "Gene abnormalities", "parent": "Genetic Etiology" }] }, { "name": "Structural Etiology", "parent": "Etiology", "_children": [{ "name": "Malformations of cortical development", "parent": "Structural Etiology" }, { "name": "Vascular malformations", "parent": "Structural Etiology" }, { "name": "Hippocampal sclerosis", "parent": "Structural Etiology" }, { "name": "Hypoxic-ischemic structural abnormalities", "parent": "Structural Etiology" }, { "name": "Traumatic Brain Injury", "parent": "Structural Etiology" }, { "name": "Tumors", "parent": "Structural Etiology" }, { "name": "Porencephalic cyst", "parent": "Structural Etiology" }] }, { "name": "Metabolic Etiology", "parent": "Etiology", "_children": [{ "name": "Biotinidase and holocarboxylase synthase deficiency", "parent": "Metabolic Etiology" }, { "name": "Cerebral folate deficiency", "parent": "Metabolic Etiology" }, { "name": "Creatine disorders", "parent": "Metabolic Etiology" }, { "name": "Folinic acid responsive seizures", "parent": "Metabolic Etiology" }, { "name": "Glucose transporter 1 (GLUT1) deficiency", "parent": "Metabolic Etiology" }, { "name": "Mitochondrial disorders", "parent": "Metabolic Etiology" }, { "name": "Peroxisomal Disorders", "parent": "Metabolic Etiology" }, { "name": "Pyridoxine dependent epilepsy/PNPO deficiency", "parent": "Metabolic Etiology" }] }, { "name": "Immune Etiology", "parent": "Etiology", "_children": [{ "name": "Rasmussen syndrome", "parent": "Immune Etiology" }, { "name": "Antibody mediated etiologies", "parent": "Immune Etiology" }] }, { "name": "Infectious Etiology", "parent": "Etiology", "_children": [{ "name": "Bacterial Meningitis", "parent": "Infectious Etiology" }, { "name": "Cerebral Malaria", "parent": "Infectious Etiology" }, { "name": "Cerebral Toxoplasmosis", "parent": "Infectious Etiology" }, { "name": "CMV", "parent": "Infectious Etiology" }, { "name": "HIV", "parent": "Infectious Etiology" }, { "name": "Neurocysticercosis", "parent": "Infectious Etiology" }, { "name": "Tuberculosis", "parent": "Infectious Etiology" }, { "name": "Viral Encephalitis", "parent": "Infectious Etiology" }, { "name": "Other infections", "parent": "Infectious Etiology" }] }, { "name": "Unknown Etiology", "parent": "Etiology", "_children": [{ "name": "Febrile infection related epilepsy syndrome (FIRES)", "parent": "Unknown Etiology" }] }] } ] }]; ================================================ FILE: interactiveTreeVisualization/epilepsyClassification2017/treeFunctions.js ================================================ // ************** Generate the tree diagram ***************** var margin = { top: 50, right: 150, bottom: 50, left: 150 }, width = 2 * window.innerWidth - margin.right - margin.left, height = 4 * window.innerHeight - margin.top - margin.bottom; var i = 0, duration = 750, root; var tree = d3.layout.tree() .separation(function (a, b) { if (a.depth > 0) { depth = a.depth } else { depth = 1 } return (a.parent === b.parent ? 2 : 3) / depth; }) .size([height, width]); //var tree = d3.layout.tree() // .size([height, width]); var diagonal = d3.svg.diagonal() .projection(function (d) { return [d.y, d.x]; }); var svg0 = d3.select("body").append("svg") .attr("width", width + margin.right + margin.left) .attr("height", height + margin.top + margin.bottom) .attr("style", "background-color:white") svg = svg0.append("g") .attr("transform", "translate(" + margin.left + "," + margin.top + ")"); root = treeData[0]; root.x0 = height / 2; root.y0 = 0; update(root); d3.select(self.frameElement).style("height", "500px"); // ************** functions to update the tree diagram ***************** function update(source) { var levelWidth = [1]; var childCount = function (level, n) { if (n.children && n.children.length > 0) { if (levelWidth.length <= level + 1) levelWidth.push(0); levelWidth[level + 1] += n.children.length; n.children.forEach(function (d) { childCount(level + 1, d); }); } }; childCount(0, root); var newHeight = d3.max(levelWidth) * 