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.

Advantages

• Free computation resources: GitHub action provides 20 concurrent jobs with 2-core each. The computation power is equal to a 40-core workstation, much faster than running it on most laptops/desktops.
• Faster data transfer: The raw dMRI data are usually huge and can be up to several GB per scan, but tractography and related metrics are substantially smaller at MB size. Using DSI Studio Cloud, the amount of data transfer can be dramatically reduced.

Requirements

• dMRI data stored on OpenNeuro
• A GitHub account (free)

Limitations

• Not more than 256 scans data: There is a maximum of 256 jobs per workflow run. DSI Studio will still generate SRC and FIB files for downloading, but fiber tracking cannot be executed due to the this limit.

Examples Dataset

• (OpenNeuro ds002087) Datasets with and without deliberate head movements for detection and imputation of dropout in diffusion MRI
• (OpenNeuro ds001378) SCA2 Diffusion Tensor Imaging

Pipeline

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

Steps

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

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

3. 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.

4. 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

DS NUMBER	DWI COUNT	NAME
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)