From e83c28423f1262f9178352ea8125da862ec3954c Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Thu, 24 Nov 2022 12:01:13 +0100 Subject: [PATCH 1/4] update: add as many available coordinates as possible --- docs/builtin.rst | 88 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 88 insertions(+) diff --git a/docs/builtin.rst b/docs/builtin.rst index cc51b5948..cb090e889 100644 --- a/docs/builtin.rst +++ b/docs/builtin.rst @@ -315,9 +315,97 @@ Planned 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 + * - 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. + * - 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 + * - 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 + * - 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. + * - 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. + + Planned ~~~~~~~ -- 2.52.0 From 76024e6850bfcd89c660de506e745df9454770f4 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Thu, 24 Nov 2022 12:01:44 +0100 Subject: [PATCH 2/4] update: add planned coordinates --- docs/builtin.rst | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/docs/builtin.rst b/docs/builtin.rst index cb090e889..6783c297d 100644 --- a/docs/builtin.rst +++ b/docs/builtin.rst @@ -409,6 +409,30 @@ Available Planned ~~~~~~~ +.. list-table:: + :widths: auto + :header-rows: 1 + + * - Name + - Publication + * - Emotional scene and face processing + - | 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 + * - Motor execution network + - | 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. + Masks ----- -- 2.52.0 From e0d39eeb46e633dea9d041c478e8c3391f130146 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Thu, 24 Nov 2022 12:05:00 +0100 Subject: [PATCH 3/4] chore: newline cleanup for builtin.rst --- docs/builtin.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/builtin.rst b/docs/builtin.rst index 6783c297d..129be664d 100644 --- a/docs/builtin.rst +++ b/docs/builtin.rst @@ -456,13 +456,13 @@ Available * - Vickery-Patil (Gray Matter) - | ``GM_prob0.2`` - 0.0.1 - - | Vickery, Sam, & Patil, Kaustubh. (2022). + - | 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`` - 0.0.1 - - | Vickery, Sam, & Patil, Kaustubh. (2022). + - | Vickery, Sam, & Patil, Kaustubh. (2022). | Chimpanzee and Human Gray Matter Masks [Data set]. Zenodo. | https://doi.org/10.5281/zenodo.6463123 -- 2.52.0 From 67daaef551601d9ee374acdbc0bfb9edf6d49446 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Thu, 24 Nov 2022 14:49:33 +0100 Subject: [PATCH 4/4] docs: update further coordinates list --- docs/builtin.rst | 58 ++++++++++++++++++++++++++++++++++++++---------- 1 file changed, 46 insertions(+), 12 deletions(-) diff --git a/docs/builtin.rst b/docs/builtin.rst index 129be664d..84bb10ce0 100644 --- a/docs/builtin.rst +++ b/docs/builtin.rst @@ -359,13 +359,18 @@ Available | 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 - * - Extended multiple-demand network + * - Missing formal name - ``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. + - 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 @@ -373,6 +378,21 @@ Available | 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 + - ``extMDN`` + - 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 @@ -381,6 +401,14 @@ Available | 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 @@ -389,6 +417,18 @@ Available | 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 @@ -415,7 +455,7 @@ Planned * - Name - Publication - * - Emotional scene and face processing + * - 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). @@ -426,12 +466,6 @@ Planned | and Functional-Connectivity Evidence. | Journal of Cognitive Neuroscience, Volume 33(9), Pages 1716–1752 (2021). | https://doi.org/10.1162/jocn_a_01616 - * - Motor execution network - - | 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. Masks -- 2.52.0