Hi, What seems to be happening is that I insert this command: tkmedit subject_id brainmask.mgz rh.white -aux T1.mgz -aux-surface lh.white -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt it should show me the subcortical segmentation overlayed with the pial, white, and orig surface lines shown. It no longer shows me this after I made some control points in the coronal view.
[image: Inline image 1] This is what should show [image: Inline image 2] Why is this? Talia On Mon, Jul 28, 2014 at 10:40 AM, Talia Raney talia.raney@gmail.com wrote:
Hi, I'm having issues with tkmedit. I'm doing visual inspection and I checked tkregister to be sure that the white matter is outlined in the functional image. However, when I open tkmedit for surface and cortical segmentation, it doesn't show up the red and green lines that distinguish the boundaries of the grey and white matter. It had previously and I put a few control points but now it doesn't show up at all. Why might this be and how can it be fixed? Thanks! Talia
Hi Talia, this is a Problem with x11 forwarding. Everything works fine if you use VNC instead. Caspar
On Thursday, July 31, 2014, Talia Raney talia.raney@gmail.com wrote:
Hi, What seems to be happening is that I insert this command: tkmedit subject_id brainmask.mgz rh.white -aux T1.mgz -aux-surface lh.white -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt it should show me the subcortical segmentation overlayed with the pial, white, and orig surface lines shown. It no longer shows me this after I made some control points in the coronal view.
[image: Inline image 1] This is what should show [image: Inline image 2] Why is this? Talia On Mon, Jul 28, 2014 at 10:40 AM, Talia Raney <talia.raney@gmail.com javascript:_e(%7B%7D,'cvml','talia.raney@gmail.com');> wrote:
Hi, I'm having issues with tkmedit. I'm doing visual inspection and I checked tkregister to be sure that the white matter is outlined in the functional image. However, when I open tkmedit for surface and cortical segmentation, it doesn't show up the red and green lines that distinguish the boundaries of the grey and white matter. It had previously and I put a few control points but now it doesn't show up at all. Why might this be and how can it be fixed? Thanks! Talia
What gets printed out to the terminal? Can you load it through the interface?
On 07/31/2014 11:37 AM, Caspar M. Schwiedrzik wrote:
Hi Talia, this is a Problem with x11 forwarding. Everything works fine if you use VNC instead. Caspar
On Thursday, July 31, 2014, Talia Raney <talia.raney@gmail.com mailto:talia.raney@gmail.com> wrote:
Hi, What seems to be happening is that I insert this command: tkmedit subject_id brainmask.mgz rh.white -aux T1.mgz -aux-surface lh.white -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt it should show me the subcortical segmentation overlayed with the pial, white, and orig surface lines shown. It no longer shows me this after I made some control points in the coronal view. Inline image 1 This is what should show Inline image 2 Why is this? Talia On Mon, Jul 28, 2014 at 10:40 AM, Talia Raney <talia.raney@gmail.com <javascript:_e(%7B%7D,'cvml','talia.raney@gmail.com');>> wrote: Hi, I'm having issues with tkmedit. I'm doing visual inspection and I checked tkregister to be sure that the white matter is outlined in the functional image. However, when I open tkmedit for surface and cortical segmentation, it doesn't show up the red and green lines that distinguish the boundaries of the grey and white matter. It had previously and I put a few control points but now it doesn't show up at all. Why might this be and how can it be fixed? Thanks! Talia
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Caspar M. Schwiedrzik -
Douglas N Greve -
Talia Raney