FastSurferCNN.mri_segstats

FreeSurfer’s mri_segstats command line interface for segstats.py.

mri_segstats.py translates the mri_segstats options listed in its help to segstats.py; other options of mri_segstats are not supported.

Limitations

These supported options do not behave like mri_segstats (FreeSurfer 8.1.0):

• –sqr, –sqrt, –abs, –mul and –div modify the partial volume image (–pv, or –i without –pv), so they change the volumes, but not the intensity statistics. mri_segstats applies them to –i only.

• Without –pv, mri_segstats.py corrects partial volume effects with –i. mri_segstats reports the number of voxels as the volume, unless –pv is passed.

• mri_segstats.py needs –i or –pv to compute the table, mri_segstats reports the number of voxels and the volume of each segmentation also without them.

• –robust keeps the voxel of single-voxel segmentations, where mri_segstats keeps no voxel and reports nan, and rejects percentages of 50 and above, where mri_segstats keeps no voxel of some segmentations.

FastSurferCNN.mri_segstats.format_cmdline_args(args)

Format the commandline arguments of the segstats script.

FastSurferCNN.mri_segstats.make_arguments()

Create an argument parser object with all parameters of the script.

FastSurferCNN.mri_segstats.parse_arguments(argv=None)

Parse the command line argv and apply the parse actions, e.g. –no-global-stats or the eTIV ratios.

FastSurferCNN.mri_segstats.print_and_exit(args)

Print the commandline arguments of the segstats script to stdout and exit.