.. include:: links.inc .. _builtin: Built-in Pipeline Components ============================ Data Grabber ------------ .. Provide a list of the DataGrabbers that are implemented or planned. Access: Valid options are - Open - Open with registration - Restricted Type/config: this should mention whether the class is built-in in the core of junifer or needs to be imported from a specific configuration in the `junifer.configs` module. State: this should indicate the state of the dataset. Valid options are - Planned - In Progress - Done Version added: If the status is "Done", the junifer version in which the dataset was added. Else, a link to the Github issue or pull request implementing the dataset. Links to github can be added by using the following syntax: :gh:`` Available ~~~~~~~~~ .. list-table:: :widths: auto :header-rows: 1 * - Class - Description - Access - Type/Config - State - Version Added * - :class:`.DataladHCP1200` - `HCP OpenAccess dataset `_ - Open with registration - Built-in - Done - 0.0.1 * - :class:`.JuselessDataladUKBVBM` - | UKB VBM dataset preprocessed with CAT. | Available for Juseless only. - Restricted - ``junifer.configs.juseless`` - Done - 0.0.1 * - :class:`.JuselessDataladCamCANVBM` - | CamCAN VBM dataset preprocessed with CAT. | Available for Juseless only. - Restricted - ``junifer.configs.juseless`` - Done - 0.0.1 * - :class:`.DataladAOMICID1000` - `AOMIC 1000 dataset `_ - Open without registration - Built-in - Done - 0.0.1 * - :class:`.DataladAOMICPIOP1` - `AOMIC PIOP1 dataset `_ - Open without registration - Built-in - Done - 0.0.1 * - :class:`.DataladAOMICPIOP2` - `AOMIC PIOP2 dataset `_ - Open without registration - Built-in - Done - 0.0.1 * - :class:`.JuselessDataladAOMICID1000VBM` - | AOMIC ID1000 VBM dataset. | Available for Juseless only. - Restricted - ``junifer.configs.juseless`` - Done - 0.0.1 * - :class:`.JuselessDataladIXIVBM` - | `IXI VBM dataset `_. | Available for Juseless only. - Restricted - ``junifer.configs.juseless`` - Done - 0.0.1 * - :class:`.JuselessUCLA` - | UCLA fMRIPrep dataset. | Available for Juseless only. - Restricted - ``junifer.configs.juseless`` - Done - 0.0.1 Planned ~~~~~~~ .. list-table:: :widths: auto :header-rows: 1 * - Name - Description - Access - Type/Config - Reference * - ENKI - ENKI dataset for Juseless - Restricted - ``junifer.configs.juseless`` - :gh:`47` Preprocessor ------------ .. Provide a list of the Preprocessors that are implemented or planned. State: this should indicate the state of the preprocessor. Valid options are - Planned - In Progress - Done Version added: If the status is "Done", the junifer version in which the preprocessor was added. Else, a link to the Github issue or pull request implementing the preprocessor. Links to github can be added by using the following syntax: :gh:`` Available ~~~~~~~~~ .. list-table:: :widths: auto :header-rows: 1 * - Class - Description - State - Version Added * - :class:`.fMRIPrepConfoundRemover` - Remove confounds from ``fMRIPrep``-ed data - Done - 0.0.1 * - :class:`.SpaceWarper` - | Warp / transform data from one space to another | (subject-native or other template spaces) - Done - 0.0.4 * - ``Smoothing`` - | Apply smoothing to data, particularly useful when dealing with | ``fMRIPrep``-ed data - In Progress - :gh:`161` .. Planned ~~~~~~~ Marker ------ .. Provide a list of the Markers that are implemented or planned. State: this should indicate the state of the marker. Valid options are - Planned - In Progress - Done Version added: If the status is "Done", the junifer version in which the marker was added. Else, a link to the Github issue or pull request implementing the marker. Links to github can be added by using the following syntax: :gh:`` Available ~~~~~~~~~ .. list-table:: :widths: auto :header-rows: 1 * - Class - Description - State - Version Added * - :class:`.ParcelAggregation` - Apply parcellation and perform aggregation function - Done - 0.0.1 * - :class:`.FunctionalConnectivityParcels` - Compute functional connectivity over parcellation - Done - 0.0.1 * - :class:`.CrossParcellationFC` - Compute functional connectivity across two parcellations - Done - 0.0.1 * - :class:`.SphereAggregation` - Spherical aggregation using mean - Done - 0.0.1 * - :class:`.FunctionalConnectivitySpheres` - Compute functional connectivity over spheres placed on coordinates - Done - 0.0.1 * - :class:`.RSSETSMarker` - Compute root sum of squares of edgewise timeseries - Done - 0.0.1 * - :class:`.ReHoParcels` - Calculate regional homogeneity over parcellation - Done - 0.0.1 * - :class:`.ReHoSpheres` - Calculate regional homogeneity over spheres placed on coordinates - Done - 0.0.1 * - :class:`.ALFFParcels` - Calculate (f)ALFF and aggregate using parcellations - Done - 0.0.1 * - :class:`.ALFFSpheres` - Calculate (f)ALFF and aggregate using spheres placed on coordinates - Done - 0.0.1 * - :class:`.EdgeCentricFCParcels` - | Calculate edge-centric functional connectivity over parcellation, as | found in | `Jo et al. (2021) `_ - Done - 0.0.2 * - :class:`.EdgeCentricFCSpheres` - | Calculate edge-centric functional connectivity over spheres placed on | coordinates, as found in | `Jo et al. (2021) `_ - Done - 0.0.2 * - :class:`.TemporalSNRParcels` - Calculate temporal signal-to-noise ratio using parcellations - Done - 0.0.2 * - :class:`.TemporalSNRSpheres` - | Calculate temporal signal-to-noise ratio using spheres placed on | coordinates - Done - 0.0.2 * - :class:`.HurstExponent` - | Calculate Hurst exponent of a time series as found in | `Peng et al. (1995) `_ - Done - 0.0.4 * - :class:`.MultiscaleEntropyAUC` - | Calculate AUC of multiscale entropy of a time series as found in | `Costa et al. (2002) `_ - Done - 0.0.4 * - :class:`.PermEntropy` - | Calculate permutation entropy of a time series as found in | `Bandt at al. (2002) `_ - Done - 0.0.4 * - :class:`.RangeEntropy` - | Calculate range entropy of a time series as found in | `Omidvarnia et al. (2018) `_ - Done - 0.0.4 * - :class:`.RangeEntropyAUC` - | Calculate AUC of range entropy of a time series as found in | `Omidvarnia et al. (2018) `_ - Done - 0.0.4 * - :class:`.SampleEntropy` - | Calculate sample entropy of a time series as found in | `Richman et al. (2000) `_ - Done - 0.0.4 Planned ~~~~~~~ .. list-table:: :widths: auto :header-rows: 1 * - Name - Description - Reference * - Connectedness - Compute connectedness - :gh:`34` Parcellation ------------ .. Provide a list of the Parcellations that are implemented or planned. Version added: The junifer version in which the parcellation was added. Available ~~~~~~~~~ .. list-table:: :widths: auto :header-rows: 1 * - Name - Options - Keys - Template Spaces - Version Added - Publication * - Schaefer - ``n_rois``, ``yeo_networks`` - | ``Schaefer900x7``, ``Schaefer1000x7``, ``Schaefer100x17``, | ``Schaefer200x17``, ``Schaefer300x17``, ``Schaefer400x17``, | ``Schaefer500x17``, ``Schaefer600x17``, ``Schaefer700x17``, | ``Schaefer800x17``, ``Schaefer900x17``, ``Schaefer1000x17`` - ``MNI152NLin6Asym`` - 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). | https://doi.org/10.1093/cercor/bhx179 * - SUIT - ``space`` - ``SUITxMNI``, ``SUITxSUIT`` - ``SUIT``, ``MNI152Lin6Asym`` - 0.0.1 - | Diedrichsen, J. | A spatially unbiased atlas template of the human cerebellum. | NeuroImage, Volume 33(1), Pages 127–138 (2006). | https://doi.org/10.1016/j.neuroimage.2006.05.056 * - Tian - ``scale``, ``space``, ``magneticfield`` - | ``TianxS1x3TxMNI6thgeneration``, ``TianxS1x7TxMNI6thgeneration``, | ``TianxS2x3TxMNI6thgeneration``, ``TianxS2x7TxMNI6thgeneration``, | ``TianxS3x3TxMNI6thgeneration``, ``TianxS3x7TxMNI6thgeneration``, | ``TianxS4x3TxMNI6thgeneration``, ``TianxS4x7TxMNI6thgeneration``, | ``TianxS1x3TxMNInonlinear2009cAsym``, | ``TianxS2x3TxMNInonlinear2009cAsym``, | ``TianxS3x3TxMNInonlinear2009cAsym``, | ``TianxS4x3TxMNInonlinear2009cAsym`` - ``MNI152NLin6Asym``, ``MNI152NLin2009cAsym`` - 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). | https://doi.org/10.1038/s41593-020-00711-6 * - AICHA - ``version`` - ``AICHA_v1``, ``AICHA_v2`` - ``MNI152Lin6Asym`` - 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). | https://doi.org/10.1016/j.jneumeth.2015.07.013 * - Shen - ``year``, ``n_rois`` - | ``Shen_2013_50``, ``Shen_2013_100``, ``Shen_2013_150``, | ``Shen_2015_268``, ``Shen_2019_368`` - ``MNI152NLin2009cAsym`` - 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). | https://doi.org/10.1016/j.neuroimage.2013.05.081. | 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). | https://doi:10.1038/nn.4135 * - Yan - ``n_rois``, ``yeo_networks``, ``kong_networks`` - | ``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`` - ``MNI152NLin6Asym`` - 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). | https://doi.org/10.1016/j.neuroimage.2023.120010 * - Brainnetome - ``threshold`` - ``Brainnetome_thr0``, ``Brainnetome_thr25``, ``Brainnetome_thr50`` - ``MNI152NLin6Asym`` - 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). | https://doi.org/10.1093/cercor/bhw157 Planned ~~~~~~~ .. list-table:: :widths: auto :header-rows: 1 * - 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). | http://doi.org/10.1016/j.neuroimage.2006.01.021 * - Glasser - | Glasser, M.F., Coalson, T.S., Robinson, E.C. et al. | A multi-modal parcellation of human cerebral cortex. | Nature (2016). | http://doi.org/10.1038/nature18933 * - AAL - | Rolls, E.T., Huang, C.C., Lin, C.P., et al. | Automated anatomical labelling atlas 3. | NeuroImage, Volume 206 (2020). | https://doi.org/10.1016/j.neuroimage.2019.116189 * - Mindboggle 101 - | Klein, A., & Tourville, J. | 101 labeled brain images and a consistent human cortical labeling | protocol. | Frontiers in Neuroscience (2012). | http://doi.org/10.3389/fnins.2012.00171/abstract * - 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). | http://doi.org/10.1016/j.neuroimage.2010.06.010. * - 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). | https://doi.org/10.1093/cercor/bhw157 * - 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). | https://doi.org/10.1152/jn.00339.2011 | 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). | https://doi.org/10.1152/jn.00338.2011 Coordinates ----------- .. Provide a list of the Coordinates that are implemented or planned. Version added: The junifer version in which the parcellation was added. Available ~~~~~~~~~ .. list-table:: :widths: auto :header-rows: 1 * - Name - Keys - Version Added - Publication * - Cognitive action control - ``CogAC`` - 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). | https://doi.org/10.1016/j.neubiorev.2014.11.003. * - Cognitive action regulation - ``CogAR`` - 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). | https://doi.org/10.1016/j.neubiorev.2018.04.022. * - Default mode network - ``DMNBuckner`` - 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). | https://doi.org/10.1152/jn.00783.2009 | 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). | https://doi.org/10.1196/annals.1440.011 * - Missing formal name - ``extDMN`` - 0.0.1 - Missing publication details * - Empathic processing - ``Empathy`` - 