From 11505789882ea72f1b0e2801995ba141876d5e7e Mon Sep 17 00:00:00 2001 From: Jon Clayden Date: Fri, 2 Apr 2021 12:25:13 +0100 Subject: [PATCH] README tweaks --- README.Rmd | 4 ++-- README.md | 12 ++++++------ 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/README.Rmd b/README.Rmd index bb2e54a6..97d4f3ad 100644 --- a/README.Rmd +++ b/README.Rmd @@ -2,7 +2,7 @@ knitr::opts_chunk$set(collapse = TRUE) ``` -[![CRAN version](http://www.r-pkg.org/badges/version/divest)](https://cran.r-project.org/package=divest) [![Build Status](https://travis-ci.org/jonclayden/divest.svg?branch=master)](https://travis-ci.org/jonclayden/divest) [![Build status](https://ci.appveyor.com/api/projects/status/lc8v02uc1ywkskrc?svg=true)](https://ci.appveyor.com/project/jonclayden/divest) [![Coverage Status](https://coveralls.io/repos/github/jonclayden/divest/badge.svg?branch=master)](https://coveralls.io/github/jonclayden/divest?branch=master) [![Dependencies](https://tinyverse.netlify.com/badge/divest)](https://tinyverse.netlify.app) +[![CRAN version](http://www.r-pkg.org/badges/version/divest)](https://cran.r-project.org/package=divest) [![CI Status](https://github.com/jonclayden/divest/actions/workflows/ci.yaml/badge.svg)](https://github.com/jonclayden/divest/actions/workflows/ci.yaml) [![Coverage Status](https://coveralls.io/repos/github/jonclayden/divest/badge.svg?branch=master)](https://coveralls.io/github/jonclayden/divest?branch=master) [![Dependencies](https://tinyverse.netlify.com/badge/divest)](https://tinyverse.netlify.app) # An R interface to dcm2niix @@ -25,7 +25,7 @@ remotes::install_github("jonclayden/divest") The package's key function is `readDicom`, which scans a directory containing DICOM files, stacks related data into merged 3D or 4D images where appropriate, and returns a list of `niftiImage` objects. For example, -```{r} +```{r, results="hide"} library(divest) path <- system.file("extdata", "raw", package="divest") images <- readDicom(path, interactive=FALSE, verbosity=-1) diff --git a/README.md b/README.md index 82a258ad..06906daf 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ -[![CRAN version](http://www.r-pkg.org/badges/version/divest)](https://cran.r-project.org/package=divest) [![Build Status](https://travis-ci.org/jonclayden/divest.svg?branch=master)](https://travis-ci.org/jonclayden/divest) [![Build status](https://ci.appveyor.com/api/projects/status/lc8v02uc1ywkskrc?svg=true)](https://ci.appveyor.com/project/jonclayden/divest) [![Coverage Status](https://coveralls.io/repos/github/jonclayden/divest/badge.svg?branch=master)](https://coveralls.io/github/jonclayden/divest?branch=master) [![Dependencies](https://tinyverse.netlify.com/badge/divest)](https://tinyverse.netlify.app) +[![CRAN version](http://www.r-pkg.org/badges/version/divest)](https://cran.r-project.org/package=divest) [![CI Status](https://github.com/jonclayden/divest/actions/workflows/ci.yaml/badge.svg)](https://github.com/jonclayden/divest/actions/workflows/ci.yaml) [![Coverage Status](https://coveralls.io/repos/github/jonclayden/divest/badge.svg?branch=master)](https://coveralls.io/github/jonclayden/divest?branch=master) [![Dependencies](https://tinyverse.netlify.com/badge/divest)](https://tinyverse.netlify.app) # An R interface to dcm2niix @@ -29,10 +29,6 @@ The package's key function is `readDicom`, which scans a directory containing DI library(divest) path <- system.file("extdata", "raw", package="divest") images <- readDicom(path, interactive=FALSE, verbosity=-1) -## [dcm2niix WARNING] Unable to determine manufacturer (0008,0070), so conversion is not tuned for vendor. -## [dcm2niix WARNING] All images appear to be a single slice - please check slice/vector orientation -## [dcm2niix WARNING] Check that 2D images are not mirrored. -## [dcm2niix WARNING] Unable to determine manufacturer (0008,0070), so conversion is not tuned for vendor. ``` The conversion is interactive by default, prompting the user to select which series to convert, but here we simply convert everything non-interactively. The minimal test dataset provided with the package contains two images from each of two acquisitions. (It is incomplete, hence the warnings.) We can see the basic properties of a converted composite image by printing it. @@ -62,7 +58,7 @@ attributes(images[[i]]) ## [1] "mm" "s" ## ## $.nifti_image_ptr -## +## ## ## $.nifti_image_ver ## [1] 1 @@ -177,6 +173,10 @@ It is also possible to obtain information about the available DICOM series witho ```r names(scanDicom(path)) ## [dcm2niix info] Found 4 DICOM file(s) +## [dcm2niix WARNING] Unknown manufacturer +## [dcm2niix WARNING] Unknown manufacturer +## [dcm2niix WARNING] Unknown manufacturer +## [dcm2niix WARNING] Unknown manufacturer ## [1] "label" "rootPath" "files" ## [4] "seriesNumber" "seriesDescription" "patientName" ## [7] "studyDate" "echoTime" "repetitionTime"