ANTsX neuroimaging-derived structural phenotypes of UK Biobank

Feature ranking across FSL, FreeSurfer, and ANTsX IDPs for predicting UKBB sociodemographic targets

Target	Data ID	Brief Description	ML Technique
Age	21003-2.0	Age (years) at imaging visit	linear regression
Fluid intelligence score	20191-0.0	Number of correct answers (of 13)	linear regression
Neuroticism score	20127-0.0	Summary of 12 behaviour domains	sparse regression
Numeric memory	20240-0.0	Maximum digits remembered correctly	sparse regression
Body mass index	21001-2.0	Impedance-based body composition	linear regression
Townsend deprivation index	189-0.0	Material deprivation measure	linear regression
Genetic sex	22001-0.0	Sex from genotyping	linear regression
Hearing difficulty	2247-2.0	Any difficulty? Yes/No	linear regression
Risk taking	2040-2.0	Do you take risks? Yes/No	linear regression
Same sex intercourse	2159-2.0	Ever had? Yes/No	DenseNet
Smoking	1249-2.0	Daily, occasionally, or $\leq 2$ times?	DenseNet
Alcohol	1558-2.0	Six frequency categories $^\dagger$	DenseNet

$\dagger$: Daily, 3-4 times/week, 1-2 times/week, 1-3 times/month, special occasions only, and never.

Couple notes:

For each sociodemographic variable, only the top performing ML technique for grouped set of all IDPs is used for the rankings below. For the majority of the variables listed above, this was linear regression.
Rankings are based on "variable importance" as determined by the ML technique (e.g., vi from the vip R package for linear regression).
Only the top 25 are listed. This can be easily modified to include more.

Age (linear regression)

Age

Package	Pipeline	Feature
ANTsX	Atropos	Cerebellum
FreeSurfer	ASEG	Volume of WM-hypointensities (whole brain)
ANTsX	Cereb	L\_III volume
FreeSurfer	ASEG	Volume of CerebralWhiteMatter (left hemisphere)
FreeSurfer	ASEG	Volume of CerebralWhiteMatter (right hemisphere)
FreeSurfer	ASEG	Volume of CC-Central (whole brain)
FreeSurfer	ASEG	Volume of SupraTentorial (whole brain)
FSL	Other	Continuous Volume of grey matter
FreeSurfer	ASEG	Volume of TotalGray (whole brain)
FreeSurfer	ASEG	Volume of Cortex (left hemisphere)
FreeSurfer	ASEG	Volume of VentricleChoroid (whole brain)
FreeSurfer	ASEG	Volume of Cortex (right hemisphere)
ANTsX	Cereb	CerebellarCSF volume
FreeSurfer	ASEG	Volume of VentralDC (right hemisphere)
ANTsX	DKT Volume	Right cerebellum exterior
FreeSurfer	ASEG	Volume of VentralDC (left hemisphere)
ANTsX	Cereb	CerebellarWhiteMatter volume
FreeSurfer	ASEG	Volume of SubCortGray (whole brain)
ANTsX	DKT Volume	Cerebellar vermal lobules VI VII
ANTsX	DKT Volume	Left caudate
FreeSurfer	ASEG	Volume of Amygdala (right hemisphere)
ANTsX	DKT Volume	Right lateral ventricle
ANTsX	Atropos	BrainStem
FreeSurfer	ASEG	Volume of Cerebellum-Cortex (left hemisphere)
FreeSurfer	ASEG	Volume of Caudate (left hemisphere)

FluidIntelligenceScore (linear regression)

