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
dolphinede@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 greve@nmr.mgh.harvard.edu An: dolphinede dolphinede@aol.com; freesurfer 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
dolphinede@aol.com mailto:dolphinede@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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> An: dolphinede <dolphinede@aol.com mailto:dolphinede@aol.com> Cc: freesurfer <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
dolphinede@aol.com mailto:dolphinede@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
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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