| Type: | Package |
| Title: | Example Data from the Multi-Modal MRI 'Reproducibility' Resource |
| Version: | 1.7.3 |
| Date: | 2020-07-02 |
| Author: | John Muschelli <muschellij2@gmail.com> |
| Maintainer: | John Muschelli <muschellij2@gmail.com> |
| Description: | Multi-modal magnetic resonance imaging ('MRI') data from the 'Kirby21' 'reproducibility' study https://www.nitrc.org/projects/multimodal/, including functional and structural imaging. |
| License: | GPL-2 |
| LazyData: | true |
| LazyLoad: | true |
| Imports: | utils, stats, git2r |
| RoxygenNote: | 7.1.0 |
| URL: | https://www.nitrc.org/projects/multimodal/, http://dx.doi.org/10.1016/j.neuroimage.2010.11.047 |
| Encoding: | UTF-8 |
| Suggests: | testthat (≥ 2.1.0) |
| NeedsCompilation: | no |
| Packaged: | 2020-07-02 18:19:56 UTC; johnmuschelli |
| Repository: | CRAN |
| Date/Publication: | 2020-07-02 18:40:02 UTC |
Return All Modalities
Description
Return the modalities for images where packages were developed
Usage
all_modalities()
Value
Vector of characters
Copy Kirby21 Data to an output directory
Description
Copies files from Kirby21 Package to an output directory
Usage
copy_kirby21_data(copydir, ...)
Arguments
copydir |
Output directory for data |
... |
Arguments to pass to |
Value
Logical if files are copied
Examples
on_cran = !identical(Sys.getenv("NOT_CRAN"), "true")
on_ci <- nzchar(Sys.getenv("CI"))
local_run = grepl("musch", tolower(Sys.info()[["user"]]))
run_example = !on_cran || on_ci || local_run
if (run_example) {
tdir = tempfile()
dir.create(tdir)
outdir = tempdir()
surv_installed = "kirby21.survey" %in% installed.packages()
if (!surv_installed) {
testthat::expect_error(
download_kirby21_data("SURVEY",
force = FALSE))
} else {
download_kirby21_data("SURVEY",
force = FALSE)
}
res = download_kirby21_data("SURVEY", outdir = outdir, force = TRUE)
if (!surv_installed) {
try({remove.packages("kirby21.survey")})
}
copy_kirby21_data(copydir = tdir, outdir = outdir)
}
Delete Kirby21 Imaging Data
Description
This function allows users to remove specific modalities for Kirby21 data sets. This allows this package to be on CRAN
Usage
delete_kirby21_data(modality = kirby21.base::all_modalities(), outdir = NULL)
Arguments
modality |
modality of images that are to be downloaded. You must have the package downloaded for that modality. |
outdir |
output directory for files to download. It will default to the directory of the corresponding package for the data. |
Value
Nothing is returned
Examples
on_cran = !identical(Sys.getenv("NOT_CRAN"), "true")
on_ci <- nzchar(Sys.getenv("CI"))
local_run = grepl("musch", tolower(Sys.info()[["user"]]))
run_example = !on_cran || on_ci || local_run
if (run_example) {
outdir = tempdir()
res = download_kirby21_data("SURVEY", outdir = outdir, force = TRUE)
delete_kirby21_data("SURVEY", outdir = outdir)
}
Download Kirby21 Imaging Data
Description
This function allows users to download specific modalities for Kirby21 data sets. This allows this package to be on CRAN
Usage
download_kirby21_data(
modality = kirby21.base::all_modalities(),
progress = TRUE,
force = FALSE,
outdir = NULL
)
Arguments
modality |
modality of images that are to be downloaded. You must have the package downloaded for that modality. |
progress |
Should verbose messages be printed when downloading the data |
force |
If the package of that modality is not installed stop. If
|
outdir |
output directory for files to download. It will default to the directory of the corresponding package for the data. |
Value
A logical indicating the data is there.
Examples
on_cran = !identical(Sys.getenv("NOT_CRAN"), "true")
on_ci <- nzchar(Sys.getenv("CI"))
local_run = grepl("musch", tolower(Sys.info()[["user"]]))
run_example = !on_cran || on_ci || local_run
if (run_example) {
outdir = tempdir()
res = download_kirby21_data("SURVEY", outdir = outdir)
}
Get IDs with Data in Package
Description
Return the IDs for the people scanned available in the kirby21 packages
Usage
get_ids()
Value
Vector of numeric ids
Get Image Filenames
Description
Return the filenames for the images
Usage
get_image_filenames(...)
Arguments
... |
arguments passed to |
Examples
get_image_filenames()
Get Image Filenames in a data.frame
Description
Return a data.frame of filenames for the images
Usage
get_image_filenames_df(
ids = get_ids(),
modalities = all_modalities(),
visits = c(1, 2),
long = TRUE,
warn = TRUE,
outdir = NULL
)
get_image_filenames_matrix(...)
get_image_filenames_list(...)
get_image_filenames_list_by_visit(...)
get_image_filenames_list_by_subject(...)
Arguments
ids |
ID to return |
modalities |
vector of image modalities within
|
visits |
Vector of scan indices to return (1 or 2 or both) |
long |
if |
warn |
if |
outdir |
output directory for files to download. It will default to the directory of the corresponding package for the data. |
... |
arguments passed to |
Value
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 Filenames of Par files
Description
Return the filenames for the par files
Usage
get_par_filenames(
ids = get_ids(),
modalities = c("FLAIR", "MPRAGE", "T2w", "fMRI", "DTI"),
visits = c(1, 2)
)
Arguments
ids |
ID to return |
modalities |
vector of image modalities within
|
visits |
Vector of scan indices to return (1 or 2 or both) |
Value
Data.frame of filenames
Examples
get_par_filenames()
Kirby 21 Demographics
Description
A dataset containing demographic information for kirby21 data sets
Format
A data frame with 21 rows and 3 columns.
Source
https://www.nitrc.org/frs/?group_id=313
All Modalities and the Corresponding package
Description
Return the modalities for images and the packages that contain them
Usage
modality_df()
Value
data.frame of two columns:
modality: modality of image
package: package that contains it
Kirby 21 Subject Identifiers to NITRC Visit Identifiers
Description
A dataset containing the mapping from the Subject IDs from the Kirby demographics to the KKI2009 identifiers on NITRC
Format
A data frame with 42 rows and 4 columns