{"action":"created","issue":{"url":"https://api.github.com/repos/incf-nidash/nidm/issues/281","labels_url":"https://api.github.com/repos/incf-nidash/nidm/issues/281/labels{/name}","comments_url":"https://api.github.com/repos/incf-nidash/nidm/issues/281/comments","events_url":"https://api.github.com/repos/incf-nidash/nidm/issues/281/events","html_url":"https://github.com/incf-nidash/nidm/pull/281","id":65667736,"number":281,"title":"Definitions of HRF terms (current status: uncurated)","user":{"login":"cmaumet","id":5374264,"avatar_url":"https://avatars.githubusercontent.com/u/5374264?v=3","gravatar_id":"","url":"https://api.github.com/users/cmaumet","html_url":"https://github.com/cmaumet","followers_url":"https://api.github.com/users/cmaumet/followers","following_url":"https://api.github.com/users/cmaumet/following{/other_user}","gists_url":"https://api.github.com/users/cmaumet/gists{/gist_id}","starred_url":"https://api.github.com/users/cmaumet/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cmaumet/subscriptions","organizations_url":"https://api.github.com/users/cmaumet/orgs","repos_url":"https://api.github.com/users/cmaumet/repos","events_url":"https://api.github.com/users/cmaumet/events{/privacy}","received_events_url":"https://api.github.com/users/cmaumet/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/incf-nidash/nidm/labels/nidm-results","name":"nidm-results","color":"f7c6c7"},{"url":"https://api.github.com/repos/incf-nidash/nidm/labels/Terms","name":"Terms","color":"bfdadc"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":13,"created_at":"2015-04-01T12:03:41Z","updated_at":"2015-04-15T18:27:26Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/incf-nidash/nidm/pulls/281","html_url":"https://github.com/incf-nidash/nidm/pull/281","diff_url":"https://github.com/incf-nidash/nidm/pull/281.diff","patch_url":"https://github.com/incf-nidash/nidm/pull/281.patch"},"body":"Following #248, this issue is open to discuss the definitions of the terms used to model the hemodynamic response function (HRF):\r\n\r\nFirst, let's define the parent class and its associated object property:\r\n - **nidm:HemodynamicResponseFunctionBasis**: A basis function, part of a set of functions that is convolved with the anticipated neural responses to obtain the anticipated hemodynamic responses. (adapted from the definition suggested by @jbpoline in #248).\r\n - **nidm:hasHRFBasis**: Hemodynamic response function basis used to model the anticipated hemodynamic response.\r\n\r\nDefinitions for children of *nidm:HemodynamicResponseFunctionBasis*:\r\n- **nidm:HemodynamicResponseFunction**: Hemodynamic response function basis that can on its own be used to represent the idealised hemodynamic response function.\r\n - **nidm:GammaDifferenceHRF**: Hemodynamic response function which is a linear combination of two Gamma functions.\r\n   - **fsl:GammaDifferenceHRF**:  Hemodynamic response function which is a mixture of two Gamma functions - a standard positive function at normal lag, and a small, delayed, inverted Gamma, which attempts to model the late undershoot (definition adapted from http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/feat5/detail.html). This is the default in FSL.\r\n    - **spm:GammaDifferenceHRF**: Hemodynamic response function which is a linear combination two Gamma functions and is denoted by \"canonical HRF\" in SPM. This is the default in SPM.\r\n - **nidm:GammaHRF**: Hemodynamic response function which is a Gamma function.\r\n   - **afni:GammaHRF**: Hemodynamic response function which is a pre-defined Gamma function. This is the default in AFNI (-GAM option to 3ddeconvolve, or implied via afni_proc.py).\r\n    - ~~**fsl:GammaHRF**: Hemodynamic response function basis that is a Gamma variate (in fact a normalisation of the probability density function of the Gamma function); width and lag can be altered (definition adapted from http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/feat5/detail.html).~~\r\n - **nidm:GaussianHRF** ~~**fsl:GaussianHRF**~~: Hemodynamic response function which is a gaussian kernel.\r\n - ~~fsl:NoHRF~~: \r\n\r\n- **nidm:HemodynamicResponseFunctionDerivative**: Hemodynamic response function basis which is the derivative of an hemodynamic response function.