6. Built-in Pipeline Components#
6.1. Data Grabber#
6.1.1. Available#
Class |
Description |
Access |
Type/Config |
State |
Version Added |
|---|---|---|---|---|---|
Open with registration |
Built-in |
Done |
0.0.1 |
||
UKB VBM dataset preprocessed with CAT.
Available for Juseless only.
|
Restricted |
|
Done |
0.0.1 |
|
CamCAN VBM dataset preprocessed with CAT.
Available for Juseless only.
|
Restricted |
|
Done |
0.0.1 |
|
Open without registration |
Built-in |
Done |
0.0.1 |
||
Open without registration |
Built-in |
Done |
0.0.1 |
||
Open without registration |
Built-in |
Done |
0.0.1 |
||
AOMIC ID1000 VBM dataset.
Available for Juseless only.
|
Restricted |
|
Done |
0.0.1 |
|
Available for Juseless only.
|
Restricted |
|
Done |
0.0.1 |
|
UCLA fMRIPrep dataset.
Available for Juseless only.
|
Restricted |
|
Done |
0.0.1 |
6.1.2. Planned#
Name |
Description |
Access |
Type/Config |
Reference |
|---|---|---|---|---|
ENKI |
ENKI dataset for Juseless |
Restricted |
|
6.2. Preprocessor#
6.2.1. Available#
Class |
Description |
State |
Version Added |
|---|---|---|---|
Remove confounds from |
Done |
0.0.1 |
|
Warp / transform data from one space to another
(subject-native or other template spaces)
|
Done |
0.0.4 |
|
|
Apply smoothing to data, particularly useful when dealing with
fMRIPrep-ed data |
In Progress |
6.3. Marker#
6.3.1. Available#
Class |
Description |
State |
Version Added |
|---|---|---|---|
Apply parcellation and perform aggregation function |
Done |
0.0.1 |
|
Compute functional connectivity over parcellation |
Done |
0.0.1 |
|
Compute functional connectivity across two parcellations |
Done |
0.0.1 |
|
Spherical aggregation using mean |
Done |
0.0.1 |
|
Compute functional connectivity over spheres placed on coordinates |
Done |
0.0.1 |
|
Compute root sum of squares of edgewise timeseries |
Done |
0.0.1 |
|
Calculate regional homogeneity over parcellation |
Done |
0.0.1 |
|
Calculate regional homogeneity over spheres placed on coordinates |
Done |
0.0.1 |
|
Calculate (f)ALFF and aggregate using parcellations |
Done |
0.0.1 |
|
Calculate (f)ALFF and aggregate using spheres placed on coordinates |
Done |
0.0.1 |
|
Done |
0.0.2 |
||
Calculate edge-centric functional connectivity over spheres placed on
coordinates, as found in
|
Done |
0.0.2 |
|
Calculate temporal signal-to-noise ratio using parcellations |
Done |
0.0.2 |
|
Calculate temporal signal-to-noise ratio using spheres placed on
coordinates
|
Done |
0.0.2 |
|
Calculate Hurst exponent of a time series as found in
|
Done |
0.0.4 |
|
Calculate AUC of multiscale entropy of a time series as found in
|
Done |
0.0.4 |
|
Calculate permutation entropy of a time series as found in
|
Done |
0.0.4 |
|
Calculate range entropy of a time series as found in
|
Done |
0.0.4 |
|
Calculate AUC of range entropy of a time series as found in
|
Done |
0.0.4 |
|
Calculate sample entropy of a time series as found in
|
Done |
0.0.4 |
6.3.2. Planned#
Name |
Description |
Reference |
|---|---|---|
Connectedness |
Compute connectedness |
6.4. Parcellation#
6.4.1. Available#
Name |
Options |
Keys |
Template Spaces |
Version Added |
Publication |
|---|---|---|---|---|---|
Schaefer |
|
Schaefer900x7, Schaefer1000x7, Schaefer100x17,Schaefer200x17, Schaefer300x17, Schaefer400x17,Schaefer500x17, Schaefer600x17, Schaefer700x17,Schaefer800x17, Schaefer900x17, Schaefer1000x17 |
|
0.0.1 |
Schaefer, A., Kong, R., Gordon, E.M. et al.
