Hello, Bruce,
Thanks a lot!
Now I come to Round. 1,
I use command lines below for reference subject # 1 (base_1)
%%%
mris_register -curv $FREESURFER_HOME/subjects/base_1/surf/lh.sphere
$FREESURFER_HOME/subjects/base_1/surf/my_template0_lh.tif
$FREESURFER_HOME/subjects/base_1/surf/
no, you shouldn't run 2 and 3. sulc and curv are *not* surface formats,
so the code dies trying to read them as such
On Fri, 13 Nov 2009, Guang Zeng
wrote:
>
> Hello, Bruce,
>
> Thanks a lot for your help!
> I ran 4 commands, and results are shown below:
>
> 1.
>
Hello, Bruce,
Thanks a lot for your help!
I ran 4 commands, and results are shown below:
1.
%%%
mris_make_template lh smoothwm 018_S_0425_20060419_CN my_template0.tif
creating new parameterization...
processing subject 018_S_
Use mri_surf2vol to create volumes. You can binarize aparc+aseg.mgz to
give a mask of an area (use --match), then take the intersection of the
mask with the surface-in-volume.
doug
Martin Ystad wrote:
> Hi,
> I'm working on a fractal dimension analysis of the pial- and
> white-matter surface.
I think it does not include both, so yes you should add them.
On Fri, 13 Nov
2009, Matt Clarkson wrote:
> Hi Bruce,
>
> in general, the vents look good. So, just one more question, if I may. I
> notice that the segmentation labels have ventricles and choroid-plexus.
> So, in the wmparc.stats, an
Hi Bruce,
in general, the vents look good. So, just one more question, if I may. I notice
that the segmentation labels have ventricles and choroid-plexus.
So, in the wmparc.stats, and aseg.stats, does the volume of the left lateral
ventricle include the left choroid plexus, or should I add both
Hi Matt,
are the ventricles labeled properly in the aseg? If so, then you probably
don't need to do anything. If not, then you'll need to manually edit
them, and run from there forward (-make all should do it).
cheers,
Bruce
On Fri, 13 Nov
2009, Matt Clarkson wrote:
> Hi Bruce,
>
> Thanks. So
Hi Bruce,
Thanks. So it sounds like FreeSurfer 4.5 should now be adequately filling
ventricles in the general case, and that -bigventricles offers didn't reach a
level of robustness you were happy with, so best to avoid that? What about the
flag -fillven on mri_edit_wm_with_aseg? Any use?
In t
Hi,
I'm working on a fractal dimension analysis of the pial- and
white-matter surface. The matlab script that calculates the fractal
dimension needs binary nifti-files as input. Since FreeSurfer creates
the surfaces I need, here's what I want to do:
I'd like to convert the pial and white-matter
Hi Matt,
yes, the filling procedure has evolved and is better in current versions
than previous ones.
cheers,
Bruce
On Fri, 13 Nov 2009, Matt Clarkson wrote:
> Hi Bruce,
>
> I agree with your point, however this method was instigated by a previous
> person at our institution, so I'm looking
Hi Bruce,
I agree with your point, however this method was instigated by a previous
person at our institution, so I'm looking at it afresh. Also, the addition of
regions 4, 43, 5 and 44 does do "something". I agree though that when I look at
wm.mgz using tkmedit on a vanilla FreeSurfer run, it
Hi Matt,
the -bigventricles stuff is something I messed with for a while, but didn't
get to work robustly and haven't gotten back to it. I'm not sure I
understand your fix though. If the aseg properly labels the ventricles,
then they should be filled in the wm.mgz, and if the aseg doesn't, then
Hi Reddy,
the nu isn't smoothing them, it's what we call the "conform" process -
interpolating to 1mm isotropic. Your voxels are 1.25x1.25x1.2, which is
almost 90% larger than 1mm iso, so when we upsample them there is a bunch
of interpolation.
cheers
Bruce
On Fri, 13 Nov 2009, Mr k hanimire
Hi Guang,
it still needs the ?h.sphere files as those are used to establish the
spherical coordinate system.
cheers,
Bruce
On Thu, 12 Nov 2009, Guang Zeng wrote:
>
> Hi, there,
>
> I am going to make our own template. Based on the introduction in FreeSurfer
> WIKI "The Surface Registration Pro
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