FluidIntelligenceScore

Package	Pipeline	Feature
FSL	FAST	Volume of grey matter in Amygdala (right)
FreeSurfer	ASEG	Volume of CC-Mid-Anterior (whole brain)
ANTsX	DKT Thickness	Left paracentral
FSL	FAST	Volume of grey matter in Intracalcarine Cortex (right)
FSL	Other	Continuous Volume of peripheral cortical grey matter
ANTsX	DKT Thickness	Left superior frontal
FSL	FAST	Volume of grey matter in Amygdala (left)
ANTsX	DKT Thickness	Left inferior temporal
FSL	FAST	Volume of grey matter in Middle Temporal Gyrus - posterior division (left)
ANTsX	DKT Volume	Left hippocampus
FreeSurfer	DKT Thickness	Mean thickness of superiorparietal (left hemisphere)
FreeSurfer	DKT Thickness	Mean thickness of isthmuscingulate (right hemisphere)
FreeSurfer	ASEG	Volume of Inf-Lat-Vent (left hemisphere)
FSL	FAST	Volume of grey matter in Superior Temporal Gyrus - posterior division (right)
FreeSurfer	ASEG	Volume of Cortex (left hemisphere)
FSL	FAST	Volume of grey matter in X Cerebellum (left)
FreeSurfer	DKT Thickness	Mean thickness of fusiform (right hemisphere)
FreeSurfer	ASEG	Volume of Cortex (right hemisphere)
ANTsX	Cortical	Left rostral middle frontal volume
FreeSurfer	HippAmyg	Volume of subiculum-body (right hemisphere)
FreeSurfer	HippAmyg	Volume of HATA (right hemisphere)
FreeSurfer	HippAmyg	Volume of CA4-body (right hemisphere)
FreeSurfer	HippAmyg	Volume of Hippocampal-tail (right hemisphere)
FreeSurfer	HippAmyg	Volume of parasubiculum (right hemisphere)
ANTsX	DKT Thickness	Left caudal middle frontal

NeuroticismScore (sparse regression)

NeuroticismScore

Package	Pipeline	Feature
FSL	FAST	Volume of grey matter in Amygdala (right)
FreeSurfer	DKT Thickness	Mean thickness of superiortemporal (right hemisphere)
FreeSurfer	DKT Thickness	Mean thickness of posteriorcingulate (left hemisphere)
FSL	Other	Continuous Volume of peripheral cortical grey matter
ANTsX	DKT Thickness	Left supramarginal
FreeSurfer	DKT Thickness	Mean thickness of posteriorcingulate (right hemisphere)
FreeSurfer	DKT Thickness	Mean thickness of isthmuscingulate (left hemisphere)
ANTsX	DKT Thickness	Right posterior cingulate
ANTsX	DKT Thickness	Left lateral orbitofrontal
FreeSurfer	HippAmyg	Volume of AV (right hemisphere)
FreeSurfer	DKT Thickness	Mean thickness of lateralorbitofrontal (left hemisphere)
FreeSurfer	DKT Thickness	Mean thickness of superiorparietal (right hemisphere)
ANTsX	DKT Thickness	Right supramarginal
FreeSurfer	DKT Thickness	Mean thickness of superiortemporal (left hemisphere)
FreeSurfer	DKT Thickness	Mean thickness of inferiortemporal (left hemisphere)
ANTsX	DKT Thickness	Left precentral
FreeSurfer	DKT Thickness	Mean thickness of transversetemporal (left hemisphere)
FreeSurfer	DKT Thickness	Mean thickness of lingual (left hemisphere)
FreeSurfer	DKT Thickness	Mean thickness of isthmuscingulate (right hemisphere)
ANTsX	DKT Thickness	Left posterior cingulate
FreeSurfer	DKT Thickness	Mean thickness of rostralanteriorcingulate (right hemisphere)
FreeSurfer	DKT Thickness	Mean thickness of lateralorbitofrontal (right hemisphere)
FreeSurfer	HippAmyg	Volume of AV (left hemisphere)
ANTsX	DKT Thickness	Left isthmus cingulate
ANTsX	DKT Thickness	Right precentral

NumericMemory (sparse regression)

