sure, mris_anatomical_stats can do this. Look at the annot and BA*.label files in tksurfer (in the subject's label directory) to see which ones have areas you are interested in. Many of these are already reported by default in the stats dir.
cheers, Bruce
On Tue, 30 Mar 2010, Janani Dhinakaran wrote:
I managed to rerun recon-all completely and get the cortex out with tkmedit jan aparc+aseg.mgz I wonder if there is a way of specifying particular areas like extracting and measuring the volumes or thickness of regions like the sensorimotor cortex or broca's area?
Thank you
On 16 March 2010 12:14, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
does the file /home/s0964091/Desktop/jan/mri/aparc.a2005s+aseg.mgz exist? Did recon-all complete properly?
On Tue, 16 Mar 2010, Janani Dhinakaran wrote:
Hello,
With reference to this mail- Re: [Freesurfer] Extracting ROIs from aparc.a2009s+aseg.mgzI tried introducing segments to my image
ERROR: Loading Segmentation aparc.a2005s+aseg.mgz Couldn't import the segmentation volume. Tkmedit wouldn't read the segmentation you specified. This could be because the segmentation volume wasn't a valid COR volume directory.
The following is what happened in the text shell. s0964091@CRIC-0012:~$ tkmedit jan orig.mgz -segmentation aparc.a2005s+aseg.mgz ERROR: cannot find /home/s0964091/Desktop/jan/mri/aparc.a2005s+aseg.mgz LoadSegmentationVolume main aparc.a2005s+aseg.mgz /usr/local/freesurfer/FreeSurferColorLUT.txt Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl %
So it loaded Orig but without segments. How do I rectify this?
Thank you.
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