fsbrain (version 0.5.3)

fslong.subjects.finished: Find completely run FreeSurfer long subjects in a recon-all long output folder.

Description

This finds all subjects for which the FreeSurfer long pipeline finished. It can work without a subjects file, by scanning the directory names to find all potential subjects. It checks only whether the expected folder for each subject exists. For a subject named 'subject1' and 2 timepoints, these folders are checked for existence: subject1, subject1_MR1, subject1_MR2, subject1_MR1.long.subject1, subject1_MR2.long.subject1

Usage

fslong.subjects.finished(
  subjects_dir,
  subjects_to_check = NULL,
  timepoints = seq.int(2)
)

Value

a named list with entries 'subjects_okay' and 'subjects_missing_dirs'. Each of these two keys contains a vector of character strings, the respective subjects (a subset if 'subjects_to_check'). In 'subjects_okay' are all subjects for which the expected long directories were found, the rest is in 'subjects_missing_dirs'.

Arguments

subjects_dir

char, the recon-all long output directory

subjects_to_check

a vector of chars, the subject names (the cross-sectional names, without the '_MR1' or '_MR2' or 'long' suffixes). If NULL, the folder will be scanned for subjects, by looking for all '_MR1' folders and stripping the '_MR1' suffix.

timepoints

vector of integers, the timepoints to check. E.g., c(1,2) or seq.int(2) if you want to check scan timepoints '_MR1' and 'MR2'.