{"id":19252286,"url":"https://github.com/sccn/nima","last_synced_at":"2025-08-01T11:13:28.720Z","repository":{"id":150759711,"uuid":"327718222","full_name":"sccn/NIMA","owner":"sccn","description":null,"archived":false,"fork":false,"pushed_at":"2024-07-25T20:43:38.000Z","size":10986,"stargazers_count":0,"open_issues_count":1,"forks_count":0,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-01-05T06:43:06.388Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"MATLAB","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sccn.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2021-01-07T20:30:24.000Z","updated_at":"2024-07-25T20:43:41.000Z","dependencies_parsed_at":null,"dependency_job_id":"fe5c52f5-db2d-43a3-a6ec-bda8066ae741","html_url":"https://github.com/sccn/NIMA","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sccn%2FNIMA","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sccn%2FNIMA/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sccn%2FNIMA/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sccn%2FNIMA/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sccn","download_url":"https://codeload.github.com/sccn/NIMA/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":240347944,"owners_count":19787236,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-09T18:26:15.596Z","updated_at":"2025-02-23T16:50:55.322Z","avatar_url":"https://github.com/sccn.png","language":"MATLAB","funding_links":[],"categories":[],"sub_categories":[],"readme":"![P159_separatealpha.png](images/P159_separatealpha.png)\n\nThe NIMA EEGLAB plugin\n-------------------------------------------------------------\n\nNIMA stands for Nima's Images from Measure-projection Analysis. Measure\nProjection Toolbox (MPT) is a published method (Bigdely-Shamlo et al.,\n2013), and for his wiki page see [this\nlink](https://sccn.ucsd.edu/wiki/MPT). MPT's nice visualization\nfunctions are stripped and re-wrapped into a stand-alone dipole\nvisualizer that does not have dependency on MPT. As a GUI, a menu item\nappears under STUDY tab. The main function, nimasImagesfromMpA() can be\nused also as a stand-alone command line function.\n\nWhat you can do with the optional inputs (12/07/2018 updated)\n-------------------------------------------------------------\n\n-   Specifying the colors and Alpha values separately for each\n    blob/voxel clusters.\n-   Specifying which MRI image and blob/voxel-cluster projections to\n    show.\n\nGUI, Blobs, and Voxels\n----------------------\nGUI image can be seen in the screenshot below. This visualization works\non 3-D Gaussian-blurred dipole locations, called (probabilistic) *dipole\ndensity*, which requires two parameters to determine the spatial\nspreading, namely full-width half-maximum (FWHM) in mm and number of\nsigma to truncate the Gaussian (can be specified as optional input,\ndefault 3 sigma; sigma == FWHM/2.355). Also, users are requested to\ndetermine the spatial resolution by determining isometric voxel size,\nwhich could be from 2 mm to 8 mm by increment of 1 mm. The final\nvisualization can be made either using blob or voxels, and the\ntransparency can be specified as Alpha (0-1 as invisible-solid). As an\noptional input, the order and the RGB triplets of the color assignment\nfor the selected clusters can be specified as 'blobColor', \\[1 0 0; 0 1\n0; 0 0 1\\] which will give you R, G, B for the specified three clusters\nin this order. In the screenshot below, compare scalp topographies, blob\nimages, and voxel images of Cluster 5, 6, 16. My colleague told me the\nvoxel image reminds him of Minecraft.\n\n![Nimafigure01.png](images/Nimafigure01.png)\n\nComparison with std_dipoleDensity()\n-----------------------------------\n\nstd_dipoleDensity() currently allows up to 5 clusters to be plotted in\none head space. Compared with this function, images from NIMA can embody\ntransparency and more fine-tuned spatial resolution.\n\n![Dipfitcomparison.png](images/Dipfitcomparison.png)\n\nVoxel Size Comparison for Blob Images\n-------------------------------------\n\nFWHM = 8 mm, number of sigma to truncate Gaussian = 3. From top left to\nright, Voxel Size = 2 mm, 3 mm, 4 mm. From bottom left to right, 5 mm, 6\nmm, and 7 mm.\n\n![Blob_from2to7mm.png](images/Blob_from2to7mm.png)\n\nVoxel Size Comparison for Voxel Images\n--------------------------------------\n\nFWHM = 8 mm, number of sigma to truncate Gaussian = 3. From top left to\nright, Voxel Size = 2 mm, 3 mm, 4 mm. From bottom left to right, 5 mm, 6\nmm, and 7 mm.\n\n![Voxels_from2to7mm.png](images/Voxels_from2to7mm.png)\n\nFWHM Size Comparison\n--------------------\n\nNumber of sigma to truncate Gaussian = 3. From top left to right, FWHM =\n8 mm, 12 mm, 16 mm. From bottom left to right, 20 mm, 24 mm, and 28 mm.\n\n![Voxels_fwhm8to28mm.png](images/Voxels_fwhm8to28mm.png)\n\nAlpha Comparison\n----------------\n\nFWHM = 8 mm, number of sigma to truncate Gaussian = 3. Top row, voxel\nplot. Bottom row, blob plot. From left to right, Alpha = 0.1, 0.3, 0.5,\n0.7, 0.9.\n\n![Alphacomparison.png](images/Alphacomparison.png)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsccn%2Fnima","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsccn%2Fnima","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsccn%2Fnima/lists"}