From a83d6072a4b517c30fc5659f28c996db8c114cb9 Mon Sep 17 00:00:00 2001 From: Robert Smith Date: Tue, 9 Aug 2022 15:38:20 +1000 Subject: [PATCH 1/2] DWI derivatives: Compulsory "parameter" entity While the specification states that the "parameter" entity must always be defined---even if all model parameters are encoded within a single image, in which case value "all" must be used---two of the demonstrative examples did not obey such. --- .../05-diffusion-derivatives.md | 28 +++++++++---------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/src/05-derivatives/05-diffusion-derivatives.md b/src/05-derivatives/05-diffusion-derivatives.md index 3d019ff8..1fc75d5d 100644 --- a/src/05-derivatives/05-diffusion-derivatives.md +++ b/src/05-derivatives/05-diffusion-derivatives.md @@ -435,11 +435,11 @@ another. my_diffusion_pipeline/ sub-01/ dwi/ - sub-01_tensor.nii.gz + sub-01_parameter-all_tensor.nii.gz sub-01_tensor.json ``` - Dimensions of NIfTI image "`sub-01_tensor.nii.gz`": *I*x*J*x*K*x6 ([parameter vectors](#data-param)) + Dimensions of NIfTI image "`sub-01_parameter-all_tensor.nii.gz`": *I*x*J*x*K*x6 ([parameter vectors](#data-param)) Contents of JSON file: @@ -450,7 +450,7 @@ another. "ReferenceAxes": "xyz", "Parameters": { "FitMethod": "ols", - "OutlierRejection": False + "OutlierRejection": false } } ``` @@ -461,18 +461,18 @@ another. my_diffusion_pipeline/ sub-01/ dwi/ - sub-01_desc-wm_csd.nii.gz - sub-01_desc-wm_csd.json - sub-01_desc-gm_csd.nii.gz - sub-01_desc-gm_csd.json - sub-01_desc-csf_csd.nii.gz - sub-01_desc-csf_csd.json + sub-01_parameter-wm_csd.nii.gz + sub-01_parameter-wm_csd.json + sub-01_parameter-gm_csd.nii.gz + sub-01_parameter-gm_csd.json + sub-01_parameter-csf_csd.nii.gz + sub-01_parameter-csf_csd.json sub-01_csd.json ``` - Dimensions of NIfTI image "`sub-01_desc-wm_csd.nii.gz`": *I*x*J*x*K*x45 ([spherical harmonics](#data-sh)) - Dimensions of NIfTI image "`sub-01_desc-gm_csd.nii.gz`": *I*x*J*x*K*x1 ([spherical harmonics](#data-sh)) - Dimensions of NIfTI image "`sub-01_desc-csf_csd.nii.gz`": *I*x*J*x*K*x1 ([spherical harmonics](#data-sh)) + Dimensions of NIfTI image "`sub-01_parameter-wm_csd.nii.gz`": *I*x*J*x*K*x45 ([spherical harmonics](#data-sh)) + Dimensions of NIfTI image "`sub-01_parameter-gm_csd.nii.gz`": *I*x*J*x*K*x1 ([spherical harmonics](#data-sh)) + Dimensions of NIfTI image "`sub-01_parameter-csf_csd.nii.gz`": *I*x*J*x*K*x1 ([spherical harmonics](#data-sh)) Contents of file "`sub-01_csd.json`" (common to all [intrinsic](#paramdef-intrinsic) model parameter images): @@ -488,7 +488,7 @@ another. } ``` - Contents of JSON file "`sub-01_desc-wm_csd.json`": + Contents of JSON file "`sub-01_parameter-wm_csd.json`": ```JSON { @@ -503,7 +503,7 @@ another. } ``` - Contents of JSON file "`sub-01_desc-gm_csd.json`": + Contents of JSON file "`sub-01_parameter-gm_csd.json`": ```JSON { From c7cfbafb7d0269eab621c928f7f779183cc9243b Mon Sep 17 00:00:00 2001 From: Robert Smith Date: Wed, 10 Aug 2022 19:42:06 +1000 Subject: [PATCH 2/2] DWI derivatives: Resolution between content changes Resolves bids-standard/bids-bep016#52 (making "parameter" entity compulsory) against bids-standard/bids-bep016#51 (changing key for that parameter from "parameter" to "param"). --- .../05-diffusion-derivatives.md | 26 +++++++++---------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/src/05-derivatives/05-diffusion-derivatives.md b/src/05-derivatives/05-diffusion-derivatives.md index cf476c8f..62e5a77d 100644 --- a/src/05-derivatives/05-diffusion-derivatives.md +++ b/src/05-derivatives/05-diffusion-derivatives.md @@ -435,11 +435,11 @@ another. my_diffusion_pipeline/ sub-01/ dwi/ - sub-01_parameter-all_tensor.nii.gz + sub-01_param-all_tensor.nii.gz sub-01_tensor.json ``` - Dimensions of NIfTI image "`sub-01_parameter-all_tensor.nii.gz`": *I*x*J*x*K*x6 ([parameter vectors](#data-param)) + Dimensions of NIfTI image "`sub-01_param-all_tensor.nii.gz`": *I*x*J*x*K*x6 ([parameter vectors](#data-param)) Contents of JSON file: @@ -461,18 +461,18 @@ another. my_diffusion_pipeline/ sub-01/ dwi/ - sub-01_parameter-wm_csd.nii.gz - sub-01_parameter-wm_csd.json - sub-01_parameter-gm_csd.nii.gz - sub-01_parameter-gm_csd.json - sub-01_parameter-csf_csd.nii.gz - sub-01_parameter-csf_csd.json + sub-01_param-wm_csd.nii.gz + sub-01_param-wm_csd.json + sub-01_param-gm_csd.nii.gz + sub-01_param-gm_csd.json + sub-01_param-csf_csd.nii.gz + sub-01_param-csf_csd.json sub-01_csd.json ``` - Dimensions of NIfTI image "`sub-01_parameter-wm_csd.nii.gz`": *I*x*J*x*K*x45 ([spherical harmonics](#data-sh)) - Dimensions of NIfTI image "`sub-01_parameter-gm_csd.nii.gz`": *I*x*J*x*K*x1 ([spherical harmonics](#data-sh)) - Dimensions of NIfTI image "`sub-01_parameter-csf_csd.nii.gz`": *I*x*J*x*K*x1 ([spherical harmonics](#data-sh)) + Dimensions of NIfTI image "`sub-01_param-wm_csd.nii.gz`": *I*x*J*x*K*x45 ([spherical harmonics](#data-sh)) + Dimensions of NIfTI image "`sub-01_param-gm_csd.nii.gz`": *I*x*J*x*K*x1 ([spherical harmonics](#data-sh)) + Dimensions of NIfTI image "`sub-01_param-csf_csd.nii.gz`": *I*x*J*x*K*x1 ([spherical harmonics](#data-sh)) Contents of file "`sub-01_csd.json`" (common to all [intrinsic](#paramdef-intrinsic) model parameter images): @@ -488,7 +488,7 @@ another. } ``` - Contents of JSON file "`sub-01_parameter-wm_csd.json`": + Contents of JSON file "`sub-01_param-wm_csd.json`": ```JSON { @@ -503,7 +503,7 @@ another. } ``` - Contents of JSON file "`sub-01_parameter-gm_csd.json`": + Contents of JSON file "`sub-01_param-gm_csd.json`": ```JSON {