fsbrain (version 0.2.1)

qc.from.segstats.table: Perform data quality check based on a segstats table.

Description

Determine subjects that potentially failed segmentation, based on segstats table data. The input table file must be a segmentation or parcellation table, generated by running the FreeSurfer tools 'aparcstats2table' or 'asegstats2table' for your subjects.

Usage

qc.from.segstats.table(
  filepath,
  z_threshold = 2.8,
  verbosity = 1L,
  num_bad_regions_allowed = 1L
)

Arguments

filepath

path to input file, a tab-separated file generated by running 'aparcstats2table' or 'asegstats2table'. The command line in the system shell would be something like 'aparcstats2table_bin --subjectsfile $subjects_file --meas $measure --hemi $hemi -t $aparc_output_table'.

z_threshold

numerical, the cutoff value for considering a subject an outlier (in standard deviations).

verbosity

integer, controls the output to stdout. 0=off, 1=normal, 2=verbose.

num_bad_regions_allowed

integer, the number of regions in which subjects are allowed to be outliers without being reported as potentially failed segmentation

Value

vector of character strings, the subject identifiers which potentially failed segmentation