Dear FreeSurfer Users,
I ran recon -all on my structural image and created ROI masks (using
mri_label2vol) based on FreeSurfer's cortical parcellation. I'd like to use
these masks for further analysis with FSL. However, it seems that the ROI
masks generated with mri_label2vol have different header
Hi Katica
what format was the input image to recon-all? Can you verify that tkmedit
has the directions correct (that is what it labels as anterior is actually
anatomically anterior, etc...). If so, then the talairach just failed and
you will need to either try an alternative (like the MNI or S
exactly, or measures derived them them like whole-brain volume
cheers
Bruce
On Sun, 5 Jan 2014, Yuliya
Yoncheva wrote:
Hello Bruce,
thank you very much for your fast response and clarifying that potential
voxels outside the pial surface do not impact cortical measures.
Best,
Yuliya
On S
Hello Bruce,
thank you very much for your fast response and clarifying that potential
voxels outside the pial surface do not impact cortical measures.
Best,
Yuliya
On Sun, Jan 5, 2014 at 3:40 PM, Bruce Fischl wrote:
> Hi Yuliya
>
> they are included if they are inside of the ?h.pial surface.
Hi Octavian
it's not so easy to reduce the bandwidth in the T2-space sequences, but
certainly you can try. Geometry-matched just means that the FOV and
matrix sizes are the same.
cheers
Bruce
On Fri, 3 Jan 2014, Octavian Lie wrote:
Dear Bruce,
Best wishes for 2014!
I will heed your advice
Hi Yuliya
they are included if they are inside of the ?h.pial surface. We don't use
the cortex aseg label as it is in general less accurate than the surfaces.
cheers
Bruce
On Sun, 5 Jan 2014, Yuliya Yoncheva wrote:
Dear FreeSurfer community,
I am visually inspecting the quality of my recon -
Hi Bruce
Yes I am - sorry to not have mentioned
Tudor
On 5 January 2014 17:00, Bruce Fischl wrote:
> Hi Tudor
> Are you doing the editing with tkmedit?
> Cheers
> Bruce
>
> > On Jan 5, 2014, at 6:20 AM, Tudor Popescu wrote:
> >
> > Hi everyone and happy new year!
> >
> > I made a couple of man
Hi Tudor
Are you doing the editing with tkmedit?
Cheers
Bruce
> On Jan 5, 2014, at 6:20 AM, Tudor Popescu wrote:
>
> Hi everyone and happy new year!
>
> I made a couple of manual edits to a wm.mgz file and then relaunched part of
> that subject's recon (-autorecon2-wm -autorecon3). After it fi
Hi everyone and happy new year!
I made a couple of manual edits to a wm.mgz file and then relaunched part
of that subject's recon (-autorecon2-wm -autorecon3). After it finished,
however, the wm.mgz had lost its manual edits - even though I had saved the
edited version under the same name, in the
