DSI Studio Cloud

DSI Studio Cloud is a GitHub repository that uses GitHub’s cloud computing resource to analyze diffusion MRI data. It can construct tractography and analyze its diffusion and shape metrics. The code can be extended to accomplish any command line functions provided in DSI Studio.

DSI Studio Cloud makes uses of the GitHub-hosted runner, a virtual machine hosted by GitHub, to process dMRI data. The GitHub-Action scripts in the DSI Studio Cloud get data from OpenNeuro to the GitHub runners and processe them using DSI Studio.




Examples Dataset


The DSI Studio Cloud pipeline includes preprocessing (eddy correction and align ac-pc), quality check, automatic fiber tracking, region-based analysis, and connectivity matrix. image


  1. Fork the repository: Click on the Fork button in the upper right corner.

  1. Enable Actions: Click on the Actions menu and confirm I understand my workflows, go ahead and enable them.

  1. Run Actions: Under the same Actions menu, click on Auto-Track (OpenNeuro) on the left and click run workflow on the right.

Setup Parameters:

Parameters Descriptions
OpenNeuro Accession Number the DS number of the OpenNeuro data. (e.g. ds001378)
Preprocessing: Eddy Correction specify whether to correct DWI data using FSL eddy.
Preprocessing: Align AC-PC specify whether to resample DWI to align ac-pc.
Pipeline: Region Analysis the region analysis pipeline calculates the averages value of metrics in the atlas regions.
Pipeline: Connectivity Matrix the connectivity matrix pipeline calculates the whole-brain connectivity matrix using the atlas parcellations.
Pipeline: Automatic Fiber Tracking the automatic fiber tracking pipeline maps tracts of interests and calculates their diffusion and shape metrics.
Options: Atlases specify the atlases to be used in region analysis or connectivity matrix. Full list of atlases
Options: Tracts of Interest specify the tracts to be mapped used in automatic fiber tracking. Partial name accepted. Full list of tracts

Click on Run workflow to start.

  1. Download Results:

Once completed, the FIB files, tract files, and tract metrics can be downloaded from the Release on the right of the repository.