Local-Global Parcellation of the Human Cerebral Cortex from
Intrinsic Functional Connectivity MRI
Cerebral Cortex, Volume 28(9), Pages 3095–3114 (2018).
|
SUIT |
|
|
|
0.0.1 |
Diedrichsen, J.
A spatially unbiased atlas template of the human cerebellum.
NeuroImage, Volume 33(1), Pages 127–138 (2006).
|
Tian |
|
TianxS1x3TxMNI6thgeneration, TianxS1x7TxMNI6thgeneration,TianxS2x3TxMNI6thgeneration, TianxS2x7TxMNI6thgeneration,TianxS3x3TxMNI6thgeneration, TianxS3x7TxMNI6thgeneration,TianxS4x3TxMNI6thgeneration, TianxS4x7TxMNI6thgeneration,TianxS1x3TxMNInonlinear2009cAsym,TianxS2x3TxMNInonlinear2009cAsym,TianxS3x3TxMNInonlinear2009cAsym,TianxS4x3TxMNInonlinear2009cAsym |
|
0.0.1 |
Tian, Y., Margulies, D.S., Breakspear, M. et al.
Topographic organization of the human subcortex
unveiled with functional connectivity gradients.
Nature Neuroscience, Volume 23, Pages 1421–1432 (2020).
|
AICHA |
|
|
|
0.0.3 |
Joliot, M., Jobard, G., Naveau, M. et al.
AICHA: An atlas of intrinsic connectivity of homotopic areas.
Journal of Neuroscience Methods, Volume 254, Pages 46-59 (2015).
|
Shen |
|
Shen_2013_50, Shen_2013_100, Shen_2013_150,Shen_2015_268, Shen_2019_368 |
|
0.0.3 |
Shen, X., Tokoglu, F., Papademetris, X., Constable, R.T.
Groupwise whole-brain parcellation from resting-state fMRI data
for network node identification.
NeuroImage, Volume 82 (2013).
Finn, E.S., Shen, X., Scheinost, D., et al.
Functional connectome fingerprinting: identifying individuals using
patterns of brain connectivity.
Nature Neuroscience, Volume 18(11), Pages 1664-1671 (2015).
|
Yan |
|
Yan100xYeo7, Yan200xYeo7, Yan300xYeo7,Yan400xYeo7, Yan500xYeo7, Yan600xYeo7,Yan700xYeo7, Yan800xYeo7, Yan900xYeo7,Yan1000xYeo7,Yan100xYeo17, Yan200xYeo17, Yan300xYeo17,Yan400xYeo17, Yan500xYeo17, Yan600xYeo17,Yan700xYeo17, Yan800xYeo17, Yan900xYeo17,Yan1000xYeo17,Yan100xKong17, Yan200xKong17, Yan300xKong17,Yan400xKong17, Yan500xKong17, Yan600xKong17,Yan700xKong17, Yan800xKong17, Yan900xKong17,Yan1000xKong17 |
|
0.0.3 |
Yan, X., Kong, R., Xue, A., et al.
Homotopic local-global parcellation of the human cerebral cortex from
resting-state functional connectivity.
NeuroImage, Volume 273 (2023).
|
Brainnetome |
|
|
|
0.0.4 |
Fan, L., Li, H., Zhuo, J., et al.
The Human Brainnetome Atlas: A New Brain Atlas Based on Connectional
Architecture
Cerebral Cortex, Volume 26(8), Pages 3508–3526 (2016).
|
6.4.2. Planned#
Name |
Publication |
|---|---|
Desikan-Killiany |
Desikan, R.S., Ségonne, F., Fischl, B. et al.
An automated labeling system for subdividing the human cerebral cortex
on MRI scans into gyral based regions of interest.
NeuroImage, Volume 31(3), Pages 968-980 (2006).
|
Glasser |
Glasser, M.F., Coalson, T.S., Robinson, E.C. et al.
A multi-modal parcellation of human cerebral cortex.
Nature (2016).
|
AAL |
Rolls, E.T., Huang, C.C., Lin, C.P., et al.
Automated anatomical labelling atlas 3.
NeuroImage, Volume 206 (2020).
|
Mindboggle 101 |
Klein, A., & Tourville, J.
101 labeled brain images and a consistent human cortical labeling
protocol.
Frontiers in Neuroscience (2012).
|
Destrieux |
Destrieux, C., Fischl, B., Dale, A., & Halgren, E.
