Yes, that looks right to me doug On 04/05/2012 11:50 AM, Irwin, William wrote: > Thanks, Doug. > > I actually want lobar both GM and WM. > > So would this be the correct syntax to generate lobar GM and WM labels? > > mri_aparc2aseg --s<subject> --labelwm --rip-unknown --ctxseg aparc+aseg.mgz > --annot lobe > > Yes, I started to do as you suggest with tkmedit using FreeView, but I > thought there might be a less manual way of doing this. > > Thanks, > Wil > > |-----Original Message----- > |From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] > |Sent: Thursday, April 05, 2012 8:30 AM > |To: Irwin, William > |Cc: freesurfer@nmr.mgh.harvard.edu > |Subject: Re: [Freesurfer] lobar WM volumes > | > |You don't need to do 2b if all you want are the lobar wm segmentations. > |2b should just copy the cortical labels into the new seg. > | > |mri_segstats --seg mri/newseg.mgz --sum stats/newseg.stats --pv > |mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent -- > |subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units > |MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab newcolortable -- > |subject<subject> > | > | > |You can load the newseg.mgz into tkmedit as both a segmentation (-seg) and > |as the aux volume. When you click on a point, you can see the seg value > |associated with the given label. > | > |doug > | > | > | > |On 04/04/2012 11:15 PM, Irwin, William wrote: > |> Hi Doug- > |> > |> I wanted to follow up on this procedure and ask for a bit of > clarification. As > |an extension from Ines' efforts, I believe one can produce a ' lobe+aseg.mgz' > |lobar volume with both WM and GM for both RH and LH. > |> > |> 1: > |> mri_annotation2label --s<subject> --hemi rh --lobesStrict lobe > |> mri_annotation2label --s<subject> --hemi lh --lobesStrict lobe > |> > |> 2(a): > |> mri_aparc2aseg --s<subject> --labelwm --annot lobe > |> > |> 2(b) > |> mri_aparc2aseg --s<subject> --rip-unknown --ctxseg aparc+aseg.mgz -- > |annot lobe > |> I'm not sure if this the correct syntax to be analogous to that for WM in > 2(a). > |> > |> What would be the correct syntax to combine 2(a) and 2(b) into one > |command? > |> > |> 3: > |> Per your suggestion for syntax, this can be found in recon-all.log > following > |that for wmparc (and I have identified that). There is similar syntax for > |GM/ctx. I'm not sure if the following would need to be slightly modified for > |my objective: > |> > |> mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv > |> mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent > |> --subcortgray --in mri/norm.mgz --in-intensity-name norm > |> --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol > |> --totalgray --ctab /usr/local/freesurfer/ASegStatsLUT.txt > |> --subject<subject> > |> > |> But, before proceeding with the step 3, how can one determine the lobar > |label numbers assigned such that a custom LUT can be created. The output of > |the 2(b) (if the syntax is correct) indicates that 8 entries are read > (Frontal, > |Temporal, Parietal, Occipital for LH and RH?). > |> > |> Thanks for your help. > |> > |> -Wil > |> > |> |-----Original Message----- > |> |From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] > |> |Sent: Monday, April 02, 2012 10:39 AM > |> |To: freesurfer@nmr.mgh.harvard.edu > |> |Subject: Re: [Freesurfer] lobar WM volumes > |> | > |> |use mri_segstats. You can look in subjid/scripts/recon-all.log for > |> |example command lines (look for the one with wmparc). The command > |> |will require a color table. The ones in the log file will use the > |> |default table, but this will not have the numbers/names of your > |> |lobar regions, so you'll need to create a new color table (or add to the > one > |that is there). > |> |doug > |> | > |> |On 04/02/2012 12:58 PM, Inês Violante wrote: > |> |> Dear all, > |> |> > |> |> I need to obtain the white matter volume per lobe for a given > |> |> numer of > |> |subjects. > |> |> I started by using the following: > |> |> > |> |> mri_annotation2label --subject<subjid> --hemi rh --lobesStrict > lobe > |> |> > |> |> mri_aparc2aseg --s<subjid> --labelwm --annot lobe > |> |> > |> |> and now I have a lobe+aseg.mgz file. How can I create a stats > |> |> file containing the wm volume for each lobe? > |> |> > |> |> Thank you, > |> |> > |> |> ines > |> |> > |> |> _______________________________________________ > |> |> 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 > |> | > |> > |> > |> > |> > | > |-- > |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 > | > | > | > |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. > > > >
-- 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
