you mean the coefficients from Siemens? Actually Jenni has had a lot of
recent experience messing around with Allegra data. If you want to put one
on the file drop we'll take a look (do they look okay?)
Bruce
On Mon, 10 Jul 2006, Russell
Poldrack wrote:
not yet - we are working on getting t
not yet - we are working on getting the coordinates on this end to do that, so we should hopefully be able to do so fairly soon.cheersrpOn Jul 10, 2006, at 5:01 PM, Bruce Fischl wrote:Hi Russ,are you gradient unwarping them?BruceOn Mon, 10 Jul 2006, Russell Poldrack wrote: hi - I've been trying to
Hi Russ,
are you gradient unwarping them?
Bruce
On Mon, 10 Jul 2006, Russell Poldrack wrote:
hi - I've been trying to run a set of MP-RAGE images collected on our allegra
through the first part of the autorecon process, and I've run into somewhat
of a problem with the skull-stripping. In all
hi - I've been trying to run a set of MP-RAGE images collected on our allegra through the first part of the autorecon process, and I've run into somewhat of a problem with the skull-stripping. In all 8 of the brains that I have tried, there is a substantial amount of scalp left over after stripping
check the talairach transform and see if it's reasonable. If it is, feel
free to put the nu.mgz on our drop site (with the talairach.xfm) and I'll
take a look.
cheers,
Bruce
On Mon, 10 Jul 2006, Don Hagler wrote:
I am getting an error running mri_normalize (as part of recon-all) on a
particul
I am getting an error running mri_normalize (as part of recon-all) on a
particular subject's volume.
Here is the command from recon-all:
mri_normalize -g 1 nu.mgz T1.mgz
Here is the output:
WM removal version
using max gradient = 1.000
reading from nu.mgz...
normalizing image...
talairach trans
Sasha,
These and other papers are available in PDF format in the references
section at the bottom of this page:
http://surfer.nmr.mgh.harvard.edu/fswiki
Nick
On Mon, 2006-07-10 at 17:23 -0400, Bruce Fischl wrote:
> yes:
>
>
>
> if you use surface recons
>
>
>
> Fischl B, Salat DH, van der
oops, ignore the "if you use surface recons" part of this
On Mon, 10 Jul
2006, Bruce Fischl wrote:
yes:
if you use surface recons
Fischl B, Salat DH, van der Kouwe AJW, Makris N, Ségonne F, Dale
AM. Sequence-Independent Segmentation of Magnetic Resonance Images.
NeuroImage 23 Suppl
yes:
if you use surface recons
Fischl B, Salat DH, van der Kouwe AJW, Makris N, Ségonne F, Dale
AM. Sequence-Independent Segmentation of Magnetic Resonance Images.
NeuroImage 23 Suppl 1, S69-84.
Fischl B, Salat D, Busa E, Albert M, Dieterich M, Haselgrove C,
van der Kouwe A, Killiany R, Ke
Dear all,
I am interested in learning more about the details of subcortical
segmentation, in particular how the basal ganglia structure boundaries
are determined. Is there any literature I may refer to?
Thanks,
Sasha
Disclaimer:
The materials in this e-mail are private and may contain Protec
the aseg will be different, since it's voxel-based (and typically not as
accurate as the surfaces)
On Mon, 10 Jul 2006 [EMAIL PROTECTED] wrote:
Is this true of the aseg files as well? I tried *double-checking* the
mris_anatomical_stats by using the aseg file in MatLab (assigning values
to the
Yes, it is true for both (and the aparc+aseg.mgz). This puzzled me when
I first wrote mri_aparc2aseg (which creates the aparc+aseg.mgz file).
[EMAIL PROTECTED] wrote:
Is this true of the aseg files as well? I tried *double-checking* the
mris_anatomical_stats by using the aseg file in MatL
Is this true of the aseg files as well? I tried *double-checking* the
mris_anatomical_stats by using the aseg file in MatLab (assigning values
to the voxel-intensities, counting them up, etc, etc) and the numbers came
up different. Is that why? Probably not the best method now that I think
about
actually it's the total gray matter volume (sum of thickness*surface area)
On Mon, 10 Jul 2006, Bagnato, Francesca (NIH/NINDS) [E] wrote:
I just mean to ask if such a mean take into account the different
surfaces area and correct for that (e.g. geometric mean).
Thanks Francesca
-Original M
I just mean to ask if such a mean take into account the different
surfaces area and correct for that (e.g. geometric mean).
Thanks Francesca
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Monday, July 10, 2006 2:04 PM
To: Bagnato, Francesca (NIH/NINDS) [E]
Cc: Pelle
not sure I understand what you mean. It is the mean across the surface. As
such it will be corrupted by non-cortical regions such as the callosum,
although they are only a small % of the surface. If you want to get rid of
them you can draw a cortical label and pass it to mris_anatomical_stats
w
Bruce: is this an average weighted on the surface of the cortices or
just a pure arithmetic mean?
Thanks,
Francesca
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Monday, July 10, 2006 1:50 PM
To: Pellegrini, Stefano (NIH/NINDS) [F]
Cc: freesurfer
Subject: Re: [Free
Hi everybody,
I have a small problem with an old version of freesurfer. I am studing
some data that someone analyzed some months ago using the old version
of freesurfer. I am looking for the mean cortical thickness of each
hemisphere, but I have found only the thickness af each single area of
do you mean the mean across the entire cortex? If so,
mris_anatomical_stats will give you that.
On Mon, 10 Jul 2006, Stefano
Pellegrini wrote:
Hi everybody,
I have a small problem with an old version of freesurfer. I am studing some
data that someone analyzed some months ago using the old v
It is only cortical. And you don't want to use ?h.ribbon.mgz as this is
quantized to 1mm^3 and will be less accurate than mris_anatomical stats.
doug
[EMAIL PROTECTED] wrote:
Hi,
I am attempting to assess (& compare) total cortical gray matter volume in
a series of subjects (schiz vs.
Hi Derin,
mris_anatomical_status gives you only cortical gray matter.
cheers,
Bruce
On Mon, 10 Jul
2006 [EMAIL PROTECTED] wrote:
Hi,
I am attempting to assess (& compare) total cortical gray matter volume in
a series of subjects (schiz vs. control), and was wondering if the tabular
mris_an
Hi,
I am attempting to assess (& compare) total cortical gray matter volume in
a series of subjects (schiz vs. control), and was wondering if the tabular
mris_anatomical_stats gm output consisted of only cortical gm, or included
subcortical and other nuclei as well. I've searched the wiki, articl
I guess you could compute the cog in native coords, then convert those
coords to tal (would probably be the same thing as starting in tal).
Having said that, I don't have anything which will compute the cog
along the surface. The right way to do it is to map the label to the
sphere, compute th
Hi List,
we have some problems with inorm-sess and some data sets. No matter how
we set -tresh (well, 0.1, 0.5, 0.75 or 1.0) some of our functional runs
produce errors/warnings. (and the "INFO: no voxels found under
thershold" messages, but they look benign).
The warning are mostly divides by
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