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 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