50; // 50 pixels per line tree = tree.size([newHeight, width]); // Compute the new tree layout. var nodes = tree.nodes(root).reverse(), links = tree.links(nodes); // Normalize for fixed-depth. nodes.forEach(function (d) { d.y = d.depth * 350; }); // Update the nodes… var node = svg.selectAll("g.node") .data(nodes, function (d) { return d.id || (d.id = ++i); }); // Enter any new nodes at the parent's previous position. var nodeEnter = node.enter().append("g") .attr("class", "node") .attr("transform", function (d) { return "translate(" + source.y0 + "," + source.x0 + ")"; }) .on("click", click); nodeEnter.append("circle") .attr("r", 1e-6) .style("fill", function (d) { return d._children ? "lightsteelblue" : "#fff"; }); nodeEnter.append("text") .attr("x", function (d) { return d.children || d._children ? -13 : 13; }) .attr("dy", ".35em") .attr("text-anchor", function (d) { return d.children || d._children ? "end" : "start"; }) .text(function (d) { return d.name; }) .style("fill-opacity", 1e-6); // Transition nodes to their new position. var nodeUpdate = node.transition() .duration(duration) .attr("transform", function (d) { return "translate(" + d.y + "," + d.x + ")"; }); nodeUpdate.select("circle") .attr("r", 10) .style("fill", function (d) { return d._children ? "lightsteelblue" : "#fff"; }); nodeUpdate.select("text") .style("fill-opacity", 1); // Transition exiting nodes to the parent's new position. var nodeExit = node.exit().transition() .duration(duration) .attr("transform", function (d) { return "translate(" + source.y + "," + source.x + ")"; }) .remove(); nodeExit.select("circle") .attr("r", 1e-6); nodeExit.select("text") .style("fill-opacity", 1e-6); // Update the links… var link = svg.selectAll("path.link") .data(links, function (d) { return d.target.id; }); // Enter any new links at the parent's previous position. link.enter().insert("path", "g") .attr("class", "link") .attr("d", function (d) { var o = { x: source.x0, y: source.y0 }; return diagonal({ source: o, target: o }); }) // Transition links to their new position. link.transition() .duration(duration) .attr("d", diagonal); // Transition exiting nodes to the parent's new position. link.exit().transition() .duration(duration) .attr("d", function (d) { var o = { x: source.x, y: source.y }; return diagonal({ source: o, target: o }); }) .remove(); // Stash the old positions for transition. nodes.forEach(function (d) { d.x0 = d.x; d.y0 = d.y; }); } // Toggle children on click. function click(d) { if (d.children) { d._children = d.children; d.children = null; } else { d.children = d._children; d._children = null; } update(d); } function expand(d) { var children = (d.children) ? d.children : d._children; if (d._children) { d.children = d._children; d._children = null; } if (children) children.forEach(expand); } function collapse(d) { if (d.children) { d._children = d.children; d._children.forEach(collapse); d.children = null; } } function expandAll() { expand(root); update(root); } function collapseAll() { root.children.forEach(collapse); collapse(root); update(root); } // ************** functions to save the tree diagram ***************** // Set-up the export button d3.select('#saveButton').on('click', function () { var svgString = getSVGString(svg0.node()); svgString2Image(svgString, 1 * width, 1 * height, 'png', save); // passes Blob and filesize String to the callback function save(dataBlob, filesize) { saveAs(dataBlob, 'D3 vis exported to PNG.png'); // FileSaver.js function } }); // Below are the functions that handle actual exporting: // getSVGString ( svgNode ) and svgString2Image( svgString, width, height, format, callback ) function getSVGString(svgNode) { svgNode.setAttribute('xlink', 'http://www.w3.org/1999/xlink'); var cssStyleText = getCSSStyles(svgNode); appendCSS(cssStyleText, svgNode); var serializer = new XMLSerializer(); var svgString = serializer.serializeToString(svgNode); svgString = svgString.replace(/(\w+)?:?xlink=/g, 'xmlns:xlink='); // Fix