OpenNeuro DWI Data List

ds000009 24 The generality of self-control
ds000030 262 UCLA Consortium for Neuropsychiatric Phenomics LA5c Study
ds000031 44 MyConnectome
ds000113 20 Forrest Gump
ds000114 1 A test-retest fMRI dataset for motor, language and spatial attention functions.
ds000117 11 Multisubject multimodal face processing
ds000201 76 The Stockholm Sleepy Brain Study: Effects of Sleep Deprivation on Cognitive and Emotional Processing in Young and Old
ds000206 319 DWI Traveling Human Phantom Study
ds000221 228 ds000221_R1.0.0
ds000244 12 Individual Brain Charting
ds001021 1 NKI-sample
ds001226 72 BTC_preop
ds001242 52 Examining effects of arousal on responses to salient and non-salient stimuli in younger and older adults
ds001378 50 SCA2 Diffusion Tensor Imaging
ds001419 1 thoughtExperiment
ds001499 4 BOLD5000
ds001590 45 Feature Discrimination
ds001595 1 Test dataset for XCP software
ds001743 12 Unilateral Glaucoma 3T dMRI
ds001771 80 InterTVA. A multimodal MRI dataset for the study of inter-individual differences in voice perception and identification.
ds001796 64 Bilingualism and the brain
ds001875 27 TheVirtualBrain Macaque MRI
ds001894 113 Longitudinal Brain Correlates of Multisensory Lexical Processing in Children
ds001907 81 ANT: Healthy aging and Parkinson’s disease
ds001919 266 Spinal Cord MRI Public Database (Multi-subjects)
ds001928 40 Functional Connectivity of Music-Induced Analgesia in Fibromyalgia
ds001942 60 Auditory localization with 7T fMRI
ds002080 58 BTC_postop
ds002087 2 Datasets with and without deliberate head movements for detection and imputation of dropout in diffusion MRI
ds002185 22 Human Olfaction Without Apparent Olfactory Bulbs
ds002307 37 individual_dMRI_fMRI
ds002330 132 Neuroimaging predictors of creativity in healthy adults
ds002366 33 Emotion regulation in the Ageing Brain, University of Reading, BBSRC
ds002374 1 3AM straight reproducibility phantoms
ds002393 19 Spinal Cord MRI Public Database (Single-subject)
ds002543 96 Learning, Inhibitory Control, and Perception
ds002602 56 The Reading Brain Project L2 Adults
ds002634 40 Project_larynx
ds002685 23 IBC
ds002785 422 AOMIC-PIOP1
ds002790 453 AOMIC-PIOP2
ds002843 262 Cognitive Training
ds003011 30 Social Processes Initiative in Neurobiology of the Schizophrenia(s) Traveling Human Phantoms
ds003027 36 plp_nf1_dMRI_fMRI
ds003047 18 DTI data from ‘Fiber architecture in the ventromedial striatum and its relation with the bed nucleus of the stria terminalis’
ds003097 3670 AOMIC-ID1000
ds003171 17 Modeling an auditory stimulated brain under altered states of consciousness using the generalized ising model
ds003346 137 SUDMEX_CONN: The Mexican dataset of cocaine use disorder patients.
ds003367 50 Ascending arousal network connectivity during recovery from traumatic coma
ds003416 3934 MASiVar: Multisite, Multiscanner, and Multisubject Acquisitions for Studying Variability in Diffusion Weighted Magnetic Resonance Imaging
ds003424 56 Identification of an Amygdala-Thalamic Circuit That Acts as a Central Gain Mechanism in Taste Perception
ds003495 48 dStreamUpgrade
ds003505 64 VEPCON: Source imaging of high-density visual evoked potentials with multi-scale brain parcellations and connectomes
ds003508 110 Language Learning Aptitude dataset
ds003563 8 Data from: Comprehensive ultrahigh resolution whole brain in vivo MRI dataset as a human phantom
ds003599 133 White matter deficits in cocaine use disorder V1.0
ds003604 377 A longitudinal neuroimaging dataset on language processing in children ages 5, 7, and 9 years old
ds003813 1 Fitlins - Example
ds003959 12 Soma and Neurite Density MRI (SANDI) of the in-vivo mouse brain
ds003974 52 The Reading Brain Project L1 Adults
ds003988 56 The Reading Brain Project L2 Adults
ds003989 3 Structural, diffusion and rs-functional MRI data in Macaque Monkeys
ds004024 7 TMS-EEG-MRI-fMRI-DWI data on paired associative stimulation and connectivity (Shirley Ryan AbilityLab, Chicago, IL)
ds004069 2872 Queensland Twin Adolescent Brain (QTAB)
ds004078 24 A synchronous multimodal neuroimaging dataset to study brain language processing
ds004097 40 An open-access accelerated adult equivalent of the ABCD Study neuroimaging dataset (a-ABCD)
ds004146 2871 Queensland Twin Adolescent Brain (QTAB)
ds004161 96 Turone Sheep Chronic Stress (TSCS)
ds004215 303 The NIMH Intramural Healthy Volunteer Dataset
ds004299 978 Characterizing habit learning in the human brain at the individual and group levels: a multi-modal MRI study
ds004305 64 Mapping neuroinflammation in vivo with diffusion-MRI in rats given a systemic lipopolysaccharide challenge
ds004441 28 Rat_diffusion_STZ
ds004498 21 Perinatal Stroke
ds004513 29 The energetic costs of the human connectome
ds004632 27 DTI readouts for designing a preclinical stem-cell therapy trial in experimental stroke
ds004640 2 Sustaining wakefulness: Brainstem connectivity in human consciousness
ds004737 76 CS-DSI
ds004742 1 White matter tract
ds004744 17 White matter tract and peaks