{"action":"created","comment":{"url":"https://api.github.com/repos/poldracklab/fmriprep/pulls/comments/206629148","pull_request_review_id":142078131,"id":206629148,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDIwNjYyOTE0OA==","diff_hunk":"@@ -24,27 +24,26 @@\n                    \"that is robust to differences in scan acquisition protocols and that requires \"\n                    \"minimal user input, while providing easily interpretable and comprehensive \"\n                    \"error and output reporting.\")\n-__longdesc__ = (\"This package is a functional magnetic resonance image preprocessing pipeline \"\n-                \"that is designed to provide an easily accessible, state-of-the-art interface \"\n-                \"that is robust to differences in scan acquisition protocols and that requires \"\n-                \"minimal user input, while providing easily interpretable and comprehensive error \"\n-                \"and output reporting. This open-source neuroimaging data processing tool is \"\n-                \"being developed as a part of the MRI image analysis and reproducibility platform \"\n-                \"offered by the CRN. This pipeline is heavily influenced by the `Human Connectome \"\n-                \"Project analysis pipelines \"\n-                \"<https://github.com/Washington-University/Pipelines>`_ and, as such, the \"\n-                \"backbone of this pipeline is a python reimplementation of the HCP \"\n-                \"`GenericfMRIVolumeProcessingPipeline.sh` script. However, a major difference is \"\n-                \"that this pipeline is executed using a `nipype workflow framework \"\n-                \"<http://nipype.readthedocs.io/en/latest/>`_. This allows for each call to a \"\n-                \"software module or binary to be controlled within the workflows, which removes \"\n-                \"the need for manual curation at every stage, while still providing all the \"\n-                \"output and error information that would be necessary for debugging and \"\n-                \"interpretation purposes. The fmriprep pipeline primarily utilizes FSL tools, but \"\n-                \"also utilizes ANTs tools at several stages such as skull stripping and template \"\n-                \"registration. This pipeline was designed to provide the best software \"\n-                \"implementation for each state of preprocessing, and will be updated as newer and \"\n-                \"better neuroimaging software become available.\")\n+__longdesc__ = \"\"\"\\\n+Preprocessing of functional MRI (fMRI) involves numerous steps to clean and standardize\n+data before statistical analysis. Generally, researchers create ad hoc preprocessing\n+workflows for each new dataset, building upon a large inventory of tools available for\n+each step. The complexity of these workflows has snowballed with rapid advances in MR data\n+acquisition and image processing techniques. We introduce fMRIPrep, an analysis-agnostic\n+tool that addresses the challenge of robust and reproducible preprocessing for task-based\n+and resting fMRI data. FMRIPrep automatically adapts a best-in-breed workflow to the\n+idiosyncrasies of virtually any dataset, ensuring high-quality preprocessing with no\n+manual intervention. By introducing visual assessment checkpoints into an iterative\n+integration framework for software-testing, we show that fMRIPrep robustly produces\n+high-quality results on a diverse fMRI data collection comprising participants from\n+54 different studies in the OpenfMRI repository. We review the distinctive features of\n+fMRIPrep in a qualitative comparison to other preprocessing workflows. FMRIPrep achieves\n+higher spatial accuracy as it introduces less uncontrolled spatial smoothness than commonly\n+used preprocessing tools. FMRIPrep has the potential to transform fMRI research by equipping\n+neuroscientists with a high-quality, robust, easy-to-use and transparent preprocessing workflow\n+which can help ensure the validity of inference and the interpretability of their results.