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). | https://doi.org/10.1007/s00429-012-0380-y * - Extended social-affective default - ``eSAD`` - 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). | https://doi.org/10.1007/s00429-013-0698-0 * - Extended multiple-demand network - ``eMDN`` - 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). | https://doi.org/10.1016/j.neuroimage.2017.10.020. * - Motor execution - ``Motor`` - 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). | https://doi.org/10.1016/j.neuroimage.2008.04.025. * - Multitasking - ``MultiTask`` - 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). | https://doi.org/10.1007/s00429-019-01870-4 * - Physiological stress - ``PhysioStress`` - 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). | https://doi.org/10.1016/j.neuroimage.2015.06.059. * - Reward-related decision making - ``Rew`` - 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). | https://doi.org/10.1016/j.neubiorev.2010.12.012. * - Missing formal name - ``Somatosensory`` - 0.0.1 - Missing publication details * - Theory-of-mind cognition - ``ToM`` - 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). | https://doi.org/10.1007/s00429-012-0380-y * - Vigilant attention - ``VigAtt`` - 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). | https://doi.org/10.1037/a0030694 * - Working memory - ``WM`` - 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). | https://doi.org/10.1016/j.neuroimage.2011.11.050. * - Areal functional network from Power et al. (2011) - ``Power2011`` - 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). | https://doi.org/10.1016/j.neuron.2011.09.006 * - Brain maturity functional connections from Dosenbach et al. (2010) - ``Dosenbach`` - 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). | https://doi.org/10.1126/science.1194144 * - Areal functional network from Power et al. (2013) - ``Power2013`` - 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). | https://doi.org/10.1016/j.neuron.2013.07.035 * - Autobiographical Memory from Spreng et al. (2009) - ``AutobiographicalMemory`` - 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). | https://doi.org/10.1162/jocn.2008.21029 Planned ~~~~~~~ .. list-table:: :widths: auto :header-rows: 1 * - 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). | https://doi.org/10.1016/j.neuroimage.2010.10.011. * - 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). | https://doi.org/10.1162/jocn_a_01616 Mask ---- .. Provide a list of the masks that are implemented or planned. Version added: The junifer version in which the mask was added. Available ~~~~~~~~~ .. list-table:: :widths: auto :header-rows: 1 * - Name - Keys - Template Space - Version Added - Description - Publication * - Vickery-Patil (Gray Matter) - | ``GM_prob0.2`` - ``MNI152Lin6Asym`` - 0.0.1 - | Vickery, Sam, & Patil, Kaustubh. (2022). | Chimpanzee and Human Gray Matter Masks [Data set]. Zenodo. | https://doi.org/10.5281/zenodo.6463123 * - Vickery-Patil (Cortex + Basal Ganglia) - | ``GM_prob0.2_cortex`` - ``MNI152Lin6Asym`` - 0.0.1 - | Vickery, Sam, & Patil, Kaustubh. (2022). | Chimpanzee and Human Gray Matter Masks [Data set]. Zenodo. | https://doi.org/10.5281/zenodo.6463123 * - ``junifer``'s custom brain mask - | ``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``. * - ``nilearn``'s mask computed from fMRI data - | ``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 total | image histogram. See :func:`nilearn.masking.compute_epi_mask` * - ``nilearn``'s background 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. | See :func:`nilearn.masking.compute_background_mask` .. Planned ~~~~~~~ .. helpful site for creating tables: https://rest-sphinx-memo.readthedocs.io/en/latest/ReST.html#tables