Thanks for the reply. If you let me know, among the below list of steps of
current recon-all, currently which is not suitable to perform on neonates MRI
image, will really appreciate.
Autorecon Processing Stages:
Motion Correction and Conform
NU (Non-Uniform intensity normalization)
Hi Torben,
Would it be possible to send us the volume and the surface file?
Best,
Ruopeng
> On Jul 4, 2017, at 3:32 AM, Torben Lund wrote:
>
> Hello FreeSurfer Developers
>
> I'm attempting to evaluate a segmentation result from CAT12, (sorry) with the
> Freeview program. For version 1.0 su
Dear freesurfer support,
I am using the PetSurfer to process our PET data. But by default, it would only
generate stats for the segmentation with the aparc atlas.
However, I want to obtain the stats for different freesurfer atlases, like in
the freesurfer outputs (aseg,stats, ?h,BA_exvivo.stats
Hi S Das,
We are trying to release the infant pipeline by the end of the summer.
Lilla
On Tue, 4 Jul 2017, Das S. wrote:
> Dear Freesurfer expert,
> I want to perform recon-all pipeline on neonates data.Can I do so?
> I was going through some mail archives and there it is said that on T1 image
Hello Bruce,
Thank you for your advice! I really appreciate it! Happy 4th July.
Kind regards, Michael
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Bruce Fischl
Sent: 04 July 2017 20:09:10
To: Freesurfer support list
Subject: Re: [Freesurfer] lo
Hi Michael
I don't think there is really a problem here - it is just that either the
brain is oriented strangely or it indeed asymmetric. In any case the
segmentations and surfaces look accurate
cheers
Bruce
On Tue, 4 Jul 2017, Michael Davies
wrote:
Hello, I have encountered a lopsided h
Hello, I have encountered a lopsided hemisphere when analysing the data. What
procedure do i need to employ to fix the problem? Any advice would be greatly
appreciated!
Kind regards, Michael
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h
Hi Michelle
yes, you can try putting already stripped data through, or I think if you
convert the afni skull stripped volume to $subject/mri/brainmask.mgz
recon-all should recognize that it is different from the auto stripping and
use it instead
cheers
Bruce
On Tue, 4 Jul 2017, Michelle Van
Hi Manuel
it's impossible to tell from a single slice.
cheers
Bruce
On Tue, 4 Jul 2017, Manuel
Delgado wrote:
> To illustrate the previous case here there is an image in which there is a
> discrepancy between the wm surface and the smoothwm.nofix. Is it necessary
> to fix it or not?
> Thanks
>
Hi Manuel
you should examine the ?h.white and ?h.pial for accuracy, and only use the
.nofix surfaces if you are trying to figure out why the white/pial are not
as accurate as you would like
Bruce
On Tue, 4 Jul 2017, Manuel Delgado wrote:
> Dear all:
> Regarding wm edits, it is shown in the tu
sure. Can you upload the data again to our ftp site? Don't use the filedrop
- use ftp and make sure you include the cross and the long of all the
timepoints for this subject, and also the coordinates of the location you
are seeing the problem
cheers
Bruce
On Tue, 4 Jul 2017,
Bronwyn Overs
Hi All,
I am trying to visualise nodes of a brain network reconstructed using
FreeSurfer Desikan-Killiany Atlas parcellation scheme (aparc+aseg.mgz) on Brain
Net Viewer and Network Based Statistics software.
In order to do so, I need to upload a .txt file listing Freesurfer labels
coordinates
Hello,
I am just following up on this question.
Thanks!
Michelle
On Tue, Jun 27, 2017 at 4:46 PM, Michelle VanTieghem <
michelle.vantieg...@gmail.com> wrote:
> Hi Bruce,
>
> The -gcut does not appear to make any difference on our skull stripping. I
> also saw that you can change flags for water
Hello Freesurfer,
After running the first step of PETsurfer (
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer). I viewed the image it
created using freeview. When I change, the color map to Lookup Table, the
image also included the skull. How can I remove the skull from
gtmseg.mgz/prevent it f
Hello FreeSurfer Developers
I'm attempting to evaluate a segmentation result from CAT12, (sorry) with the
Freeview program. For version 1.0 superimposing a gifti surface on top of a
nifti volume works beautifully (see results here:
https://www.dropbox.com/s/lwhonnzy7n2t87x/Freeview1.0.pdf?dl=0
Dear Freesurfer expert,
I want to perform recon-all pipeline on neonates data.Can I do so?
I was going through some mail archives and there it is said that on T1 image of
neonates data we can't perform recon-all.
But again there is another paper where it says Freesurfer can perform
segmentation o
To illustrate the previous case here there is an image in which there is a
discrepancy between the wm surface and the smoothwm.nofix. Is it necessary
to fix it or not?
Thanks
--
*Manuel Delgado Alvarado, MD*
*Predoctoral Researcher*
*Neuroimaging Unit, IDIVAL*
*Avda. Cardenal Herrera Oria s/n*
*
Dear all:
Regarding wm edits, it is shown in the tutorial how to proceed with "holes"
that appear in the smoothwm.nofix. However, those holes do not necessarily
affect the wm matter surface. So is it recommendable to check if holes in
the smoothwm.nofix surface affect the real wm surface before cor
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