\n+\n+[Pre-print https://doi.org/10.1101/306951]\"\"\"","path":"fmriprep/info.py","position":44,"original_position":44,"commit_id":"7216f208f5ddd72e9626e645278846daf2946709","original_commit_id":"7216f208f5ddd72e9626e645278846daf2946709","user":{"login":"effigies","id":83442,"node_id":"MDQ6VXNlcjgzNDQy","avatar_url":"https://avatars0.githubusercontent.com/u/83442?v=4","gravatar_id":"","url":"https://api.github.com/users/effigies","html_url":"https://github.com/effigies","followers_url":"https://api.github.com/users/effigies/followers","following_url":"https://api.github.com/users/effigies/following{/other_user}","gists_url":"https://api.github.com/users/effigies/gists{/gist_id}","starred_url":"https://api.github.com/users/effigies/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/effigies/subscriptions","organizations_url":"https://api.github.com/users/effigies/orgs","repos_url":"https://api.github.com/users/effigies/repos","events_url":"https://api.github.com/users/effigies/events{/privacy}","received_events_url":"https://api.github.com/users/effigies/received_events","type":"User","site_admin":false},"body":"I don't think this link is valid RST. You can check with the PyPI pre-check from nipype:\r\n\r\nhttps://github.com/nipy/nipype/blob/master/.circleci/config.yml#L333-L344\r\n\r\nIf it seems worth adding to our own Circle workflows, it's a 30s job.","created_at":"2018-07-31T18:06:10Z","updated_at":"2018-07-31T18:06:11Z","html_url":"https://github.com/poldracklab/fmriprep/pull/1230#discussion_r206629148","pull_request_url":"https://api.github.com/repos/poldracklab/fmriprep/pulls/1230","author_association":"COLLABORATOR","_links":{"self":{"href":"https://api.github.com/repos/poldracklab/fmriprep/pulls/comments/206629148"},"html":{"href":"https://github.com/poldracklab/fmriprep/pull/1230#discussion_r206629148"},"pull_request":{"href":"https://api.github.com/repos/poldracklab/fmriprep/pulls/1230"}}},"pull_request":{"url":"https://api.github.com/repos/poldracklab/fmriprep/pulls/1230","id":205188519,"node_id":"MDExOlB1bGxSZXF1ZXN0MjA1MTg4NTE5","html_url":"https://github.com/poldracklab/fmriprep/pull/1230","diff_url":"https://github.com/poldracklab/fmriprep/pull/1230.diff","patch_url":"https://github.com/poldracklab/fmriprep/pull/1230.patch","issue_url":"https://api.github.com/repos/poldracklab/fmriprep/issues/1230","number":1230,"state":"open","locked":false,"title":"[WIP] Updating long description [skip ci]","user":{"login":"oesteban","id":598470,"node_id":"MDQ6VXNlcjU5ODQ3MA==","avatar_url":"https://avatars2.githubusercontent.com/u/598470?v=4","gravatar_id":"","url":"https://api.github.com/users/oesteban","html_url":"https://github.com/oesteban","followers_url":"https://api.github.com/users/oesteban/followers","following_url":"https://api.github.com/users/oesteban/following{/other_user}","gists_url":"https://api.github.com/users/oesteban/gists{/gist_id}","starred_url":"https://api.github.com/users/oesteban/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/oesteban/subscriptions","organizations_url":"https://api.github.com/users/oesteban/orgs","repos_url":"https://api.github.com/users/oesteban/repos","events_url":"https://api.github.com/users/oesteban/events{/privacy}","received_events_url":"https://api.github.com/users/oesteban/received_events","type":"User","site_admin":false},"body":"## Changes proposed in this pull request\r\n\r\nUpdate long description field of the package, as it is veery outdated\r\n\r\n<!--\r\nPlease describe here the main features / changes proposed for review and integration in fMRIPrep\r\nIf this PR addresses some existing problem, please use GitHub's citing tools \r\n(eg. ref #, closes # or fixes #).\r\nIf there is not an existing issue open describing the problem, please consider opening a new\r\nissue first and then link it from here (so the *fMRIPrep* community has a better understanding\r\nof ongoing development efforts and possible overlaps between contributions).\r\n-->\r\n\r\n\r\n## Documentation that should be reviewed\r\nJust that paragraph\r\n<!--\r\nPlease summarize here the main changes to the documentation that the reviewers should be aware of.\r\n-->\r\n\r\n## Pull-request guidelines:\r\n<!--\r\nPlease make sure you have read the PR guidelines below, and checked \r\nall boxes that apply at the bottom.\r\n-->\r\n1. We invite you to list yourself as a *fMRIPrep* contributor, so if your name \r\n   is not already mentioned, please modify the \r\n   [``.zenodo.json``](https://github.com/poldracklab/fmriprep/blob/master/.zenodo.json)\r\n   file with your data right above Russ' entry. Example:\r\n   ```\r\n   {\r\n      \"name\": \"Contributor, New FMRIPrep\",\r\n      \"affiliation\": \"Department of fMRI prep'ing, Open Science Made-Up University\",\r\n      \"orcid\": \"<your id>\"\r\n   },\r\n   {\r\n      \"name\": \"Poldrack, Russell A.\",\r\n      \"affiliation\": \"Department of Psychology, Stanford University\",\r\n      \"orcid\": \"0000-0001-6755-0259\"\r\n   },\r\n   ```\r\n   \r\n2. By submitting this request you acknowledge that your contributions are available under the BSD 3-Clause license.