Automatic parcellation of human cortical gyri and sulci using standard
anatomical nomenclature.
NeuroImage, Volume 53(1), Pages 1–15 (2010).
|
Fan |
Fan, L., Li, H., Zhuo, J. et al.
The human brainnetome atlas: a new brain atlas based on connectional
architecture.
Cerebral cortex, Volume 26(8), Pages 3508-3526 (2016).
|
Buckner |
Buckner, R.L., Krienen, F.M., Castellanos, A., Diaz, J.C., Yeo, B.T.T.
The organization of the human cerebellum estimated by intrinsic
functional connectivity.
Journal of Neurophysiology, Volume 106(5), Pages 2322–2345 (2011).
Yeo, B.T.T., Krienen, F.M., Sepulcre, J. et al.
The organization of the human cerebral cortex estimated by intrinsic
functional connectivity.
Journal of Neurophysiology, Volume 106(3), Pages 1125–1165 (2011).
|
6.5. Coordinates#
6.5.1. Available#
Name |
Keys |
Version Added |
Publication |
|---|---|---|---|
Cognitive action control |
|
0.0.1 |
Cieslik, E.C., Mueller, V.I., Eickhoff, C.R., Langner, R.,
Eickhoff, S.B.
Three key regions for supervisory attentional control: Evidence from
neuroimaging meta-analyses.
Neuroscience & Biobehavioral Reviews, Volume 48, Pages 22-34 (2015).
|
Cognitive action regulation |
|
0.0.1 |
Langner, R., Leiberg, S., Hoffstaedter, F., Eickhoff, S.B.
Towards a human self-regulation system: Common and distinct neural
signatures of emotional and behavioural control.
Neuroscience & Biobehavioral Reviews, Volume 90, Pages 400-410 (2018).
|
Default mode network |
|
0.0.1 |
Van Dijk, K.R., Hedden, T., Venkataraman, A. et al.
Intrinsic functional connectivity as a tool for human connectomics:
theory, properties, and optimization.
Journal of neurophysiology, Volume 103(1), Pages 297-321 (2010).
Buckner, R.L., Andrews‐Hanna, J.R., & Schacter, D.L.
The brain’s default network: anatomy, function, and relevance to
disease.
Annals of the New York Academy of Sciences, Volume 1124(1), Pages 1-38
(2008).
|
Missing formal name |
|
0.0.1 |
Missing publication details |
Empathic processing |
|
0.0.1 |
Bzdok, D., Schilbach, L., Vogeley, K. et al.
Parsing the neural correlates of moral cognition: ALE meta-analysis on
morality, theory of mind, and empathy.
Brain Structure and Function, Volume 217(4), Pages 783-796 (2012).
|
Extended social-affective default |
|
0.0.1 |
Amft, M., Bzdok, D., Laird, A.R. et al.
Definition and characterization of an extended social-affective default
network.
Brain structure & function, Volume 220, Pages 1031–1049 (2015).
|
Extended multiple-demand network |
|
0.0.1 |
Camilleri, J.A., Müller, V.I., Fox, P. et al.
Definition and characterization of an extended multiple-demand network.
NeuroImage, Volume 165, Pages 138-147 (2018).
|
Motor execution |
|
0.0.1 |
Witt, S.T., Laird, A.R., Meyerand, M.E.
Functional neuroimaging correlates of finger-tapping task variations:
An ALE meta-analysis,
NeuroImage, Volume 42(1), Pages 343-356 (2008).
|
Multitasking |
|
0.0.1 |
Worringer, B., Langner, R., Koch, I. et al.
Common and distinct neural correlates of dual-tasking and
task-switching: a meta-analytic review and a neuro-cognitive processing
model of human multitasking.
Brain structure & function, Volume 224(5), Pages 1845–1869 (2019).
|
Physiological stress |
|
0.0.1 |
Kogler, L., Müller, V.I., Chang, A. et al.
Psychosocial versus physiological stress — Meta-analyses on
deactivations and activations of the neural correlates of stress
reactions.
NeuroImage, Volume 119, Pages 235-251 (2015).
|
Reward-related decision making |
|
0.0.1 |
Liu, X., Hairston, J., Schrier, M., Fan, J.
Common and distinct networks underlying reward valence and processing
stages: A meta-analysis of functional neuroimaging studies.
