Hi
I would like to have a single white and pial surface for FEM based field
calculation in the brain. I got these surfaces by tesselating from filled.mgz
and ribbon.mgz by changing the values in the volume files. Unfortunately the
surfaces don't have the acquired quality I need. They show some t
it's because analyze doesn't store orientation information, so your
images are probably incorrectly oriented. Can you get access to the files
in a format before they were converted to dicom?
cheers
Bruce
On Thu, 6 May 2010
elsh0...@umn.edu wrote:
>
>
> -
> Hello all,
> I had two kind of files
oops, I mean before they were converted to analyze?
On Thu, 6 May 2010
elsh0...@umn.edu wrote:
>
>
> -
> Hello all,
> I had two kind of files ( img & hdr). I used fslchfiletype command to
> create nii.gz files. img and hdr files replaced by nii.gz files. I used
> mri_convert command to create 001
All,
I have generated a batch script that saves out images from tkmedit and
tksurfer which I would like to run on a cluster of workstations across
a large dataset. However, when I run the jobs remotely
tkmedit/tksurfer opens displays on my local machine. As a consequence,
if I do not remain logged
How are you going to do the test? I'm not sure what the stats file has
to do with the fsgd file ...
doug
Rajagopalan, Venkateswaran wrote:
>
> Dear All,
>
> I am new to freesurfer, i am sorry i am confused so i am posting this
> message. I have two groups i want to compare cortical thickness va
Hi Alex,
you could try the topology correction, but we've never done it on a whole
brain, so I have no idea how it will go. The two hemispheres together
aren't going to be topologically spherical given the various commisures
that connect them. Maybe you are better off simply merging the two
t
mri_surfcluster will do. BTW, cluster-based permutation is already build
into our tools (mri_glmfit and mri_glmfit-sim).
doug
Hari Bharadwaj wrote:
> Hi All,
>I was wondering if there is a command to extract connected components
> from a thresholded surface contrast map. I am trying to imple
Dear Doug,
I am sorry i got confused between the thickness files lh.thickness and
aparc.stats file i thought thickness measures from aparc.stats file is used to
look for differences in thickness. I tried mriglm command line version and it
worked so thanks, I am sorry for the confusion.
Thank
We don't actually apply the transform to the data. It is only used for
reporting purposes and to build average subjects.
doug
Tadeu Kubo wrote:
> Hi,
>
> I've been using FS, in which the Talairach transform is applied as a
> standard space for registration. Instead of the Talairach
> transform
yes, use mri_cor2label.
doug
Stefan Brauns wrote:
> Thank you for your immediate response.
>
> That will probably do it. Would I extract these labels with the
> command mri_cor2label or is there an easier way?
>
> On Thu, May 6, 2010 at 5:30 PM, Bruce Fischl
> mailto:fis...@nmr.mgh.harvard.edu>
yes, red/yellow for correlated; blue/cyan for anticorrelated
doug
John Fredy wrote:
> Hello All,
>
> We are using qdec for the analysis of relation between thickness, two
> roi: par Opercularis, par triangularis; two test: fmri broca and
> edinburgo. When I make a design with thickness, one roi
You can constrain the search to a smaller space using a label.
doug
lordowen wrote:
> Dear freesurfer developers:
>
> As I searched wiki, the freesurfer only provided whole-brain FDR and
> cluster simulation for multiple comparison correction. Is there any
> way to perform the smell volume correc
you don't need to reorient your data for FreeSurfer. Check the FSL
site/list to see what there orientation requirements are
doug
chenchunhuichina wrote:
> Hello FreeSurfer users,
> I may be asking a stupid question but it really troubled me a while.
>
> I converted dicom files to nift using dcm2n
HI,
I have a question about feat registration to standard space.
I used the following line .
cd "$featdirectory"
flirt -in example_func.nii -ref /autofs/../MNIref/MNI152_T1_1mm_brain.nii
-out funcinstd_DUMMY -omat reg/example_func2standard.mat -dof 6
reg-feat2anat --feat "$featdirectory" --subje
The standard reg is used to create a registration between the anatomical
and the mni152. This is then used if you have multiple runs that you are
combining into a higher-level (fixed effects) gfeat in mni152 space.
Technically, the quality of this registration is not so important
because it jus
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