You can also use mri_binarize with the --match flag. It does the same
thing, but you can give it multiple match values. There is also a
--ventricles option (excludes 4th ventricle).
doug
Bruce Fischl wrote:
> Hi Tommi,
>
> no, you need to also extract the left and right ventricles and the
> in
OK, I've tracked down and fixed the error. You can get a new version from:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/getrunlist
let me know if that works.
doug
Katherine Sledge Moore wrote:
> Hi,
>
> I was wondering whether there was any progress on this issue (copied
> be
Hi!
I'm trying to partition a surface into a number of random but
roughly-equally sized areas, and I've been using the
"mris_make_face_parcellation" function to do this. Is it possible to
have a finer control over the sizes of each label it generates? I only
see 7 options in: $FREESURFER_HOME/lib/
Hello,
I manually edited the aseg.mgz file for one of my participants, I was
wondering if someone could tell me how to rerun the recon-all to
ensure that these changes are incorporated in future steps and
statistics files.
Many thanks,
Jennifer
___
Frees
What version are you using?
--
On Thu, 9 Dec 2010, Jennifer Addicks wrote:
> Hello,
> I manually edited the aseg.mgz file for one of my participants, I was
> wondering if someone could tell me how to rerun the recon-all to
> ensure that these changes are incorporated in future steps and
> stati
Hello,
I ran freesurfer ReconAll process on 27 subjects using linux opensuse 11.3.
freesurfer version is 5.0.0
(freesurfer-Linux-centos4-stable-pub-v5.0.0.tar.gz). Then I ran the same
process on some of those subjects using same version of freesurfer
(freesurfer-Darwin-leopard-ppc-stable-pub-v5.0.
Hi Andrew,
these are icosahedral supertessellations, which come in fixed increments.
I guess if you generated some other partitioning of the sphere and saved it
in .ic format it would work, but you'd have to write your own.
cheers
Bruce
On Thu, 9 Dec
2010, Andrew Dumas wrote:
> Hi!
>
> I'm t
Thanks, Bruce. That might be a bit of a dead end since it sounds fairly
involved to write a spherical partitioning scheme to a .ic file. Is
there a good way to tessellate a surface with nearly-equal area labels
using any other FreeSurfer tools? Thanks again!
Andrew
On Thu, 2010-12-09 at 14:46 -0
not with our's although there are electrostatic repulsion models people
use for diffusion directions you could try
On Thu, 9 Dec 2010, Andrew Dumas
wrote:
> Thanks, Bruce. That might be a bit of a dead end since it sounds fairly
> involved to write a spherical partitioning scheme to a .ic file.
the results differ because the math operations are conducted identically
on the two platforms. each OS uses different math libs, and probably
more importantly, your processors are different (x86 vs powerpc).
the qdec analysis of each platform should give the same results though,
as the stats diff
Hi there,
Are there any Freesurfer utilities that I can use to query the file type of
an image directly? i.e., more directly than mri(s)_info. The problem is
that mris_info barfs when it gets an image that isn't a proper "surface"
file, and I'd like something that is maximally flexible. Ideally
Hi Mike,
sorry, I don't think so
Bruce
On Thu, 9 Dec 2010, Michael Waskom wrote:
> Hi there,
>
> Are there any Freesurfer utilities that I can use to query the file type of
> an image directly? i.e., more directly than mri(s)_info. The problem is
> that mris_info barfs when it gets an image th
not at the moment. the problem is that many of our files dont have
headers to them to allow making a distinction. hopefully given some
time we'd like to move to using the gifti format for surface files by
default. this file format contains meta data to allow distinguishing
file types.
n.
On Th
Hi FreeSurfer community:
I wanted to ask for general thoughts on spatial smoothing of data.
In particular, some searching of the archives reveals that a bit of
smoothing can help the quality of the data, as well as the inter-subject
registration of significance volumes.
FreeSurfer ca
Hi Joakim
yes, I believe your first point is true as you are implictly only
smoothing within gray matter on the surface, as opposed to volume smoothing
that includes CSF and even skull at larger kernel sizes.
W.r.t the optimal kernel size, that's a harder question. In general you
smooth to (1)
Bruce,
Thanks for the excellent advice!
Two immediate follow-up questions come to mind:
I've read the analyses behind the matched filter theorem, and my
follow-up question is if there would be any deleterious effects by using
a fwhm below the size of a theorized ROI (as is often the case). I've
Hi Joakim,
if the kernel is too small then you will have less noise reduction than
you might with a bigger kernel, but of course if it's enough to detect
the effect you're looking for, then you are fine.
And yes, those should use surface smoothing by default (Doug can correct me
if I'm wrong)
I want to look at the beta values for all my conditions, voxel-by-voxel (in
a specific ROI). I have 180 conditions, and am not looking at a specific
contrast.
When I open the beta.nii file produced by selxavg3-sess, and look at
configure functional overlay, there are 215 "timepoints" listed (and
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