NumericMemory

Package	Pipeline	Feature
FreeSurfer	HippAmyg	Volume of AV (right hemisphere)
FreeSurfer	DKT Thickness	Mean thickness of isthmuscingulate (left hemisphere)
FSL	Other	Continuous Volume of peripheral cortical grey matter
FreeSurfer	DKT Thickness	Mean thickness of postcentral (right hemisphere)
FreeSurfer	DKT Thickness	Mean thickness of inferiorparietal (left hemisphere)
FreeSurfer	HippAmyg	Volume of AV (left hemisphere)
FreeSurfer	DKT Thickness	Mean thickness of precuneus (left hemisphere)
ANTsX	DKT Thickness	Right lateral orbitofrontal
ANTsX	DKT Thickness	Right medial orbitofrontal
FreeSurfer	DKT Thickness	Mean thickness of lingual (left hemisphere)
FreeSurfer	DKT Thickness	Mean thickness of supramarginal (left hemisphere)
FreeSurfer	DKT Thickness	Mean thickness of isthmuscingulate (right hemisphere)
ANTsX	DKT Thickness	Right transverse temporal
FreeSurfer	DKT Thickness	Mean thickness of insula (left hemisphere)
ANTsX	DKT Thickness	Left fusiform
FreeSurfer	DKT Thickness	Mean thickness of rostralmiddlefrontal (left hemisphere)
ANTsX	DKT Thickness	Right superior temporal
ANTsX	DKT Thickness	Left lateral orbitofrontal
FreeSurfer	DKT Thickness	Mean thickness of medialorbitofrontal (right hemisphere)
FreeSurfer	DKT Thickness	Mean thickness of parsorbitalis (left hemisphere)
ANTsX	DKT Thickness	Left transverse temporal
FreeSurfer	DKT Thickness	Mean thickness of insula (right hemisphere)
ANTsX	Cortical	Left caudal middle frontal volume
FreeSurfer	DKT Thickness	Mean thickness of lateralorbitofrontal (right hemisphere)
ANTsX	DKT Thickness	Left medial orbitofrontal

BMI (linear regression)

BMI

Package	Pipeline	Feature
ANTsX	DKT Thickness	Left paracentral
FSL	FAST	Volume of grey matter in Amygdala (left)
FreeSurfer	ASEG	Volume of Cerebellum-White-Matter (right hemisphere)
ANTsX	Cereb	CerebellarGrayMatter volume
FreeSurfer	ASEG	Volume of Cerebellum-White-Matter (left hemisphere)
ANTsX	DKT Thickness	Left lingual
FreeSurfer	ASEG	Volume of EstimatedTotalIntraCranial (whole brain)
ANTsX	Atropos	BrainStem
FSL	Other	Continuous Volume of peripheral cortical grey matter (normalised for head size)
FSL	FAST	Volume of grey matter in Occipital Fusiform Gyrus (right)
FSL	FAST	Volume of grey matter in Lateral Occipital Cortex - superior division (right)
FSL	FAST	Volume of grey matter in Amygdala (right)
FSL	FAST	Volume of grey matter in Lingual Gyrus (right)
FreeSurfer	ASEG	Volume of VentralDC (right hemisphere)
FreeSurfer	ASEG	Volume of SupraTentorialNotVent (whole brain)
FSL	FAST	Volume of grey matter in Caudate (left)
FreeSurfer	DKT Thickness	Mean thickness of superiorfrontal (left hemisphere)
FSL	FAST	Volume of grey matter in Cuneal Cortex (left)
FSL	FAST	Volume of grey matter in VIIIa Cerebellum (left)
ANTsX	DKT Volume	Left thalamus proper
FSL	FAST	Volume of grey matter in Pallidum (right)
FSL	FAST	Volume of grey matter in IX Cerebellum (right)
FreeSurfer	Volume	Volume of transversetemporal (right hemisphere)
FSL	FIRST	Volume of caudate (left)
FreeSurfer	Volume	Volume of isthmuscingulate (right hemisphere)

TownsendDeprivationIndex (linear regression)

