Package kirby21.base
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- Randolph Andrews
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1 Type Package Package kirby21.base October 11, 2017 Title Example Data from the Multi-Modal MRI 'Reproducibility' Resource Version Date Author John Muschelli Maintainer John Muschelli Multi-modal magnetic resonance imaging ('MRI') data from the 'Kirby21' 'reproducibility' study < including functional and structural imaging. License GPL-2 LazyData true LazyLoad true Imports utils, stats, git2r RoxygenNote URL Encoding UTF-8 NeedsCompilation no Repository CRAN Date/Publication :30:08 UTC R topics documented: all_modalities copy_kirby21_data download_kirby21_data get_ids get_image_filenames get_image_filenames_df
2 2 copy_kirby21_data get_par_filenames kirby21_demog modality_df subject_id_to_visit_id Index 8 all_modalities Return All Modalities Return the modalities for images where packages were developed all_modalities() Vector of characters copy_kirby21_data Copy Kirby21 Data to an output directory Copies files from Kirby21 Package to an output directory copy_kirby21_data(outdir,...) outdir Output directory for data... to pass to get_image_filenames Logical if files are copied
3 download_kirby21_data 3 download_kirby21_data Download Kirby21 Imaging Data This function allows users to download specific modalities for Kirby21 data sets. This allows this package to be on CRAN download_kirby21_data(modality = kirby21.base::all_modalities(), progress = TRUE, force = FALSE) modality progress force modality of images that are to be downloaded. You must have the package downloaded for that modality. Should verbose messages be printed when downloading the data If the package of that modality is not installed stop. If force = FALSE, then this will download the data but not really install the package. A logical indicating the data is there. get_ids Get IDs with Data in Package Return the IDs for the people scanned available in the kirby21 packages get_ids() Vector of numeric ids
4 4 get_image_filenames_df get_image_filenames Get Image Filenames Return the filenames for the images get_image_filenames(...)... arguments passed to get_image_filenames_df Examples get_image_filenames() get_image_filenames_df Get Image Filenames in a data.frame Return a data.frame of filenames for the images get_image_filenames_df(ids = get_ids(), modalities = all_modalities(), visits = c(1, 2), long = TRUE, warn = TRUE) get_image_filenames_matrix(...) get_image_filenames_list(...) get_image_filenames_list_by_visit(...) get_image_filenames_list_by_subject(...)
5 get_par_filenames 5 ids modalities visits long warn ID to return vector of image modalities within c("flair", "MPRAGE", "T2w", "fmri", "DTI") to return Vector of scan indices to return (1 or 2 or both) if TRUE, each row is a subject, visit, modality pair if TRUE, warnings will be produced when packages are not installed... arguments passed to get_image_filenames_df Data.frame of filenames Examples get_image_filenames_df() get_image_filenames_matrix() get_image_filenames_list() get_image_filenames_list_by_visit() get_image_filenames_list_by_subject() get_par_filenames Get Filenames of Par files Return the filenames for the par files get_par_filenames(ids = get_ids(), modalities = c("flair", "MPRAGE", "T2w", "fmri", "DTI"), visits = c(1, 2)) ids modalities visits ID to return vector of image modalities within c("flair", "MPRAGE", "T2w", "fmri", "DTI") to return Vector of scan indices to return (1 or 2 or both) Data.frame of filenames Examples get_par_filenames()
6 6 modality_df kirby21_demog Kirby 21 Demographics A dataset containing demographic information for kirby21 data sets Format A data frame with 21 rows and 3 columns. Source modality_df All Modalities and the Corresponding package Return the modalities for images and the packages that contain them modality_df() data.frame of two columns: modality: modality of image package: package that contains it
7 subject_id_to_visit_id 7 subject_id_to_visit_id Kirby 21 Subject Identifiers to NITRC Visit Identifiers Format Source A dataset containing the mapping from the Subject IDs from the Kirby demographics to the KKI2009 identifiers on NITRC A data frame with 42 rows and 4 columns
8 Index all_modalities, 2 copy_kirby21_data, 2 download_kirby21_data, 3 get_ids, 3 get_image_filenames, 2, 4 get_image_filenames_df, 4, 4, 5 get_image_filenames_list (get_image_filenames_df), 4 get_image_filenames_list_by_subject (get_image_filenames_df), 4 get_image_filenames_list_by_visit (get_image_filenames_df), 4 get_image_filenames_matrix (get_image_filenames_df), 4 get_par_filenames, 5 kirby21_demog, 6 modality_df, 6 subject_id_to_visit_id, 7 8
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