> is at least 100 or so in the image (it can be more).
>
> 2. You shouldn't need to erase anything - just rerun recon-all
>
> cheers,
> Bruce
>
> On Tue, 29 Apr 2008, Jerry Yeou-Wei Chen wrote:
>
> Okay, thanks! I'll give that a shot... but I have a co
s, but I guess something is failing in
> your case.
>
> cheers,
> Bruce
>
>
>
> On Mon, 28 Apr 2008, Jerry Yeou-Wei Chen wrote:
>
> Hi Bruce,
> >
> > Looking at one of the successfully processed subjects in tkmedit, I
> > would
> > guesst
Sometimes nu_correct
> can create very dark images, and there are some switches you can loo through
> to correct them. Alternatively if it is the 001.mgz, mri_convert has a scale
> option you can use.
>
> cheers,
> Bruce
>
>
>
> On Fri, 25 Apr 2008, Jerry Yeou-Wei Chen
o answer (he is out-
> of-town today). I think he will ask about your scan parameters, ie, how
> is your scanner setup? It sounds as if something is not quite right in
> the data coming-off the scanner.
>
> Nick
>
>
> On Tue, 2008-04-22 at 14:26 -0400, Jerry Yeou-Wei C
gt; the mri peak is at zero, which is wrong (it should be around 116/117 or
> so).
>
> if you view nu.mgz (tkmedit -f nu.mgz), does it look ok? is it oriented
> correctly?
>
> Nick
>
>
>
>
> On Tue, 2008-04-22 at 12:28 -0400, Jerry Yeou-Wei Chen wrote:
> > Hell
Hello,
I am having trouble deciphering why I got the error attached below. Any
suggestions would be greatly appreciated!
Thanks,
- Jerry
Tue Apr 22 10:15:22 EDT 2008
talairach_avi done
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#
[
uld be fwhm.dat
> along with the y.fsgd.
>
> > How did I miss that???
> > Thanks!
> > - Jerry
> >
> > On Thu, Apr 17, 2008 at 3:01 PM, Doug Greve <[EMAIL PROTECTED]>
> > wrote:
> >
> >> there should be a fwhm.dat file in the output.
> &g
How did I miss that???
Thanks!
- Jerry
On Thu, Apr 17, 2008 at 3:01 PM, Doug Greve <[EMAIL PROTECTED]>
wrote:
> there should be a fwhm.dat file in the output.
>
> doug
>
>
> Jerry Yeou-Wei Chen wrote:
>
> Hello,
>
> I have a question regarding performing Mon
Hello,
I have a question regarding performing Monte Carlo simulations when a custom
design matrix is being used.
The wiki says that "For both MC simulations, you must supply the smoothness
of your data as Full-Width/Half-Max (FWHM) of the residual. This can be
obtained from the ResidualFWHM value
erated and called y.mgh).
>
> The fsgdPlot.tcl problem is (was) unrelated to this.
>
> Nick
>
>
> On Sun, 2008-04-13 at 16:08 -0400, Jerry Yeou-Wei Chen wrote:
> > Hello,
> >
> > I am getting the following error when I try to load an FSGD file in
> > tksurfe
Hello,
I am getting the following error when I try to load an FSGD file in
tksurfer. The stats were processed using a custom design matrix without
error and I am able to view the results.
FSGD file doesn't contain a PlotFile entry.
Error loading GDF
/scratch/freesurfer/subjects/adina/descic39_all
That was the problem!
Thanks!
- Jerry
On Thu, Apr 10, 2008 at 5:55 PM, Doug Greve <[EMAIL PROTECTED]>
wrote:
> I think the problem is that the last line is a blank line. Remove that
> and retry.
>
> doug
>
> Jerry Yeou-Wei Chen wrote:
>
> I am getting the followi
940126218, which is not a matrix.
could not allocate 822685706 x 805908489 matrix
Cannot allocate memory
unsupported matlab format -849662976 (unknown)
Cannot allocate memory*
On Thu, Apr 10, 2008 at 11:02 AM, Jerry Yeou-Wei Chen <[EMAIL PROTECTED]>
wrote:
> Thanks for the clarification, Do
Hello,
Are regressors mean centered for mri_glmfit?
Judging by one of my previous Xg.dat files, it does not appear so.
If not, I plan to manually enter my design matrix, with mean centered
regressors.
Do I need to enter the corresponding values in the FSGD file as mean
centered? or can they remai
t;
> Explicitly specify the design matrix. Can be in simple text or in matlab4
> format. If matlab4, you can save a matrix with save('X.mat','X','-v4');
>
> It does not need/expect any extension.
>
>
> doug
>
>
> Jerry Yeou-Wei Chen wrote:
>
ry
On Wed, Apr 9, 2008 at 4:58 PM, Jerry Yeou-Wei Chen <[EMAIL PROTECTED]>
wrote:
> Great! Thanks!
> - Jerry
>
>
> On Wed, Apr 9, 2008 at 3:50 PM, Doug Greve <[EMAIL PROTECTED]>
> wrote:
>
> >
> > You can pass custom design and contrast matrices
Hi,
Just a very quick question about the glmdir flag for mri_glmfit when running
the group analysis via command line:
If I am interested in multiple contrasts, can glmdir be the same for
subsequent iterations of mri_glmfit with different contrast vectors?
(I understand that each contrast comes up
Hello,
I would like to know how to examine an interaction between continuous
variables.
In SPM, my understanding is that a new interaction regressor, comprised of
the product of the two continuous variables of interest, can be coded and
entered into the model.
Would this be appropriate for CTA grou
Hello,
The attached image shows a plot generated from a design with one continuous
variable (gender) and three continuous variables (called N, E, P), analyzed
using the "old" method via command line rather than QDEC. For mri_glmfit,
the DODS option was used and the contrast was 0 0 1 -1 0 0 0 0 (t
Hello,
I would like to know why we are limited to 4 regressors in the design
specification within the QDEC GUI.
If I understand correctly, there is no such limitation in the "old" method
(via command line).
Thanks,
- Jerry
___
Freesurfer mailing list
Free
Hello,
We ran into the following error during autorecon2 with one subject:
mri_fill: could not find any points where lh and rh wm are nbrs
It has been suggested to another user that the "-noaseg" flag be used.
(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06560.html)
However,
Hello Freesurfer Forum,
We have a question about the M matrix, found in the
.mgz file header.
We loaded an .mgz file into Matlab and took a look at
the affine transform matrix M from the header:
M(1,:) = [-1 0 0 132.7486];
M(2,:) = [ 0 0 1 -105.7281];
M(3,:) = [ 0 -1 0 131.7424];
M
this works
mri_convert -it dicom /home/omid/freesurfer/subjects/IBS_raw/_orig_/csd/E703S2I1.MR /home/omid/freesurfer/subjects/IBS_raw/csd/mri/orig/001.mgz
Jerry Yeou-Wei Chen wrote:
Hello,
We have been having difficulties importing GE .MR files into FreeSurfer.
We have tried a numbe
23 matches
Mail list logo
