Your ROI must be listed in the color table, so you'll need to create a custom color table. For this you will need the ID eventually assigned to your ROI. To find this out, load the wmparc your created in tkmedit as both a segmentation and as the aux volume. When you click on your ROI, the tkmedit control window should show the name of your ROI. The "aux" field will show a value. This is the value you need. doug
dolphin...@aol.com wrote: > Hi Doug, > > thanks a lot for your reply. > > I have run the following command to get wm volume stats of my ROI: > > > mri_segstats --seg > /Users/dolphinede/Desktop/Probanden/ARS23/mri/wmparc.mgz --sum > /Users/dolphinede/Desktop/Probanden/ARS23/stats/wmparc.stats --pv > /Users/dolphinede/Desktop/Probanden/ARS23/mri/norm.mgz --excludeid 0 > --brain-vol-from-seg --brainmask > /Users/dolphinede/Desktop/Probanden/ARS23/mri/brainmask.mgz --in > /Users/dolphinede/Desktop/Probanden/ARS23/mri/norm.mgz > --in-intensity-name norm --in-intensity-units MR --etiv --subject > ARS23 --surf-wm-vol --ctab > /Applications/freesurfer//FreeSurferColorLUT.txt > > But I think it is not right cause my ROI, my annotation is not listed > there in the wmparc.stats. I thought that with my annotation i did > modify my wmparc.mgz and this yields to a new wmparc.stats. > > > Best regards > > Daniel... > > > > > > > -----Ursprüngliche Mitteilung----- > Von: Douglas N Greve <gr...@nmr.mgh.harvard.edu> > An: dolphinede <dolphin...@aol.com>; freesurfer > <freesurfer@nmr.mgh.harvard.edu> > Verschickt: Mo, 31 Okt 2011 3:20 pm > Betreff: Re: [Freesurfer] white matter volume in a ROI > > Use mri_segstats. You can look in the recon-all.log file in > subject/scripts. Find the call to mri_segstats used to generate the > wmparc stats, copy it and make the customizations you need. > doug > > dolphin...@aol.com <mailto:dolphin...@aol.com> wrote: > > Hi Doug, > > > > to get the white matter volume of my ROI-label, i have done the > > following steps: > > > > 1. mris_label2annot > > (mris_label2annot --s ZPN20 --h lh --ctab > > /Users/dolphinede/Desktop/Probanden/ZPN20/label/aparc.annot.ctab --a > > myaparc --l lh.cluster1.labe/.label --nhits nhits.mgh) > > > > > > 2. mri_aparc2aseg, with my real ROI label and a dumy label for the > > other hemisphere. > > > > mri_aparc2aseg --s ZPN20 --labelwm --hypo-as-wm --rip-unknown > > --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz --annot myaparc/ > > > > How do i get from the wmparc.mgz the white matter volume for my ROI > > label/myaparc ? > > Should i use mris_wm_volume? > > > > Best regards > > > > Daniel... > > > > > > > > > > > > -----Ursprüngliche Mitteilung----- > > Von: Douglas N Greve <gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu>> > > An: dolphinede <dolphin...@aol.com <mailto:dolphin...@aol.com>>; freesurfer > > <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > Verschickt: Di, 25 Okt 2011 5:05 pm > > Betreff: Re: [Freesurfer] white matter volume in a ROI > > > > > > Yes, I see what you mean. mri_aparc2aseg is hard coded to accept both > > hemis. The easiest way around it is just to create a dummy label for the > > right hemisphere. > > doug > > > > dolphin...@aol.com <mailto:dolphin...@aol.com> <mailto:dolphin...@aol.com > > <mailto:dolphin...@aol.com?>> wrote: > > > Hi Doug, > > > > > > thanks a lot your advice. > > > > > > I created an annnotation of my ROI-label as called > > > lh.cluster1.labe.label with the command line: > > > > > > /mris_label2annot --s ZPN20 --h lh --ctab > > > //Users/dolphinede/Desktop/Probanden/ZPN20/label/aparc.annot.ctab --a > > > myaparc --l lh.cluster1.labe/.label --nhits nhits.mgh > > > > > > This works fine. After that i have used your commmand in this way: > > > > > > m/ri_aparc2aseg --s ZPN20 --labelwm --hypo-as-wm --rip-unknown > > > --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz --annot myaparc/ > > > > > > and i get the following error, which is cause that i have no > > > lh.cluster1.labe.label in the right hemisphere: > > > > > > /Loading lh annotations from > > > /Users/dolphinede/Desktop/Probanden/ZPN20/label/lh.myaparc.annot > > > reading colortable from annotation file... > > > colortable with 36 entries read (originally > > > //Users/dolphinede/Desktop/Probanden/ZPN20/label/aparc.annot.ctab) > > > > > > Reading rh white surface > > > /Users/dolphinede/Desktop/Probanden/ZPN20/surf/rh.white > > > > > > Reading rh pial surface > > > /Users/dolphinede/Desktop/Probanden/ZPN20/surf/rh.pial > > > > > > Loading rh annotations from > > > /Users/dolphinede/Desktop/Probanden/ZPN20/label/rh.myaparc.annot > > > could not read annot file > > > /Users/dolphinede/Desktop/Probanden/ZPN20/label/rh.myaparc.annot > > > No such file or directory > > > ERROR: MRISreadAnnotation() failed > > > /Users/dolphinede/Desktop/Probanden/ZPN20/label/rh.myaparc.annot/ > > > > > > The question i have is if all these steps are right and/if i have to > > > do some more steps to get white matter volume of my annotation and > > > where i can find it? > > > > > > Excuse my numerous questions but I am just a freesurfer-beginner... > > > > > > Best regards > > > > > > Daniel > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -----Ursprüngliche Mitteilung----- > > > Von: Douglas N Greve <gr...