Hello everybody,
Since I was corresponding with a few persons separetly, it required resending
the same information to all of them.
So I am getting back to the general forum with my still unsolved problem.
To recap: when I run recaon-all pipeline as below:
[iwob...@huxley FMRI]$ recon-all -autor
Hi, Freesurfers
I need to know how can I generate a label or ROI of one subcortical
structure.
Thanks,
Kelly
Veja quais são os assuntos do momento no Yahoo! +Buscados
http://br.maisbuscados.yah
Hi Kelly,
sorry, I meant to answer. mri_extract_label will make a binary ROI out of
the aparc+aseg which you can use as an ROI. The indices for the different
structures are in $FREESURFER_HOME/FreeSurferColorLUT.txt
cheers,
Bruce
On Fri, 29 May 2009, Kelly Silva
wrote:
Hi, Freesurfers
Hi Elina,
what version are you running? Presumably this doesn't get fixed
correctly by the auto-topology-fixer? This defect is probably not visible
in any one slice. There is a trail of voxels that connect the temporal lobe
to the main body of the white matter. You'll need to erase some to rem
Iwo,
If you do
ls $FREESURFER_HOME/bin
Do you see mri_nu_correct.mni there?
If you do, this message might help you:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06793.html
Essentially, you have to make sure the nu_correct uses perl so you need to
make sure it knows where it's
Iwo
To find where Perl is type:
*which perl*
---
Pedro Paulo de M. Oliveira Junior
2009/5/29 Allison Stevens
> Iwo,
> If you do
> ls $FREESURFER_HOME/bin
>
> Do you see mri_nu_correct.mni there?
>
> If you do, this message might help you:
> http://www.mail-archive.com/freesurfer@nmr.mgh.harva
Dear Mr or Ms
Is there any way that we can obtain curvature value of the pial surface? I am
not sure whether lh.curv is the curvature file that I want. How can I calculate
the mean curvature, Gauss curvature of the pial surface and the GM/WM interface?
Is there any built-in function in freesu
Thanks Pedro, I was just thinking about it.
Iwo
From: Pedro Paulo de Magalhães Oliveira Junior
To: Iwo Bohr
Cc: Freesurfer@nmr.mgh.harvard.edu
Sent: Friday, 29 May, 2009 14:26:01
Subject: Re: [Freesurfer] brainmask.mgz recan-all and nu_correct error
Iwo
To
You can find this information in:
/stats/?h.aparc.stats
Allison
--
On Fri, 29 May 2009, Zhangyuanchao wrote:
Dear Mr or Ms
Is there any way that we can obtain curvature value of the pial surface? I am
not sure whether lh.curv is the curvature file that I want. How can I calculate
the me
Hello Alison,
Thank you very much for your advice. At least I know where the problem is, even
though it doesn't look like I can solve it at the moment, since I have no
writing rights to the file and our administrator is ... guess where? away in
Boston, at Freesurfer and your home :)
Hopefully I'
The current version of Freesurfer calculates numerous curvature-based
functions by default in the recon stream. If you look in the "surf"
directory for a reconstructed surface, you'll see several "curvature"
files that end in "*.crv".
By default, these are created for the gray/white junction surf
To get Rudolph's curv stats in the current freesurfer version, you'll
need to run this:
recon-all -s subjid -curvstats
(or add the -curvstats after -all if you havent processed your subjects
yet).
It only takes a minute to run.
N.
On Fri, 2009-05-29 at 10:37 -0400, Rudolph Pienaar wrote:
> The
When I compare the thickness measure among subjects, I have to resample and
smooth the thickness, so that each data have the same number of vertices and
which are in correspondence with one another across subjects.
Now I have .curv files or .sulc files for each subject and would like to make
yes, you can. There's no right answer for FWHM, but people usually use
5-20mm.
doug
Zhangyuanchao wrote:
When I compare the thickness measure among subjects, I have to
resample and smooth the thickness, so that each data have the same
number of vertices and which are in correspondence with o
Zhangyuanchao wrote:
By the way, could you recommend me relevant papers that calculates the
following indices :
Check the Freesurfer wiki... Our papers on "curvature methodologies" as
well as "wavelet decomposition" have pdfs available.
--
Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nm
Hi,
I was wondering if there was a way to compare t1 or t2 maps between 2 subjects
using the volume brain as opposed to the surface brain.
To be specific I have two brains which are T1 maps. I want to see the
differences in T1's between the two brains. How would i go about doing this.
I hope i
Hi Sam,
you could either do this on a structure-by-structure basis using the aseg
labels, or in Tal coords, or potentially in one of the nonlinear
coordinate systems we provide (if that were needed). mri_vol2vol can be
used for tal. Let us know which you prefer and we'll point you in the
righ
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