root xlink without namespace svgString = svgString.replace(/NS\d+:href/g, 'xlink:href'); // Safari NS namespace fix return svgString; function getCSSStyles(parentElement) { var selectorTextArr = []; // Add Parent element Id and Classes to the list selectorTextArr.push('#' + parentElement.id); for (var c = 0; c < parentElement.classList.length; c++) if (!contains('.' + parentElement.classList[c], selectorTextArr)) selectorTextArr.push('.' + parentElement.classList[c]); // Add Children element Ids and Classes to the list var nodes = parentElement.getElementsByTagName("*"); for (var i = 0; i < nodes.length; i++) { var id = nodes[i].id; if (!contains('#' + id, selectorTextArr)) selectorTextArr.push('#' + id); var classes = nodes[i].classList; for (var c = 0; c < classes.length; c++) if (!contains('.' + classes[c], selectorTextArr)) selectorTextArr.push('.' + classes[c]); } // Extract CSS Rules var extractedCSSText = ""; for (var i = 0; i < document.styleSheets.length; i++) { var s = document.styleSheets[i]; try { if (!s.cssRules) continue; } catch (e) { if (e.name !== 'SecurityError') throw e; // for Firefox continue; } var cssRules = s.cssRules; for (var r = 0; r < cssRules.length; r++) { if (contains(cssRules[r].selectorText, selectorTextArr)) extractedCSSText += cssRules[r].cssText; } } return extractedCSSText; function contains(str, arr) { return arr.indexOf(str) === -1 ? false : true; } } function appendCSS(cssText, element) { var styleElement = document.createElement("style"); styleElement.setAttribute("type", "text/css"); styleElement.innerHTML = cssText; var refNode = element.hasChildNodes() ? element.children[0] : null; element.insertBefore(styleElement, refNode); } } function svgString2Image(svgString, width, height, format, callback) { var format = format ? format : 'png'; var imgsrc = 'data:image/svg+xml;base64,' + btoa(unescape(encodeURIComponent(svgString))); // Convert SVG string to data URL var canvas = document.createElement("canvas"); var context = canvas.getContext("2d"); canvas.width = width; canvas.height = height; var image = new Image(); image.onload = function () { context.clearRect(0, 0, width, height); context.drawImage(image, 0, 0, width, height); canvas.toBlob(function (blob) { var filesize = Math.round(blob.length / 1024) + ' KB'; if (callback) callback(blob, filesize); }); }; image.src = imgsrc; } ================================================ FILE: interactiveTreeVisualization/epilepsyClassification2017/treeStyle.css ================================================ .node { cursor: pointer; } .node circle { fill: #fff; stroke: steelblue; stroke-width: 3px; } .node text { font: 12px sans-serif; } .link { fill: none; stroke: #ccc; stroke-width: 3px; } .button { background-color: #ccc; color: black; border: none; padding: 15px 32px; border-radius: 8px; text-align: center; text-decoration: none; display: inline-block; font-size: 14px; transition-duration: 0.4s; cursor: pointer; } .button:hover { background-color:steelblue; } ================================================ FILE: matlabCode/anat/createBIDS_T1w_json_full.m ================================================ % Template Matlab script to create a BIDS compatible file: % % sub-01_ses-01_run-01_acq-FullExample_T1w.json % % This example lists only the REQUIRED, RECOMMENDED and OPTIONAL fields. % When adding additional metadata please use CamelCase % Writing json files relies on the JSONio library % https://github.com/bids-standard/bids-matlab % % Make sure it is in the matab/octave path try bids.bids_matlab_version; catch warning('%s\n%s\n%s\n%s', ... 'Writing the JSON file seems to have failed.', ... 'Make sure that the following library is in the matlab/octave path:', ... 'https://github.com/bids-standard/bids-matlab'); end %% clear; this_dir = fileparts(mfilename('fullpath')); root_dir = fullfile(this_dir, '..', filesep, '..'); project = 'templates'; sub_label = '01'; ses_label = '01'; run_label = '01'; % The OPTIONAL acq-