Neuroscience & Biobehavioral Reviews, Volume 35(5), Pages 1219-1236
(2011).
|
Missing formal name |
|
0.0.1 |
Missing publication details |
Theory-of-mind cognition |
|
0.0.1 |
Bzdok, D., Schilbach, L., Vogeley, K. et al.
Parsing the neural correlates of moral cognition: ALE meta-analysis on
morality, theory of mind, and empathy.
Brain Structure and Function, Volume 217(4), Pages 783-796 (2012).
|
Vigilant attention |
|
0.0.1 |
Langner, R., & Eickhoff, S.B.
Sustaining attention to simple tasks: a meta-analytic review of the
neural mechanisms of vigilant attention.
Psychological bulletin, Volume 139 4, Pages 870-900 (2013).
|
Working memory |
|
0.0.1 |
Rottschy, C., Langner, R., Dogan, I. et al.
Modelling neural correlates of working memory: A coordinate-based
meta-analysis.
NeuroImage, Volume 60, Pages 830-846 (2012).
|
Areal functional network from Power et al. (2011) |
|
0.0.2 |
Power, J. D., Cohen, A. L., Nelson, S. M. et al.
Functional network organization of the human brain.
Neuron, Volume 72(4), Pages 665–678 (2011).
|
Brain maturity functional connections from Dosenbach et al. (2010) |
|
0.0.2 |
Dosenbach, N.U.F., Nardos, B., Cohen, A.L. et al.
Prediction of Individual Brain Maturity Using fMRI
Science, Volume 329(5997), Pages 1358-1361 (2010).
|
Areal functional network from Power et al. (2013) |
|
0.0.4 |
Power, J. D., Schlaggar, B. L., Lessov-Schlaggar, C. N., &
Petersen, S. E.
Evidence for hubs in human functional brain networks.
Neuron, Volume 79(4), Pages 798–813 (2013).
|
Autobiographical Memory from Spreng et al. (2009) |
|
0.0.4 |
Spreng, R. N., Mar, R. A., Kim, A. S. N.
The Common Neural Basis of Autobiographical Memory, Prospection,
Navigation, Theory of Mind, and the Default Mode: A Quantitative
Meta-analysis.
Journal of Cognitive Neuroscience, Volume 21(3), Pages 489–510 (2009).
|
6.5.2. Planned#
Name |
Publication |
|---|---|
Emotional scene and face processing (EmoSF) |
Sabatinelli, D., Fortune, E.E., Li, Q. et al.
Emotional perception: Meta-analyses of face and natural scene
processing.
NeuroImage, Volume 54(3), Pages 2524-2533 (2011).
|
Perceptuo-motor network |
Heckner, M.K., Cieslik, E.C., Eickhoff, S.B. et al.
The Aging Brain and Executive Functions Revisited: Implications from
Meta-analytic and Functional-Connectivity Evidence.
Journal of Cognitive Neuroscience, Volume 33(9), Pages 1716–1752 (2021).
|
6.6. Mask#
6.6.1. Available#
Name |
Keys |
Template Space |
Version Added |
Description - Publication |
|---|---|---|---|---|
Vickery-Patil (Gray Matter) |
GM_prob0.2 |
|
0.0.1 |
Vickery, Sam, & Patil, Kaustubh. (2022).
Chimpanzee and Human Gray Matter Masks [Data set]. Zenodo.
|
Vickery-Patil (Cortex + Basal Ganglia) |
GM_prob0.2_cortex |
|
0.0.1 |
Vickery, Sam, & Patil, Kaustubh. (2022).
Chimpanzee and Human Gray Matter Masks [Data set]. Zenodo.
|
|
compute_brain_mask |
Adapts to the target data |
0.0.2 |
Compute the whole-brain, gray-matter or white-matter mask using
the template and the resolution from the target image. The
templates are obtained via
templateflow. |
|
compute_epi_mask |
Adapts to the target data |
0.0.2 |
Compute a brain mask from fMRI data. This is based on an heuristic
proposed by T.Nichols: find the least dense point of the histogram,
between fractions
lower_cutoff and upper_cutoff of the totalimage histogram. See
nilearn.masking.compute_epi_mask() |
|
compute_background_mask |
Adapts to the target data |
0.0.2 |
Compute a brain mask for the images by guessing the value of the
background from the border of the image.
|