The following are examples of atlases provided with ExploreASL:

MNI structural 21, provides lobar regions. ROI summary from the MNI structural atlas, which contains large/lobar ROIs, which can serve as a quick overview/summary of the data. The cerebellum ROI was replaced by the cerebellum atlas from FSLatlas FNIRT.

Three vascular regions (ACA, MCA and PCA bilateral), also from Tatu et al. 22

Three labeling vascular regions (LCA, RCA and PCA bilateral) from Tatu et al. 22 together with a WM mask.

FEAST-based regions (three vascular regions split into proximal, middle and distal regions, resulting in a total of 9 vascular regions). These are vascular regions from the FEAST PreDiva paper 23. The original vascular territories from Tatu et al. 22 were divided into proximal, intermediate and distal territories based on their estimated arterial transit time (ATT) in this paper 23. If we expect vascular pathology, we might see more or less effects in the proximal vs. distal vascular ROIs.

Harvard-Oxford cortical ROI24. Note that the HO-atlas is initially probabilistic, here the CONN-toolbox version is used [ref]. This cortical parcellation by the Harvard-Oxford atlas is a standard, accepted, atlas in NeuroImaging. ROIs are small though, so if we do not find effects this could also be an SNR (translating into a statistical power) issue.

Harvard-Oxford subcortical ROIs (Subcortical parcellation by the Harvard-Oxford (HO) atlas, same as above) and the thalamus atlas (parcellation of the thalamus by its connectivity).

How to use the Atlases

In order to use these atlases, or others, one just needs to add that information to the dataPar.json, following what it is said here, in the sub-chapter "Masking and atlas parameters". Example of dataPar.json with defined atlases:

{"x": { "dataset": { "subjectRegexp": "^\\d{3}$", "exclusion": ""}, "SESSIONS": ["ASL_1","ASL_2"], "S":{"Atlases": ["Thalamus", "HOcort_CONN", "TotalGM","Tatu_ACA_MCA_PCA_Prox_Med_Dist"]}, "Q":{ "BackgroundSuppressionNumberPulses": 2, "LabelingType": "CASL", "Initial_PLD": 1800, "LabelingDuration": 1800, "SliceReadoutTime": 30, }}}