{"id":17030321,"url":"https://github.com/vsoch/nidmviewer","last_synced_at":"2025-04-12T12:12:04.545Z","repository":{"id":57446159,"uuid":"44032286","full_name":"vsoch/nidmviewer","owner":"vsoch","description":"NIDM Results Viewer","archived":false,"fork":false,"pushed_at":"2018-07-05T22:42:10.000Z","size":7665,"stargazers_count":3,"open_issues_count":12,"forks_count":3,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-04-12T12:12:01.998Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://vsoch.github.io/nidmviewer/","language":"CSS","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/vsoch.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2015-10-10T23:35:32.000Z","updated_at":"2018-12-20T16:33:29.000Z","dependencies_parsed_at":"2022-09-02T23:40:54.741Z","dependency_job_id":null,"html_url":"https://github.com/vsoch/nidmviewer","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vsoch%2Fnidmviewer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vsoch%2Fnidmviewer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vsoch%2Fnidmviewer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vsoch%2Fnidmviewer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/vsoch","download_url":"https://codeload.github.com/vsoch/nidmviewer/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248565078,"owners_count":21125417,"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":"2024-10-14T08:06:10.120Z","updated_at":"2025-04-12T12:12:04.520Z","avatar_url":"https://github.com/vsoch.png","language":"CSS","funding_links":[],"categories":[],"sub_categories":[],"readme":"# nidm-viewer\n\nNIDM Results Viewer\n\n - parses peak coordinates and associated brain maps\n - interactive coordinate browsing\n - save image to file (export)\n - produces html code for embedding, or local viewer\n - uses [font brain](http://vsoch.github.io/font-brain) for nidm and brain imaging icons\n\n\n## Documentation\nComplete documentation [is available](http://nidmviewer.readthedocs.org/en/latest/)\n\n### Installation\nTo install\n\n```\npip install nidmviewer\n```\n\nTo install development version:\n```\npip install git+git://github.com/vsoch/nidmviewer.git\n```\n\n### Running Examples\n\n#### Command Line\n\nWhen installing with setup.py, an executable, `nidmviewer` is installed in your bin to view nidm files on the fly. Here we will run an example using a local file (nidm.ttl) for which the excursion set maps are served from a webserver (neurovault) and the full paths represented in the `excsetmap_location` parameter in the turtle file.  This use case coincides with downloading a nidm.ttl and wanting to look at (remotely hosted) maps.\n\n```\nnidmviewer neurovault/nidm.ttl --port 8833\nStarting up the nidmviewer!\nFound results matching query.\n/tmp/tmpuwfuszb9\nServing nidmviewer at port 8833\n127.0.0.1 - - [24/Jan/2018 12:03:43] \"GET /pycompare.html HTTP/1.1\" 200 -\nCreated new window in existing browser session.\n\n```\n\nThe browser should open up automatically to the url.\n\nBut what if you have an entire (local) set of nidm files and images? We have a lot of images locally in the fsl folder:\n\n```\nls fsl/\nContrastStandardError_T001.nii.gz  DesignMatrix.csv          GrandMean.nii.gz                 MNI152_T1_2mm_brain.nii.gz       rendered_thresh_zstat1.png  TStatistic_T001.nii.gz\nContrastStandardError_T002.nii.gz  DesignMatrix.png          index.html                       MNI152_T1_8mm_brain_mask.nii.gz  rendered_thresh_zstat2.png  TStatistic_T002.nii.gz\nContrast_T001.nii.gz               ExcursionSet_T001.nii.gz  Mask.nii.gz                      nidm.provn                       ResidualMeanSquares.nii.gz  ZStatistic_T001.nii.gz\nContrast_T002.nii.gz               ExcursionSet_T002.nii.gz  MNI152_T1_2mm_brain_mask.nii.gz  nidm.ttl                         SearchSpaceMask.nii.gz      ZStatistic_T002.nii.gz\n```\n\nand if you look in the [examples/fsl/nidm.ttl](examples/fsl/nidm.ttl) you will see paths to files. If you naively try to serve them from (somewhere other than the same folder they live in) you are going to get a bunch of 404s. Please cd into the folder before you do this, so the web root is where the files are found:\n\n```\nnidmviewer fsl/nidm.ttl --port 8811\n```\n\n![img/example.png](img/example.png)\n\n\nYou can see the basic usage by typing the command:\n \n```\nusage: nidmviewer [-h] [--base BASE] [--port PORT]\n                  [--columns_to_remove COLUMNS_TO_REMOVE]\n                  ttl\n\ncommand line or server tool to view or compare nidm results.\n\npositional arguments:\n  ttl                   List of comma separated ttl files to parse.\n\noptional arguments:\n  -h, --help            show this help message and exit\n  --base BASE           base image (standard brain map) to use for the viewer\n                        background.\n  --port PORT           PORT to use to serve nidmviewer (default 8088).\n  --columns_to_remove COLUMNS_TO_REMOVE\n                        Comma separated list of columns to remove from viewer.\nusage: nidmviewer [-h] [--base BASE] [--port PORT]\n                  [--columns_to_remove COLUMNS_TO_REMOVE]\n                  ttl\n\ncommand line or server tool to view or compare nidm results.\n\npositional arguments:\n  ttl                   List of comma separated ttl files to parse.\n\noptional arguments:\n  -h, --help            show this help message and exit\n  --base BASE           base image (standard brain map) to use for the viewer\n                        background.\n  --port PORT           PORT to use to serve nidmviewer (default 8088).\n  --columns_to_remove COLUMNS_TO_REMOVE\n                        Comma separated list of columns to remove from viewer.\n```\n\nIf you need more substantial customization, it's recommended to use the python functions to generate your own\nhtml.\n\n#### Python\nsee [an example](examples/generate_viewer.py). This example will generate a snippet of code that you can save as an `index.html` file, and will render served alongside the images in the [examples/fsl](examples/fsl) folder.\n\n\n###### Many Thanks\n - [Papaya Viewer](https://github.com/rii-mango/Papaya), we salute you!\n - [NeuroVault](https://github.com/NeuroVault/NeuroVault) don't mess with the NeuroVault!\n\nplease [submit feedback and requests](https://github.com/vsoch/nidmviewer) or see the [demo](http://vsoch.github.io/nidmviewer)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvsoch%2Fnidmviewer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fvsoch%2Fnidmviewer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvsoch%2Fnidmviewer/lists"}