TownsendDeprivationIndex

Package	Pipeline	Feature
FSL	FAST	Volume of grey matter in Amygdala (left)
FSL	Other	Continuous Volume of peripheral cortical grey matter
FSL	FAST	Volume of grey matter in Heschl’s Gyrus (includes H1 and H2) (left)
FSL	Other	Continuous Volume of ventricular cerebrospinal fluid
FSL	Other	Continuous Volume of ventricular cerebrospinal fluid (normalised for head size)
FreeSurfer	ASEG	Volume of SupraTentorial (whole brain)
FreeSurfer	ASEG	Volume of VentralDC (left hemisphere)
FSL	FAST	Volume of grey matter in Heschl’s Gyrus (includes H1 and H2) (right)
ANTsX	SYSU WMH	Left cerebellum
FreeSurfer	ASEG	Volume of TotalGray (whole brain)
FSL	FAST	Volume of grey matter in Superior Parietal Lobule (right)
FreeSurfer	DKT Thickness	Mean thickness of superiorfrontal (right hemisphere)
ANTsX	Cereb	CerebellarGrayMatter volume
ANTsX	Cereb	L\_III volume
ANTsX	DKT Volume	Right caudal anterior cingulate
ANTsX	Cortical	Left insula volume
FreeSurfer	ASEG	Volume of SupraTentorialNotVent (whole brain)
FSL	FAST	Volume of grey matter in Thalamus (left)
ANTsX	DKT Thickness	Left superior parietal
FSL	FAST	Volume of grey matter in Inferior Temporal Gyrus - temporooccipital part (left)
FSL	FAST	Volume of grey matter in Frontal Pole (right)
FSL	FAST	Volume of grey matter in Planum Temporale (left)
ANTsX	Cereb	R\_X volume
FreeSurfer	DKT Thickness	Mean thickness of superiortemporal (left hemisphere)
FSL	FAST	Volume of grey matter in Occipital Fusiform Gyrus (left)

GeneticSex (linear regression)

GeneticSex

Package	Pipeline	Feature
ANTsX	Atropos	DeepGrayMatter
FreeSurfer	HippAmyg	Volume of AV (right hemisphere)
FreeSurfer	ASEG	Volume of VentralDC (right hemisphere)
FreeSurfer	ASEG	Volume of CerebralWhiteMatter (left hemisphere)
ANTsX	DKT Volume	Left thalamus proper
FreeSurfer	ASEG	Volume of CerebralWhiteMatter (right hemisphere)
FreeSurfer	ASEG	Volume of Cortex (right hemisphere)
FreeSurfer	ASEG	Volume of Cortex (left hemisphere)
FreeSurfer	ASEG	Volume of CC-Central (whole brain)
FSL	FIRST	Volume of accumbens (left)
FSL	FAST	Volume of grey matter in Lateral Occipital Cortex - superior division (left)
ANTsX	Cortical	Right lateral occipital volume
FSL	FAST	Volume of grey matter in Frontal Medial Cortex (left)
ANTsX	DKT Volume	Right caudate
–	–	NA
FreeSurfer	DKT Thickness	Mean thickness of paracentral (right hemisphere)
FreeSurfer	Volume	Volume of transversetemporal (left hemisphere)
ANTsX	Cereb	R\_IX thickness
ANTsX	Cortical	Left parahippocampal volume
ANTsX	Cereb	R\_VIIB thickness
FreeSurfer	HippAmyg	Volume of AV (left hemisphere)
ANTsX	Cortical	Right superior parietal volume
ANTsX	Cereb	CerebellarWhiteMatter volume
ANTsX	DKT Volume	Right inferior parietal
FSL	FAST	Volume of grey matter in Intracalcarine Cortex (right)

Hearing (linear regression)

