Hi,
I think that I know what you mean. So, if I want to get the result with A
> B > C, I should get A > B and B > C, respectively. And then, to combine
these two results.
Would you tell me detail with step by step and what command I should type
and how to type ? Or, have some reference to fol
Hi Gregory,
it's hard to tell accuracy looking at one slice, but that one looks fine.
Note that we do not generally use the cortical segmentation in the aseg -
for that we use the surfaces. So if you want to assess accuracy you
should overlay the ?h.white and ?h.pial surfaces and see if cortic
hi q. from a collaborator,
someone got a comment for 1 subject the # of vertices of sphere
file different from the length of thickness data for the same subject.
thanks
Greg.
-Original Message-
From: Deepti Pachauri [mailto:deepti.pacha...@gmail.com]
Sent: Wed 6/24/2009 1:02 AM
To: Kir
it means that an autorecon? was started for that subject and never
finished. You should be able to do recon-all -make all -s and it
will redo
what it needs to
On Thu, 9 Jul 2009, Kirk Gregory R. wrote:
hi q. from a collaborator,
someone got a comment for 1 subject the # of vertices of sph
Hi Barnali,
what do you mean you "don't get to see the pial surface"? If you type:
tksurfer lh pial
does it not show the pial? If it finished autorecon3 it should have a pial
surface for both hemis.
cheers
Bruce
On
Thu, 9 Jul 2009, Barnali Basu wrote:
Experts,
I have successfully ru
Experts,
I have successfully run recon-all (all the 3 processes autorecon1,2 and 3)
on a subject. When I see the surfaces on tksurfer, I dont get to see the
pial surface.
I gather I could construct Pial surface by running autorecon2-pial. Would
this affect in any way, since I have already finish
The newest version of FreeSurfer does not contain any changes to qdec I
believe.
Allison
--
On Thu, 9 Jul 2009, Prapti Gautam wrote:
Dear Freesurfers,
I just have some quick questions regarding qdec:
1. How many covariates does the latest version of qdec allow you to
select? I am
It's more a methodological question, and I have asked this before, but I
think it could be better discussed in the FreeSurfer community.
Several times people ask me what's the advantage of Surface based methods
like the ones used in FreeSurfer over VBM in estimating volumetric
parameters of subcor
Experts,
I have been working on Freesurfer last 5 months and initially the recon
processes were within normal time limits.
However, I am working on a different set of subjects now and its consuming
days together. For my current data,autorecon1 is fine, it stops at a
particular point in autorecon2
this is almost certainly a bug that is fixed in the current version. Try
updating and let us know if it doesn't fix the problem
On Thu, 9 Jul 2009,
Barnali Basu wrote:
Experts,
I have been working on Freesurfer last 5 months and initially the recon
processes were within normal time limits.
H
Hi PPJ
we don't use surface-based stuff for subcortical structures, although at
some point we probably will. In general the surfaces are more accurate
cortically as they let you do subvoxel positioning. I think the advantage
for subcortical structures is that we have strong priors on both the
So the topology fix, spherical registration, etc. help the positioning
for the random markov field algorithm?
And in the VBM we don't have this aid.
Is that correct?
2009/7/9, Bruce Fischl :
> Hi PPJ
>
> we don't use surface-based stuff for subcortical structures, although at
> some point we pro
Dear Freesurfer authors,
I have been working with the command line group analysis tutorial from the
freesurfer wiki website. Unfortunately I did not "qcached" my data with
recon-all. So I ran the "mris_preproc" and "mri_surf2surf" commands from the
tutorial (see below) at the end of which I g
no, all that stuff helps the surface positioning. The MRF is a separate
thing that happens before most of that
On Thu, 9 Jul 2009, Pedro Paulo de
Magalhães Oliveira Junior wrote:
So the topology fix, spherical registration, etc. help the positioning
for the random markov field algorithm?
And
Hi Mayuresh,
I think if you do:
mri_convert lh.gender_age.thickness.00.mgh#0 lh.thickness.subject0.mgh
you will extract the first frame (or #1 for the second, etc...).
cheers,
Bruce
On
Thu, 9 Jul 2009, Mayuresh Korgaonkar wrote:
Dear Freesurfer authors,
I have been working with the com
Hi,
Thank you for your response! I use the command what you said.
The terminal shows:
euler # = v-e+f = 2g-2: 154901 - 464697 + 309798 = 2 --> 0 holes
F =2V-4: 309798 = 309802-4 (0)
2E=3F:929394 = 929394 (0)
I guess that 929394 is the vertices number of surfac
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