Hi Jenni,
Sorry for the confusion. We are more familiar with our own
registration/segmentation system, where we edit before segmentation not
after. Anyway, thank you for the advice. We will edit the aseg.mgz
file instead.
Thanks again,
Jared
Jenni Pacheco wrote:
Hi Jared,
It's stil
Hi Jared,
It's still not completely clear to me what you are trying to do. By
segmentation values do you just mean the volumes that will come out of the
aseg.mgz? If thats what you mean you should make these edits to the
aseg.mgz itself.
I'm not certain what will happen if you make these e
Jenni,
Another question for you. What is the consequence of running autorecon2
after editing on the brainmask.mgz file itself. You mentioned something
about it not working if we want to obtain surfaces--what did you mean
exactly? CSF surfaces?
Ideally, we are editing the brainmask.mgz fil
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 t
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 sug
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
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:
FreeSurfe
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 and see the
images just fine, but I cannot seem to manually edit them like I can in
the segmentation fil