Hearing

Package	Pipeline	Feature
FSL	FAST	Volume of grey matter in Amygdala (left)
FSL	FAST	Volume of grey matter in Amygdala (right)
ANTsX	DKT Thickness	Right lingual
ANTsX	Cereb	L\_IX volume
ANTsX	DeepFLASH	Left aLEC
ANTsX	DKT Thickness	Left transverse temporal
FreeSurfer	Volume	Volume of caudalanteriorcingulate (left hemisphere)
FSL	FAST	Volume of grey matter in X Cerebellum (right)
FreeSurfer	Volume	Volume of medialorbitofrontal (left hemisphere)
FSL	FAST	Volume of grey matter in Temporal Fusiform Cortex - posterior division (left)
FreeSurfer	DKT Thickness	Mean thickness of posteriorcingulate (right hemisphere)
FSL	Other	Continuous Volume of grey matter
FreeSurfer	Volume	Volume of paracentral (left hemisphere)
ANTsX	DKT Volume	Right thalamus proper
ANTsX	Cereb	L\_Crus\_I volume
ANTsX	Cereb	L\_I\_II volume
FreeSurfer	Volume	Volume of inferiorparietal (left hemisphere)
FreeSurfer	DKT Thickness	Mean thickness of inferiorparietal (left hemisphere)
ANTsX	Cereb	R\_VI volume
ANTsX	DKT Volume	Right caudate
FSL	FAST	Volume of grey matter in VI Cerebellum (right)
FSL	FAST	Volume of grey matter in Parahippocampal Gyrus - posterior division (left)
FSL	FAST	Volume of grey matter in Middle Temporal Gyrus - temporooccipital part (right)
ANTsX	DKT Volume	Right middle temporal
ANTsX	Cereb	L\_Crus\_II volume

RiskTaking (linear regression)

RiskTaking

Package	Pipeline	Feature
FSL	FAST	Volume of grey matter in Amygdala (right)
FSL	FAST	Volume of grey matter in Amygdala (left)
FreeSurfer	ASEG	Volume of BrainSeg (whole brain)
FSL	FAST	Volume of grey matter in Frontal Orbital Cortex (left)
FreeSurfer	DKT Thickness	Mean thickness of parsorbitalis (left hemisphere)
FreeSurfer	HippAmyg	Volume of CL (left hemisphere)
FreeSurfer	HippAmyg	Volume of Hippocampal-tail (left hemisphere)
ANTsX	DKT Thickness	Left caudal anterior cingulate
FreeSurfer	HippAmyg	Volume of parasubiculum (left hemisphere)
FreeSurfer	HippAmyg	Volume of presubiculum-body (left hemisphere)
FreeSurfer	HippAmyg	Volume of CA3-body (left hemisphere)
FreeSurfer	HippAmyg	Volume of CA4-body (left hemisphere)
FreeSurfer	HippAmyg	Volume of subiculum-body (left hemisphere)
FreeSurfer	HippAmyg	Volume of HATA (left hemisphere)
FSL	FAST	Volume of grey matter in Temporal Fusiform Cortex - anterior division (left)
FSL	FAST	Volume of grey matter in Intracalcarine Cortex (left)
FreeSurfer	DKT Thickness	Mean thickness of lateralorbitofrontal (right hemisphere)
ANTsX	DeepFLASH	Right perirhinal
ANTsX	Cortical	Right pericalcarine volume
ANTsX	DeepFLASH	Right MTL
ANTsX	DKT Volume	Right pericalcarine
FreeSurfer	HippAmyg	Volume of AV (right hemisphere)
FreeSurfer	ASEG	Volume of Amygdala (left hemisphere)
FreeSurfer	ASEG	Volume of TotalGray (whole brain)
FreeSurfer	DKT Thickness	Mean thickness of entorhinal (left hemisphere)

SameSexIntercourse (DenseNet)

SameSexIntercourse

Package	Pipeline	Feature
–	–	GeneticSex
–	–	Age
FreeSurfer	Volume	Volume of pericalcarine (left hemisphere)
FreeSurfer	ASEG	Volume of 4th-Ventricle (whole brain)
ANTsX	DKT Thickness	Left transverse temporal
ANTsX	Cereb	R\_Crus\_II volume
FreeSurfer	DKT Thickness	Mean thickness of medialorbitofrontal (left hemisphere)
ANTsX	SYSU WMH	Right temporal
ANTsX	Cereb	CerebellarCSF volume
FSL	FAST	Volume of grey matter in Lingual Gyrus (left)
ANTsX	DKT Volume	Left pars triangularis
ANTsX	Cortical	Right pars orbitalis volume
FSL	FAST	Volume of grey matter in IX Cerebellum (vermis)
FSL	Other	Continuous Volumetric scaling from T1 head image to standard space
ANTsX	DeepFLASH	Left perirhinal
ANTsX	DKT Volume	Right pars orbitalis
ANTsX	SYSU WMH	Right brain stem
FSL	FAST	Volume of grey matter in VIIb Cerebellum (left)
ANTsX	DKT Thickness	Right pericalcarine
FSL	FAST	Volume of grey matter in Parahippocampal Gyrus - anterior division (left)
ANTsX	Cortical	Right lateral occipital volume
ANTsX	DKT Volume	Right postcentral
FSL	FAST	Volume of grey matter in Crus I Cerebellum (left)
ANTsX	DKT Volume	Right pericalcarine
FreeSurfer	DKT Thickness	Mean thickness of lingual (right hemisphere)

