Jenni,
Thanks; that was easier than I thought. I also appreciate the warning
about editing the brainmask.mgz. We will be sure to follow your
suggestion and save it as another file before editing it.
Thanks again,
Jared
Jenni Pacheco wrote:
Hi Jared,
Mechanically, yes - you would use the edit voxels tool and then use
the right button to remove the voxels you do not want.
I'm not sure I understand exactly what you are trying to do - and if
you eventually want to use Freesurfer to obtain surfaces etc, this
will not work. I'd suggest saving your brainmask as something else,
and edit that - this way you still have a viable brainmask.mgz to
obtain results with.
Jenni
On Mon, 11 Jun 2007, Jared Conley wrote:
Hi Jenni,
I am trying to edit the greyscale images of the brainmask.mgz. We
are trying to generate an ICC map with only grey/white matter and we
need to exclude a few structures that are not removed in the
skull-stripping step (i.e. some of the cranial nerves, pituitary,
etc.). I assume that I begin by using the "Edit Voxels tool (a)",
but I do not know where to go from there.
Thanks,
Jared
Jenni Pacheco wrote:
Hi Jared,
What happens when you try and edit? What type of editing are you
trying to do? Do you have the right tools selected? I'm going to
need a little bit more information on what you are doing and what is
going wrong. Thanks,
Jenni
On Mon, 11 Jun 2007, Jared Conley wrote:
FreeSurfer community,
I am attempting to manually edit brainmask.mgz in TkMedit and
cannot figured out how to do so based on the info in the Wiki. I
load the file in X11 with the command <tkmedit subjid
brainmask.mgz> and see the images just fine, but I cannot seem to
manually edit them like I can in the segmentation file. Any ideas?
Thanks,
Jared
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