Hi Mahinda, sorry for the delay, answers below

On 10/15/2012 02:13 PM, Mahinda Yogarajah wrote:

Dear Experts,

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?

Yes

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 ?

The --cortex option has it report stats for the cortex as a whole. The individual label stats should not change.

_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.

They should give the same stats for each label. Part of the difference is the reporting of various whole-brain stats (eg, --brain-vol-from-seg will compute the total brain volume based on the number of voxels in the segmentation); this measures are already in aseg.stats, but it might be convenient to have them in your new stats file. The --empty will tell it not to report labels in the colortable if they do not have any voxels in the segmentation. doug

Thanks.

Mahinda

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