18 Apr
2014
18 Apr
'14
3:32 p.m.
Hi FS community,
I had some questions regarding the mri_segstats command:
1) In the excludeid flag, are the ids the ones shown in the FreeSurferColorLUT.txt? 2) In case I would like to measure the mean intensity of the orig file as outlined in the second example in https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats:
mri_segstats --seg $SUBJECTS_DIR/bert/mri/aseg --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --nonempty --excludeid 0 --sum bert.aseg.sum --in $SUBJECTS_DIR/bert/mri/orig
is the --seg flag necessary in order to calculate only the mean intensity within the skull, or does it serve another purpose?
Thanks in advance, Panos