Hellom
I coregistered manually a aparc+aseq.nii file to my DWI-space with
tkregister2. I saved the .dat file and applied it later to the T1
image in order to apply the same spatial coregistration as to the
aparc+aseg. For woth the aparc+aseg and the T1 I used the command
mri_vol2vol
--mov
Hi Constantin,
When you used tkregister2 which volume was the target? Acoording to what
you write it was the b0 volume. So when you apply the registration to the
T1 volume, you should keep it that way.
--mov T1
--targ b0image
and no -inv is necessary.
Let me know if I misunderstood what you w
Hello Lilla,
thanks for the answer. I first used
bbregister
--s (Freesurfer Directory)
--mov b0.nii
--reg .dat
--dti
--init-fsl
Afterwards I made some minor spatial changes to the aparc+aseg,
bringing it closer to what i believed its position was on the b0space:
tkregister2
--mov b0.img
--reg
Hi Constantin,
No, now I understand what you were doing. The T1 / aparc+asge space is
your target and the diffusion space is the moving one. Your mri_vol2vol
setup should be accurate as you indicated originally. I think the problem
might be that the 2nd registration file that you are saving fr
Hi Freesurfers,
I am trying to set up both a 2 Group 1 Covariate and a 4 Group 1
Covariate analysis but just want to make sure I'm using the correct
contrast option.
For the first analyis, the two groups are Drug Pre and Drug Post,
with folate-serum level as a covaraite. We want to keep
Hi FS team,
Is it possible to project an entire annotation file from one subject's
surface to another? I haven't been able to find a command for this, but I
might just not be looking hard enough.
My intent is to project an annotation I've made on fsaverage to every
member of a cohort of 500+ subj
Hi Mike,
I think you can run mri_surf2surf with --sval-annot flag. Try
mri_surf2surf --help for more options.
Sita.
On Mon, 12 Sep 2011, mbric...@nmr.mgh.harvard.edu wrote:
> Hi FS team,
> Is it possible to project an entire annotation file from one subject's
> surface to another? I haven't
Hi Sheeva,
The pial surface is not designed to include the hippocampus and
amygdala.
Quoting from http://www.freesurfer.net/fswiki/FsTutorial/OutputData :
There are regions where the surfaces are not intended to be accurate
that you should be aware of:
* Areas around the hippocampus and
Hi all,
I'm attempting to use FreeSurfer 5.1 (version block below) to process
some older T1 scans collected on a 1.5T magnet with a native voxel size of
0.9375x0.9375x1.5mm. Overall, FreeSurfer seems to deal with these scans
just fine (resampling to 1 mm isotropic, etc.), but I'm a little co
Hi Dave,
that probably just reflects the intrinsic contrast of your images.
Depending on sequence parameters gray matter can vary w.r.t. white matter
intensity. Lower contrast will usually make things worse, but of course
it also depends on things like the noise level and the sharpness of your
for 3T scans, you could try a new flag added in v5.0.0,
-nuintensitycor-3T (include at the end of the recon-all command) which
modifies the nu_correct parameters to optimize for 3T scans, per this
paper:
http://web.mysites.ntu.edu.sg/zvitali/publications/documents/N3_NI.pdf
n.
On Mon, 2011-09-1
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