\r\n\r\n3. Use a descriptive prefix, between brackets for your PR: ``ENH`` (enhancement), ``FIX``, ``TST``, ``DOC``, ``STY``,\r\n   ``REF`` (refactor), ``CI`` (continous integration), ``MAINT`` (maintenance). Example:\r\n   ```\r\n   [ENH] Support for SB-reference in multi-band datasets\r\n   ```\r\n   For works-in-progress, add the ``WIP`` tag in addition to the descriptive prefix. \r\n   Pull-requests tagged with ``[WIP]`` will not merged in until the tag is removed.\r\n\r\n4. Your PR will be reviewed according to the following\r\n   [template](https://github.com/poldracklab/fmriprep/wiki/Reviewing-a-Pull-Request).\r\n\r\n5. Documentation is a fundamental aspect to the *glass-box* philosophy that *fMRIPrep* abides by.\r\n   Please understand that the *fMRIPrep* team may (are likely to) request you to improve the documentation\r\n   provided with this PR, within the PR or in future PRs.\r\n   \r\n\r\n**Please review and check the following**:\r\n<!-- replace the empty checkboxes [ ] below with checked ones [x] accordingly -->\r\n\r\n  - [x] I have read the [guidelines for contributions](https://github.com/poldracklab/fmriprep/blob/master/CONTRIBUTING.md).\r\n  - [x] I understand that my contributions will not be merged unless the work is\r\n        finished (i.e. no ``[WIP]`` tag remains in the title of my PR) and tests pass.\r\n  - [x] The proposed code follows the\r\n        [coding style](https://github.com/poldracklab/fmriprep/blob/master/CONTRIBUTING.md#fmriprep-coding-style-guide),\r\n        to the extent I understood them (and I will address any comments raised by the PR's reviewers in this regard).\r\n  - [ ] \\(Optional\\) I opt-out from being listed in the `.zenodo.json` file.\r\n","created_at":"2018-07-31T17:35:01Z","updated_at":"2018-07-31T18:06:11Z","closed_at":null,"merged_at":null,"merge_commit_sha":"dca73e901307873caff0ec969817b674db8075ab","assignee":null,"assignees":[],"requested_reviewers":[],"requested_teams":[],"labels":[],"milestone":null,"commits_url":"https://api.github.com/repos/poldracklab/fmriprep/pulls/1230/commits","review_comments_url":"https://api.github.com/repos/poldracklab/fmriprep/pulls/1230/comments","review_comment_url":"https://api.github.com/repos/poldracklab/fmriprep/pulls/comments{/number}","comments_url":"https://api.github.com/repos/poldracklab/fmriprep/issues/1230/comments","statuses_url":"https://api.github.com/repos/poldracklab/fmriprep/statuses/7216f208f5ddd72e9626e645278846daf2946709","head":{"label":"poldracklab:oesteban-patch-1","ref":"oesteban-patch-1","sha":"7216f208f5ddd72e9626e645278846daf2946709","user":{"login":"poldracklab","id":9287954,"node_id":"MDEyOk9yZ2FuaXphdGlvbjkyODc5NTQ=","avatar_url":"https://avatars2.githubusercontent.com/u/9287954?v=4","gravatar_id":"","url":"https://api.github.com/users/poldracklab","html_url":"https://github.com/poldracklab","followers_url":"https://api.github.com/users/poldracklab/followers","following_url":"https://api.github.com/users/poldracklab/following{/other_user}","gists_url":"https://api.github.com/users/poldracklab/gists{/gist_id}","starred_url":"https://api.github.com/users/poldracklab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/poldracklab/subscriptions","organizations_url":"https://api.github.com/users/poldracklab/orgs","repos_url":"https://api.github.com/users/poldracklab/repos","events_url":"https://api.github.com/users/poldracklab/events{/privacy}","received_events_url":"https://api.github.com/users/poldracklab/received_events","type":"Organization","site_admin":false},"repo":{"id":53175327,"node_id":"MDEwOlJlcG9zaXRvcnk1MzE3NTMyNw==","name":"fmriprep","full_name":"poldracklab/fmriprep","owner":{"login":"poldracklab","id":9287954,"node_id":"MDEyOk9yZ2FuaXphdGlvbjkyODc5NTQ=","avatar_url":"https://avatars2.githubusercontent.com/u/9287954?v=4","gravatar_id":"","url":"https://api.github.com/users/poldracklab","html_url":"https://github.com/poldracklab","followers_url":"https://api.github.com/users/poldracklab/followers","following_url":"https://api.github.com/users/poldracklab/following{/other_user}","gists_url":"https://api.github.com/users/poldracklab/gists{/gist_id}","starred_url":"https://api.github.com/users/poldracklab/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/poldracklab/subscriptions","organizations_url":"https://api.github.com/users/poldracklab/orgs","repos_url":"https://api.github.com/users/poldracklab/repos","events_url":"https://api.github.com/users/poldracklab/events{/privacy}","received_events_url":"https://api.github.com/users/poldracklab/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/poldracklab/fmriprep","description":"fMRIprep 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