\r\n - **fsl:TemporalDerivative**: Hemodynamic response function basis that is the derivative with respect to time of the FSL's Gamma Difference heamodynamic response function.\r\n - **spm:DispersionDerivative**: Hemodynamic response function basis that is the derivative with respect to spatial dispersion of the SPM's Gamma Difference heamodynamic response function.\r\n - **spm:TemporalDerivative**: Hemodynamic response function basis that is the derivative with respect to time of the SPM's Gamma Difference heamodynamic response function.\r\n\r\n- **nidm:FiniteImpulseResponseHRB** Hemodynamic response function basis which is a set of Finite impulse response (FIR) filters, with FIR the convolution kernel is represented as a set of discrete fixed-width \"impulses\" (definition adapted from http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/feat5/detail.html), denoted by TENT in AFNI.\r\n - ~~afni:FiniteImpulseResponseHRB~~\r\n - ~~fsl:FiniteImpulseResponseHRB~~\r\n - ~~spm:FiniteImpulseResponseHRB~~\r\n- **nidm:GammaHRB**: Hemodynamic response function basis which is a set of Gamma functions, also denoted by \"FLOBS\" in FSL.\r\n - ~~**fsl:GammaHRB**: Hemodynamic response function basis which is a set of Gamma variates of different widths and lags, also denoted by \"FLOBS\" in FSL (definition adapted from http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/feat5/detail.html).~~\r\n - ~~**spm:GammaHRB**: Hemodynamic response function basis which is a set of Gamma functions; window length and order can be altered.~~\r\n\r\n\r\n- **nidm:FourierHRB**: Hemodynamic response function basis which is a set of Fourier basis.\r\n  - ~~**spm:FourierHRB**: Hemodynamic response function basis which is a set of Fourier basis; window length and order can be altered.~~\r\n\r\n- **nidm:CustomHRB**: Hemodynamic response function basis which is a customised set of basis functions.\r\n  - ~~**fsl:CustomHRB**: Hemodynamic response function basis which is a customised set of basis functions, setup in a plain text file with one column for each basis function, sampled at the temporal resolution of 0.05s  (definition adapted from http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/feat5/detail.html).~~\r\n- **nidm:SineHRB** ~~**fsl:SineHRB**~~: Hemodynamic response function basis which is a set of Sine waves of differing frequencies (definition adapted from http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/feat5/detail.html).\r\n\r\n(Not sure about **afni:BLOCK**)\r\n\r\nAs presented above, I am proposing to reserve spm- fsl- and afni-specific terms for pre-defined functions (e.g. SPM canonical HRF, FSL double gamma, afni GAM), these will be defined as individuals.\r\n\r\nHow do you feel about those definitions?"},"comment":{"url":"https://api.github.com/repos/incf-nidash/nidm/issues/comments/93521942","html_url":"https://github.com/incf-nidash/nidm/pull/281#issuecomment-93521942","issue_url":"https://api.github.com/repos/incf-nidash/nidm/issues/281","id":93521942,"user":{"login":"satra","id":184063,"avatar_url":"https://avatars.githubusercontent.com/u/184063?v=3","gravatar_id":"","url":"https://api.github.com/users/satra","html_url":"https://github.com/satra","followers_url":"https://api.github.com/users/satra/followers","following_url":"https://api.github.com/users/satra/following{/other_user}","gists_url":"https://api.github.com/users/satra/gists{/gist_id}","starred_url":"https://api.github.com/users/satra/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/satra/subscriptions","organizations_url":"https://api.github.com/users/satra/orgs","repos_url":"https://api.github.com/users/satra/repos","events_url":"https://api.github.com/users/satra/events{/privacy}","received_events_url":"https://api.github.com/users/satra/received_events","type":"User","site_admin":false},"created_at":"2015-04-15T18:27:26Z","updated_at":"2015-04-15T18:27:26Z","body":"@nicholst - started sweating right here!\r\n\r\n> The good thing is that, with alphanumeric ID's, all of these labels and definitions can be easily changed in the future!\r\n\r\nonly if the concept doesn't change!\r\n"}}