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 <fis...@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. >> s0964...@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. > > -- I am the Sun, I know no darkness.
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