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

In dfsp-spirit/fsbrain: Managing and Visualizing Brain Surface Data

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)
)

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'.

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'.

dfsp-spirit/fsbrain documentation built on Nov. 28, 2024, 10:29 a.m.