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.
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.