diff --git a/R/threeBrain.R b/R/threeBrain.R index cb999bd7..c9410552 100644 --- a/R/threeBrain.R +++ b/R/threeBrain.R @@ -172,6 +172,10 @@ threeBrain <- function( "brain.finalsurfs", "synthSR.norm", "synthSR", "brain", "brainmask", "brainmask.auto", "T1" ) + allowed_fsmri_prefix <- c( + "brain.finalsurfs", "synthSR.norm", "synthSR", "brain", + "brainmask", "brainmask.auto", "T1" + ) path_mri <- file.path(fs_path, "mri", as.vector(rbind( sprintf("%s.nii.gz", allowed_mri_prefix), @@ -180,6 +184,13 @@ threeBrain <- function( ))) path_mri <- path_mri[file.exists(path_mri)] if(length(path_mri)){ path_mri <- path_mri[[1]] } + path_fsmri <- file.path(fs_path, "mri", as.vector(rbind( + sprintf("%s.nii.gz", allowed_fsmri_prefix), + sprintf("%s.nii", allowed_fsmri_prefix), + sprintf("%s.mgz", allowed_fsmri_prefix) + ))) + path_fsmri <- path_fsmri[file.exists(path_fsmri)] + if(length(path_fsmri)){ path_fsmri <- path_fsmri[[1]] } # xfm path_xfm <- file.path(fs_path, "mri", "transforms", "talairach.xfm") @@ -235,7 +246,7 @@ threeBrain <- function( } # Norig, Torig - mgz_files <- c(path_mri, path_atlas) + mgz_files <- c(path_fsmri, path_atlas) if(!length(mgz_files)) { mgz_files <- list.files( file.path(fs_path, "mri"), pattern = "\\.mg(z|h)$", all.files = FALSE,