Smoking (DenseNet)

Smoking

Package	Pipeline	Feature
FreeSurfer	ASEG	Volume of choroid-plexus (left hemisphere)
–	–	Age
ANTsX	SYSU WMH	Left parietal
ANTsX	DKT Thickness	Left pericalcarine
FreeSurfer	DKT Thickness	Mean thickness of transversetemporal (left hemisphere)
FSL	FAST	Volume of grey matter in Amygdala (left)
FreeSurfer	DKT Thickness	Mean thickness of fusiform (left hemisphere)
ANTsX	SYSU WMH	Left occipital
ANTsX	Cereb	R\_VIIIA thickness
ANTsX	Cortical	Left insula volume
FreeSurfer	HippAmyg	Volume of GC-ML-DG-body (right hemisphere)
FSL	FAST	Volume of grey matter in IX Cerebellum (vermis)
ANTsX	Cereb	L\_V thickness
ANTsX	DKT Thickness	Right precentral
FreeSurfer	DKT Thickness	Mean thickness of lingual (right hemisphere)
FSL	FIRST	Volume of amygdala (left)
FreeSurfer	DKT Thickness	Mean thickness of postcentral (left hemisphere)
FSL	FAST	Volume of grey matter in Superior Parietal Lobule (left)
–	–	GeneticSex
ANTsX	Atropos	DeepGrayMatter
FSL	FAST	Volume of grey matter in VIIIa Cerebellum (right)
FreeSurfer	Volume	Volume of precuneus (right hemisphere)
ANTsX	DKT Volume	Left thalamus proper
FreeSurfer	Volume	Volume of supramarginal (right hemisphere)
FreeSurfer	HippAmyg	Volume of parasubiculum (left hemisphere)

Alcohol (DenseNet)

Alcohol

Package	Pipeline	Feature
FreeSurfer	DKT Thickness	Mean thickness of parsopercularis (left hemisphere)
ANTsX	Cortical	Right entorhinal volume
FreeSurfer	DKT Thickness	Mean thickness of superiortemporal (right hemisphere)
FreeSurfer	DKT Thickness	Mean thickness of lateraloccipital (right hemisphere)
FSL	FAST	Volume of grey matter in Middle Temporal Gyrus - anterior division (right)
ANTsX	DKT Thickness	Right pericalcarine
ANTsX	Cortical	Right inferior temporal volume
FSL	FAST	Volume of grey matter in Subcallosal Cortex (left)
FreeSurfer	DKT Thickness	Mean thickness of lingual (right hemisphere)
ANTsX	Cortical	Left posterior cingulate volume
ANTsX	DKT Volume	Right inferior temporal
FSL	FAST	Volume of grey matter in Subcallosal Cortex (right)
–	–	Age
ANTsX	DKT Volume	Left cuneus
FSL	FAST	Volume of grey matter in VIIIb Cerebellum (right)
FreeSurfer	ASEG	Volume of Inf-Lat-Vent (right hemisphere)
ANTsX	DKT Thickness	Right rostral middle frontal
ANTsX	DKT Thickness	Left lateral occipital
FreeSurfer	Volume	Volume of rostralmiddlefrontal (right hemisphere)
ANTsX	Cortical	Right fusiform volume
ANTsX	DKT Volume	Left inferior temporal
FSL	FAST	Volume of grey matter in Inferior Frontal Gyrus - pars triangularis (right)
ANTsX	DKT Volume	Left pars opercularis
ANTsX	DeepFLASH	Left extra hippocampal
FreeSurfer	Volume	Volume of cuneus (left hemisphere)

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