{"id":399,"date":"2021-10-04T14:25:15","date_gmt":"2021-10-04T10:55:15","guid":{"rendered":"https:\/\/www.ghazizadehlab.org\/?page_id=399"},"modified":"2023-05-02T23:09:05","modified_gmt":"2023-05-02T19:39:05","slug":"resources","status":"publish","type":"page","link":"https:\/\/www.ghazizadehlab.org\/index.php\/resources\/","title":{"rendered":"Resources"},"content":{"rendered":"\t\t
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Resources<\/h1>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t
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MATres v1<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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Don’t deal with eccenctric software like AFNI and FSL. Try our all-in-one painless software for skull-stripping, atlas registration and warping. Supports humans and macaques (marmosets is in the works)<\/p>

Reference: Nadian, Mohammad Hossein, Sepideh Farmani, and Ali Ghazizadeh. “A novel methodology for exact targeting of human and non-human primate brain structures and skull implants using atlas-based 3D reconstruction.”\u00a0Journal of Neuroscience Methods<\/i>\u00a0391 (2023): 109851.<\/p>

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Code:https:\/\/github.com\/fmnh\/MATres <\/span>(courtesy of Mohammad Nadian)<\/span><\/span><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t

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Spiking Variability Decomposition<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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The code for parsing spiking variability: within trial variability n\u03c8 (aka \u03c6)\u00a0 and between trial variability (nRV) using a pricinpled approach for a doubly stochastic process.<\/span><\/p>

Reference: Fayyaz, S., Fakharian, M., & Ghazizadeh, A. (2021). Stimulus presentation can enhance spiking irregularity across subcortical and cortical regions. bioRxiv<\/em><\/span><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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Code: <\/span>var_decom<\/a> (courtesy of Saleh Fayyaz & MohammadAmin Fakharian)<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t

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Graph Learning <\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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The code for constructing graph between nodes based on partial correlations and using PC-stable algorithm<\/span><\/p>

References:\u00a0<\/span><\/p>

1) Ghazizadeh, A., Fakharian, M. A., Amini, A., Griggs, W., Leopold, D. A., & Hikosaka, O. (2020). Brain networks sensitive to object novelty, value, and their combination. Cerebral cortex communications, 1(1), tgaa034<\/em><\/span><\/p>

2) Attary T, Ghazizadeh A, (2021) Localizing sensory processing sensitivity and its subdomains within its relevant trait space: a data driven approach, Scientific Report<\/em><\/span><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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Code:\u00a0<\/span>PC_Graph_v2<\/a>\u00a0(courtesy of Mohammadhossein Nadian)<\/span><\/span><\/p>

For Attary et al 2021 data contact\u00a0us<\/a> and include your information and intended use.<\/em><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t

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Neural Spiking Deconvolution<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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\n\t\t\t\t\t\t\t\t\tThe code for parsing neural activity to events that are closely spaced<\/span>\n\nReference: Ghazizadeh, A., Fields, H. L., & Ambroggi, F. (2010). Isolating event-related neuronal responses by deconvolution. Journal of neurophysiology, 104(3), 1790-1802<\/em><\/span>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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Code: <\/span>Full and Partial deconvolution functions<\/a> (courtesy of Setayesh Radkani)<\/span><\/span><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t

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First and Second-Order Multivariate Effects<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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The procedure for computing MVE and sMVE in fMRI data (we could not find sMVE in our fMRI datasets but you are welcome to prove us wrong)<\/p>

Reference: Mansooreh Pakravan, Mojtaba Abbaszadeh, and Ali Ghazizadeh. “Coordinated multivoxel coding beyond univariate effects is not likely to be observable in fMRI data.”\u00a0NeuroImage\u00a0(2021): 118825.<\/em><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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Code:\u00a0<\/span>Crossnobis (MVE) and Geodesic (sMVE) Distances<\/a>\u00a0(courtesy of Mansooreh Pakravan)<\/span><\/span><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t

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Fractal Generation Code<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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The code for generating random fractal objects<\/span><\/p>

Reference: Ghazizadeh, A, et al “Ecological origins of object salience: Reward, uncertainty, aversiveness, and novelty.” Frontiers in neuroscience 10 (2016): 378<\/em><\/span><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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Code: <\/span>fractalmaker<\/a> (courtesy of Shinya Yamamoto)<\/span><\/span><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"

Resources MATres v1 Don’t deal with eccenctric software like AFNI and FSL. Try our all-in-one painless software for skull-stripping, atlas registration and warping. Supports humans and macaques (marmosets is in the works) Reference: Nadian, Mohammad Hossein, Sepideh Farmani, and Ali Ghazizadeh. “A novel methodology for exact targeting of human and non-human primate brain structures and […]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-399","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.ghazizadehlab.org\/index.php\/wp-json\/wp\/v2\/pages\/399","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ghazizadehlab.org\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ghazizadehlab.org\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ghazizadehlab.org\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ghazizadehlab.org\/index.php\/wp-json\/wp\/v2\/comments?post=399"}],"version-history":[{"count":40,"href":"https:\/\/www.ghazizadehlab.org\/index.php\/wp-json\/wp\/v2\/pages\/399\/revisions"}],"predecessor-version":[{"id":851,"href":"https:\/\/www.ghazizadehlab.org\/index.php\/wp-json\/wp\/v2\/pages\/399\/revisions\/851"}],"wp:attachment":[{"href":"https:\/\/www.ghazizadehlab.org\/index.php\/wp-json\/wp\/v2\/media?parent=399"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}