Nothing
#' @export
import_suma.T1 <- function(subject_name, fs_path, quiet = FALSE, dtype,
sub_type = c("brain.finalsurfs", "brainmask", "brainmask.auto", "T1"), hemisphere, ...){
sub_type <- match.arg(sub_type)
fs_path <- normalizePath(fs_path)
fname <- sprintf('%s.nii', sub_type)
src <- file.path(fs_path, 'SUMA', fname)
if( ! file.exists(src) ) {
if(!quiet){
cat2(sprintf(" * SUMA/%s is missing\n", fname), level = 'WARNING')
}
return( FALSE )
}
src <- normalizePath(src)
tname <- sprintf('%s_t1.json', subject_name)
target <-file.path(fs_path, 'RAVE', tname)
dige <- paste0(target, '.digest')
cached <- validate_digest(src, target)
if(!isFALSE(cached)){
return( TRUE )
}
# Load file
dat <- read_nifti(src)
Norig <- dat$header$get_vox2ras()
Torig <- dat$header$get_vox2ras_tkr()
volume_shape <- as.integer(dat$get_shape())
group_volume <- GeomGroup$new(name = sprintf('Volume - T1 (%s)', subject_name))
group_volume$subject_code <- subject_name
volume <- dat$get_data()
volume <- reorient_volume( volume, Torig )
# Create a datacube geom to force cache
unlink(target)
DataCubeGeom$new(
name = sprintf('T1 (%s)', subject_name), value = volume, dim = volume_shape,
half_size = volume_shape / 2, group = group_volume, position = c(0,0,0),
cache_file = target)
rm(volume)
rm(dat)
# Add file_digest, Norig, Torig to cache_digest
add_to_digest_file(
dige,
file_digest = attr(cached, 'digest'),
Norig = Norig,
Torig = Torig,
source_name = fname,
shape = volume_shape,
THREEBRAIN_DATA_VER = THREEBRAIN_DATA_VER,
.append = FALSE
)
add_to_digest_file(
file.path(fs_path, 'RAVE', 'common.digest'),
fs_volume_files = tname,
.append = TRUE
)
add_to_digest_file(
file.path(fs_path, 'RAVE', 'common.digest'),
THREEBRAIN_DATA_VER = THREEBRAIN_DATA_VER,
.append = FALSE
)
return(TRUE)
}
# import_fs('YCQ', fs_path = '~/rave_data/others/fs/', dtype = 'T1', sub_type = 'brain.finalsurfs')
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