I apologise for the repost but I was wondering if anyone could guide me with respect to deriving lobar measures and whether the commands below are correct . Thanks. M
GM Lobar Values
(1) mri_annotation2label --subject subject1 --hemi ?h --lobesStrict lobesfile
(2) mri_anatomical_stats –mgz –cortex ../label/?h.cortex.label –f ../stats/?h.lobesfiles.stats –b –a ../label/?h.lobesfile.annot subject1 ?h white
Q: Is this valid?
Q:Do I need to include that part of the command in italics (-cortex...?hcortex.label) - is it not redundant given the use of the ?h.lobesfile.annot - using one or the other does give a different result at the top of the stats file (namely NumVert, WhiteSurfArea, and mean thickness which disappears if ?h.cortex.label is not passed) - why is this ?
WM Lobar Values
(1) mri_annotation2label --subject subject1 –hemi ?h --lobesStrict lobesfile
(2) mri_aparc2seg --s subject1 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.lobar.mgz --ctxseg aparc+aseg.mgz --annot ?h.lobesfile.annot
Q: Is this valid ?
Q: Do I need all the items in italics (hypo...rip...volmask) - they are present in the recon-all logfile but not in some forum posts on similar topics.
(3a) mri_segstats --seg mri/wmparc.lobar.mgz --sum stats/wmparc.lobar.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject subject1 --surf-wm-vol --surf-ctx-vol --totalgray --ctab newcolourtable --etiv
OR
(3b) mri_segstats --seg mri/wmparc.lobar.mgz --sum stats/wmparc.lobar.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/norm.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject subject1 --surf-wm-vol --ctab newcolourtable --etiv
Q: Which of these should I be using - the latter is based on the recon-all log file, while the former is based on forum posts - what are the differences.
Thanks.
Mahinda