Hi all,
When we do recon-all, we usually do autorecon1, autorecon2, and autorecon3 in
sequence. But now suppose I have already have a very good skull-stripped
subject. I mean I don't need to do skull-stripping with freesurfer. But I want
to get greymatter and white matter, which are generated i
Hi Allison,
Thanks. I have used the command line below to separately create many label
files, each of which include vertex number and XYZ coordinates.
mri_annotation2label --subject BNC006 --hemi lh --labelbase aparc.a2009
Sorry for not declaring my intention previously. What I actually want to
Derin
OK, Allison discovered it in the depth of recon-all :-)
The control points are copied from the cross sectional by default (and
should be edited there). There is an optional flag to get them from the
base, but that has never been really tested. It only makes sense if
there is very little str
Liang,
mri_annotation2label will separate all the ROIs in the
?h.aparc.a2009s.annot - is this what you need? I'm not sure what you mean
by "mask image based on this image using 1, 2". You can merge or split
labels as well.
To display aparc.a2009s+aseg.mgz in tkmedit, you can do:
tkmedit subjid
It depends on why it failed, which is usually for one of two reasons.
The first is that the initialization failed. You can check this by
saving the initial registration by passing "--init-reg-out
init.reg.dat", then viewing this reg with tkregister2. If this is more
than 5 mm or 5 deg off, the
This is a bug in the released version of FS. Our development version is
fixed. I've put a version here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert
ythomas wrote:
> Hi,
>
> I am trying to downsample a 4D volume using mri_convert. However, it
> seems to be killing t
Hi,
I am trying to downsample a 4D volume using mri_convert. However, it
seems to be killing the 4 dimension. For example, if I do
mri_convert -voxsize 4 4 4 tmp.mgz tmp444.mgz
The original volume which is 256 x 256 x 256 x 120 becomes 64 x 64 x 64.
Thanks,
Thomas
It looks like you have 1 discrete variable with two levels and three
covariates. Three is too many for qdec, so you'll have to set up your
own FSGD. See the wiki for how to set up an FSGD. There are examples
there for many different designs.
doug
Katie Bettencourt wrote:
> Hi,
>
> I'm still t
You have done the right thing, but you need to know a little more. When
QDEC says "mean thickness" it really means the thickness at age=0, so it
is extrapolating the results back to age=0. Since you have a covariate
and you are using DODS, you have to specify an age at which to do the
test (you
Hi Helen,
That's a good question. You don't have to start at autorecon1, however.
When you run -autorecon2-wm or -autorecon2-pial one of the first steps is:
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
which is changing the brain.finalsurfs.mgz to take into account the
changes yo
sure, mris_convert will do this, or you can load it into matlab and do
what you want with it.
cheers
Bruce
On Thu, 11 Mar 2010, Yigal Agam wrote:
> Hi,
>
> Is it possible to convert a .w file to another format?
>
> Thanks,
> Yigal
> ___
> Freesurfer ma
Hi,
Is it possible to convert a .w file to another format?
Thanks,
Yigal
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Dear FS experts,
I am using CentOS 5.4. When I run tkmedit, the data looks fine. In
tksurfer, it just appears as a
sliver of surface without an error message. In console, it sticks on
reading vertex.
Somebody said this could be resolved by simply removing the package
xserver-xgl. How can I do thi
Hi,
I have a similar questionto the one listed below.
After I edit brainmask.mgz and wm.mgz, my understanding was that I could
run
autorecon2-wm
and would not have to run autorecon2-pial because -wm will run
everything else through the end of -autorecon2.
However, if brainmask.mgz is run at th
Hi,
I'm still trying to figure out how to run a regression analysis using
functional data. I found the information in using qdec, however, the
example uses a between subject design (with age/gender) and looks at
thickness measures.
I tried creating a qdec.table.dat, but I am unsure how to do it
Dear Freesurfers,
in my qdec analysis I want to compare
my patients group with a control group. The analysis should be
corrected for age effects, so I used group as discrete factor and age
as covariate. If I choose „Does the average thickness differ
between the two groups“, how can I interpretat
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