@nmr.mgh.harvard.edu > > > <mailto:gr...@nmr.mgh.harvard.edu> <mailto:gr...@nmr.mgh.harvard.edu > > > <mailto:gr...@nmr.mgh.harvard.edu?>>> > > > An: dolphinede <dolphin...@aol.com <mailto:dolphin...@aol.com> > > > <mailto:dolphin...@aol.com <mailto:dolphin...@aol.com?>>>; freesurfer > > > <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > > <mailto:freesurfer@nmr.mgh.harvard.edu > > > <mailto:freesurfer@nmr.mgh.harvard.edu?>>> > > > Verschickt: Mo, 24 Okt 2011 10:04 pm > > > Betreff: Re: [Freesurfer] white matter volume in a ROI > > > > > > It will be more involved than that. You will need to create an > > > annotation that contains your label (maybe in addition to other labels), > > > then uses mri_aparc2aseg with the --labelwm option, something like > > > > > > mri_aparc2aseg --s subject-anat --labelwm --hypo-as-wm --rip-unknown > > > --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz --annot yourannot > > > > > > doug > > > > > > dolphin...@aol.com <mailto:dolphin...@aol.com> <mailto:dolphin...@aol.com > > > <mailto:dolphin...@aol.com?>> <mailto:dolphin...@aol.com > > > <mailto:dolphin...@aol.com?> > <mailto:dolphin...@aol.com <mailto:dolphin...@aol.com?>?>> wrote: > > > > Hi Doug, > > > > > > > > thanks a lot for your answer. > > > > > > > > So i understand you right that i can get "exact" knowledge about the > > > > thickness, grey matter volume and pial surface area in my ROI, but in > > > > case of "the" ROI white matter volume, i have to look to which > > > > cortical label my ROI counts and then I use the wmparc.files for this > > > > label? > > > > > > > > Best regards > > > > > > > > Daniel Klein > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -----Ursprüngliche Mitteilung----- > > > > Von: Douglas N Greve <gr...@nmr.mgh.harvard.edu > > > > <mailto:gr...@nmr.mgh.harvard.edu> <mailto:gr...@nmr.mgh.harvard.edu > > > > <mailto:gr...@nmr.mgh.harvard.edu?>> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu?> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu?>?>>> > > > > An: dolphinede <dolphin...@aol.com <mailto:dolphin...@aol.com> > > > > <mailto:dolphin...@aol.com <mailto:dolphin...@aol.com?>> > <mailto:dolphin...@aol.com <mailto:dolphin...@aol.com?> > <mailto:dolphin...@aol.com <mailto:dolphin...@aol.com?>?>>> > > > > Cc: freesurfer <freesurfer@nmr.mgh.harvard.edu > > > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > > <mailto:freesurfer@nmr.mgh.harvard.edu > > > > <mailto:freesurfer@nmr.mgh.harvard.edu?>> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu?> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu?>?>>> > > > > Verschickt: Mo, 24 Okt 2011 4:48 pm > > > > Betreff: Re: [Freesurfer] white matter volume in a ROI > > > > > > > > For GM area and volume, you can use mris_anatomical_stats. See the > > > > recent thread on how. For the WM volume, how would you define the WM > > > > volume that corresponds to you label? We have a routine that > > > > parcellates > > > > WM based on closest proximity to a cortical label. > > > > doug > > > > > > > > dolphin...@aol.com <mailto:dolphin...@aol.com> > > > > <mailto:dolphin...@aol.com <mailto:dolphin...@aol.com?>> > > > > <mailto:dolphin...@aol.com <mailto:dolphin...@aol.com?> > <mailto:dolphin...@aol.com <mailto:dolphin...@aol.com?>?>> wrote: > > > > > Dear FreeSurfer experts, > > > > > > > > > > i have created a ROI in qdec , where i have found a significant > > > > > correlation between lgi and age. > > > > > > > > > > I mapped this ROI to all subjects. > > > > > > > > > > I am interested to compare in this ROI the pial-surface area, the > > > > > grey > > > > > matter volume and if possible the white matter volume for this > > > > > specific region and i am not sure how to do this? > > > > > > > > > > Best regards > > > > > > > > > > Daniel Klein > > > > > ------------------------------------------------------------------------ > > > > > > > > > > _______________________________________________ > > > > > Freesurfer mailing list > > > > > Freesurfer@nmr.mgh.harvard.edu > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu?>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu?> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > > > > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu?>> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu?> > <mailto:gr...@nmr.mgh.harvard.edu <mailto: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 > > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://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 <mailto:gr...@nmr.mgh.harvard.edu> > > > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu?>> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu?> > <mailto:gr...@nmr.mgh.harvard.edu <mailto: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 > > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu <mailto: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 > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto: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 > <http://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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
