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
dolphinede@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 greve@nmr.mgh.harvard.edu An: dolphinede dolphinede@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
dolphinede@aol.com mailto:dolphinede@aol.com wrote:
Hi Doug,
to get the white matter volume of my ROI-label, i have done the following steps:
- 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)
- 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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> An: dolphinede <dolphinede@aol.com mailto:dolphinede@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
dolphinede@aol.com mailto:dolphinede@aol.com <mailto:dolphinede@aol.com mailto: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 mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu?>> An: dolphinede <dolphinede@aol.com mailto:dolphinede@aol.com <mailto:dolphinede@aol.com mailto:dolphinede@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
dolphinede@aol.com mailto:dolphinede@aol.com <mailto:dolphinede@aol.com mailto:dolphinede@aol.com?> <mailto:dolphinede@aol.com mailto:dolphinede@aol.com?
<mailto: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 <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu?>
<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu? <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu??>>>
An: dolphinede <dolphinede@aol.com mailto:dolphinede@aol.com <mailto:dolphinede@aol.com mailto:dolphinede@aol.com?>
<mailto:dolphinede@aol.com mailto:dolphinede@aol.com? <mailto:dolphinede@aol.com mailto:dolphinede@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
dolphinede@aol.com mailto:dolphinede@aol.com <mailto:dolphinede@aol.com mailto:dolphinede@aol.com?> <mailto:dolphinede@aol.com mailto:dolphinede@aol.com?
<mailto: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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Phone Number: 617-724-2358 Fax: 617-726-7422
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu?> Phone Number: 617-724-2358 Fax: 617-726-7422
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@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
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