From: saad.ak...@hotmail.com
To: fsregis...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
Subject: Surface Generation Problem Pertaining to FreeSurfer
Date: Tue, 22 Feb 2011 11:43:36 +0500
Hello,
We are graduate students from Giki university, Pakistan. We are doing our
Final
Hi all,
We are trying to use -gammafit when running the mkanalysis-sess command. In
the FsFast Tutorial, the flag -gammafit 2.25 1.25 is used. Are those
numbers the default? If not, what is the default?
Thanks in advance.
Best,
Mandy Nagy
___
Freesu
So I created a weighted regression analysis to look at the effect of memory
load in a particular brain region. Basically, I weighted the paradigms by a
behavioral measure that reflected the number of items actually remembered
(as set size was increased). As far as Doug told me there are basically
use
tkmedit fsaverage orig.mgz -overlay teste_sig.mgz
doug
On 2/21/11 3:46 PM, Fernanda Palhano wrote:
Hi Bruce,
Thank you for the prompt reply.
I tried using mri_surf2vol :
mri_surf2vol --surfval
qdec/g1_g2_lh_06out/lh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh
--identity fsaverage --t
run this command
sudo rm -rf $FREESURFER_HOME
2011/2/21 Carolina Valencia
> Thanks Pedro,
>
> How I uninstall that version to re-install the correct version?
> I look for some answers and try
>
> rm -rf $FREESURFER_HOME
>
> It says that I don't have permission,how I can unistall it, if i'm the
Hi Bruce,
Thank you for the prompt reply.
I tried using mri_surf2vol :
mri_surf2vol --surfval
qdec/g1_g2_lh_06out/lh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh
--identity fsaverage --template fsaverage/mri/T1.mgz --hemi lh --o
teste_sig.mgz
gdiagno = -1
Using identity matrix for registration
Q
Hi Fernanda
if that's a surface overlay you'll need to sample it into the volume with
mri_surf2vol
cheers
Bruce
On Mon, 21 Feb 2011, Fernanda Palhano wrote:
> Hello,
>
> Does anyone knows if is it possible to overlay the surface file sig.mgh onto
> a T1 vol?
> I tried the command:
> tkmedit f
Hello,
Does anyone knows if is it possible to overlay the surface file sig.mgh onto
a T1 vol?
I tried the command:
tkmedit fsaverage T1.mgz -fthresh 2 -fmax 5 -overlay
qdec/rh-Diff-grupo1-grupo2-Intercept-thickness/sig.mgh (where 2 and 5 were
the thresholds I used in qdec),
but it seems like I hav
The rawavg.mgz and brain.mgz are of different sizes. You'll need to
transfer one to the other. You can do this with mri_vol2vol using brain
as the mov and rawavg as the target and --regheader.
doug
On 2/21/11 11:49 AM, Gabriel Go.Es. wrote:
Hello Freesurfers,
I'm trying to mask the rawavg.mg
Hello Freesurfers,
I'm trying to mask the rawavg.mgz from some subjects with the brain.mgz after
doing some manual segmentation corrections by using mri_mask command, I have
donne it before and it always works but with this subject, the command line is
excacly the same so I have no idea what
Hi Tanja, type 'coordinates' into the wiki search on our page.
doug
On 2/21/11 4:11 AM, Tetiana Dadakova wrote:
> Hello Bruce,
>
> Could you please give me a link to this coordinate tutorial. I don't
> think I can find it.
>
> Thank you,
> Tanja.
>
>
> On Wed, Feb 16, 2011 at 5:28 PM, Bruce Fischl
Hi Tanja,
Can you send us an image? Is parahippocampal white matter significantly darker
than 110?
Bruce
On Feb 21, 2011, at 6:41 AM, Tetiana Dadakova wrote:
> Dear Freesurfer users,
>
> For some of my subjects Freesurfer strongly overestimates hippocampus'
> volume. Is there any way to fix
It seems you are running the 64-bit version of FreeSurfer in a 32-bit OS
2011/2/21 Carolina Valencia
>
> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-25-generic-pae
> #44-Ubuntu SMP Fri Jan 21 19:01:46 UTC 2011 i686 GNU/Linux
>
> Thanks,
>
>
> 2011/2/21 Pedro Paulo de Magalhães Oliveira J
Please send the result of the command:
uname -a
On Mon, Feb 21, 2011 at 10:31, Carolina Valencia wrote:
> Hi Bruce,
>
> I'm experimenting problems with the installation on Ubuntu too.
> There's is warning in the welcome message, it seems that something is
> missing:
>
> freesurfer-Linux
Hi Bruce,
I'm experimenting problems with the installation on Ubuntu too.
There's is warning in the welcome message, it seems that something is
missing:
freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0
Setting up environment for FreeSurfer/FS-FAST (and FSL)
WARNING: /home/cvale
Dear Freesurfer users,
For some of my subjects Freesurfer strongly overestimates hippocampus'
volume. Is there any way to fix the segmentation of hippocampus by
e.g. adding some control points (like for white matter here
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints)?
Thank yo
Hello Bruce,
Could you please give me a link to this coordinate tutorial. I don't
think I can find it.
Thank you,
Tanja.
On Wed, Feb 16, 2011 at 5:28 PM, Bruce Fischl
wrote:
> Hi Tanja,
>
> I think Doug just put up a coordinate tutorial. For each voxel in the aseg
> label you are interested, c
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