hello,
Is there a command line tool for making a picture of a surface with
labels superimposed?
thanks in advance!
roberto
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The
Hi,
I have an label volume of the four lobes, right and left hemispheres, plus
diencephalon, brain stem and cerebellum (drawn over Colin27). I would be
happy to send it to you, and very interested in receiving any comments (in
particular, the occipital-parietal-temporal junction is quite tricky).
Just a guess: if you are using a Mac, the path for the directory
should be something like
/Users/yourname/Desktop/ etc.
instead of just
/Desktop/ etc.
hope this helps,
roberto
On Thu, Feb 18, 2010 at 10:15 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
The SUBJECTS_DIR is where you want
Hello,
I am also very interested in having a copy of colin27's FS data!
roberto
On Tue, Dec 1, 2009 at 2:53 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
Hi Mishkin,
yes, I generates surfaces for the Colin27 dataset. It actually doesn't
have great gray/white contrast, probably due to
Dear Freesurfers,
I have some mri volumes with too much neck, and I would like to crop
them. I have been trying with mri_convert --cropsize, but it does not
work. It seems that --cropsize is cropping around the center, so when
I cut the neck I also cut the top of the head... I tried changing the
, roberto toro wrote:
That will not be able to separate the only frontal WM from the rest of
the WM, isn't it? I have used FSL (a mix of bet,flirt and fnirt) with
an atlas of the lobes (that covers WM and GM) for that kind of job
roberto
On Tue, Aug 18, 2009 at 9:24 PM, Douglas N
Grevegr
Hi Roman,
did you check with tkregister2 what the transforms look like?
(use tkregister2 --mgz --s mySubjectID --fstal)
cheers,
roberto
On Wed, Jun 17, 2009 at 8:37 AM, romain valabregue
romain.valabre...@chups.jussieu.fr wrote:
Hello
I tried this new relase on 20 subject and I get the same
Dear Freesurfers,
Reading the surface segmentation paper, Dale et al 1999, it says
that in freesurfer the grey/white matter boundary is detected first
based on voxel intensity, and then by fitting locally a plane of list
variance. Is there a way to use that data to assess how clear cut the
...@nmr.mgh.harvard.edu wrote:
Hi Roberto,
you are probably better off using the surfaces for this. You can sample
inside and outside the gray/white surface and compute the contrast that way
using mri_vol2surf.
cheers,
Bruce
On Mon, 1 Jun 2009, roberto toro wrote:
Dear Freesurfers,
Reading
that way
using mri_vol2surf.
cheers,
Bruce
On Mon, 1 Jun 2009, roberto toro wrote:
Dear Freesurfers,
Reading the surface segmentation paper, Dale et al 1999, it says
that in freesurfer the grey/white matter boundary is detected first
based on voxel intensity, and then by fitting locally a plane
this reference may be relevant:
Discrete Differential-Geometry Operators for Triangulated 2-Manifolds
(Mark Meyer, Mathieu Desbrun, Peter Schröder and Alan H. Barr),
VisMath 2002
the pdf is available at:
www.multires.caltech.edu/pubs
cheers,
roberto
On Wed, Apr 29, 2009 at 9:17 PM, Richard
!
roberto
On Sat, Feb 7, 2009 at 3:37 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
Hi Roberto,
when you bring up the volume does it appear correctly in tkmedit? That is,
is the coronal view really coronal, etc?
Bruce
On Fri, 6 Feb 2009, roberto toro wrote:
Dear Freesurfers,
I
Dear Freesurfers,
I haven't been able to run recon-all in a set of subjects. All them
stop at the point of the talairach transform verification. I uploaded
one of the files here (5.3MB):
http://dl.getdropbox.com/u/74925/20070404.nii.zip
For that volume, the transform.xfm file looked indeed odd
Hi,
The problem was Neurolens' display of .mgz files.
mri_info of P.mnc and P.mgz is the same, and the display in Scuba is correct.
Thanks Bruce and Doug you for your help!
(Note for Olivier: Scuba's display [at least in my computer] is
radiological, i.e., negative X coordinates are to the
Hi,
I'm trying to figure out how to go from a coordinate in mni305 space
to a vertex index in fsaverage. In the README file that comes with
fsaverage it's stated that surface coordinates are in talairach space,
so they align with the MNI305 volume (and the talairach.xfm is the
identity). But
On 14 Mar 2007, at 00:28, Bruce Fischl wrote:
Hi Roberto,
the tal xforms will have scaling normalization in them, which I assume
you don't want?
Bruce
Hi Bruce,
you are right. I would like to know only the orientation of the head
and then compute the hemisphere size from the
On 25 Nov 2006, at 15:08, Bruce Fischl wrote:
Hi Roberto,
no, nothing built in, but you could always mask it to the label in
matlab. I guess we could provide an mris_mask utility if that would
be helpful.
thanks Bruce,
I've been trying to compute the folding index (FI) based on the
Hi,
one more question:
3. can I use mris_curvature to compute the folding index only for a
particular label (and not allways for the complete hemisphere)? I've
been using
mris_curvature path_to_mesh/lh.white, to get ICI and FI, and -min -
max -w to get the min, max, gaussian and mean
Hello,
I have a C code that reads FS surfaces and does some processing on
them. I would like to map this back to the original MRI volume.
Googling around I found that vertex coordinates may correspond to
coordinates in the COR volume but COR volumes are now
deprecatedso two
Hi,
I found the reference to D. Van Essen's paper:
Van Essen, D and Drury, H (1997) Structural and functional analyses
of human cerebral cortex using a surface-based atlas J Neurosci 17
(18):7079-7102
and the folding index is defined (from that paper) as the integral
of the product of
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