Hi NIck,
I too thought disk space might be an issue, however I''ve been running the
recon-all from a mounted partition (shared folder in Virtualbox) that has
plenty of space:
*FreeSurfer:~> df -h
FilesystemSize Used Avail Use% Mounted on
/dev/sda1 11G 9.8G 0 100% /
Research Associate
MRC Institute of Hearing Research
Nottingham, United Kingdom
Salary £26,022 – £28,178 per annum
http://www.topcareer.jobs/Vacancy/irc81869_2735.aspx
The aim of this post is to contribute to the understanding of the
pathogenesis of tinnitus in humans by analysing a large set of
Hi,
I have what I suppose is a slightly unusual question - is it possible to get
the head/face shape from a subject's MRI using FreeSurfer? I've only ever used
it to get the cortical surface, but was wondering if I could somehow extract
the head/face shape, as well.
Best
Luzia
Hello everyone !
I want to use qdec so I tried to smooth the subjects with the following
command: recon-all -s < t0001 . t0742 > -qcache (. = all my subjects !). The
tutorial said that it takes about an hour but immediately a file was created
: "-qcache" (2.95 Ko). Is it normal ? Does the proce
Hi all,
Is there a way to get freesurfer to annotate only certain selected
structures (e.g. basal ganglia). I suspect not, since the underlying model
involves spatial relationships between labels, but thought I would ask. I
am looking for any ways to speed up the annotation process. Thanks,
Hemant
Hi Luzia
the outer BEM surface that we sometimes generate for EEG/MEG inverse
analysis might do.
cheers
Bruce
On Mon, 4 Feb 2013, Troebinger, Luzia wrote:
> Hi,
>
> I have what I suppose is a slightly unusual question - is it possible to get
> the head/face shape from a subject's MRI using Fre
Hi Angela
negative sulc implies gyral, but there must be positive sulc also, no?
When you overlay sulc on an individual subject to you see red (positive) as
well as green (negative)?
cheers
Bruce
On Mon, 4 Feb 2013,
angela.fav...@unipd.it wrote:
> Dear experts,
> I am studying a group of pa
Hi Hemant
sorry, no. You can speed things up in 5.2 if you have a multi-core machine
and you specify -openmp N (where N = # of cores) on the command line.
cheers
Bruce
On Mon, 4 Feb 2013, Hemant Bokil wrote:
> Hi all,Is there a way to get freesurfer to annotate only certain selected
> structu
Dear Team,
I tried to run dt_recon and the systems says *cannot find
eddy_correct,Make sure FSL is installed*. So ,do I need to install the
whole FSL package to run this.
In Thanks
Chikku
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When I tries to download Freesurfer 5.2.0 beta source I get this error message.
cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P
dev
cvs server: cannot find module `dev' - ignored
cvs [checkout aborted]: cannot expand modules
Knut J
hi bruce and others,
are there any specific implications we should be worried about (e.g., with
qdec or surf2surf) when using an fsaverage that's from a different version
that ran the recon.
cheers,
satra
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Hi Satra,
certainly fsaverage will change if we change things in spherical
registration, or potentially elsewhere. I don't anticipate any large
changes, but I wouldn't count on them being identical
Bruce
On Mon, 4 Feb 2013,
Satrajit Ghosh wrote:
> hi bruce and others,
> are there any specific
thanks bruce. indeed, we are not expecting identical output and in these
cases that we are looking at it's all 5.x for most part.
cheers,
satra
On Mon, Feb 4, 2013 at 9:34 AM, Bruce Fischl wrote:
> Hi Satra,
>
> certainly fsaverage will change if we change things in spherical
> registration, or
Hi Luzia,
There is also a script called mkheadsurf, which will generate a high
resolution very accurate surface (not restricted by the same spherical
restrictions the BEM surfaces have). It may shrink the surface
slightly (by 1 - 2 voxels, but it should work). A description of how
we use it in MNE
thank you. Sorry but is there documentation on the wiki/anywhere on how to
create an own average?
On Fri, Feb 1, 2013 at 6:40 PM, Douglas N Greve
wrote:
> yes, unless you make your own average
> doug
> On 02/01/2013 09:42 AM, Linn Mittlestein wrote:
> > Dear Freesurfer Experts,
> >
> > Are the f
You can use the command make_average_subject:
http://surfer.nmr.mgh.harvard.edu/fswiki/make_average_subject
On Mon, 4 Feb
2013, Linn Mittlestein wrote:
thank you. Sorry but is there documentation on the wiki/anywhere on how to
create an own average?
On Fri, Feb 1, 2013 at 6:40 PM, Dougla
Yes.
On Mon, 4 Feb 2013, Varghese Chikku wrote:
Dear Team,
I tried to run dt_recon and the systems says cannot find
eddy_correct,Make sure FSL is installed. So ,do I need to install the
whole FSL package to run this.
In Thanks
Chikku
___
Fre
So I ran mri_surf2vol --help and I am still a little confused on what to
run. Where do I actually give the sig.mgh file? All the options seem to
ask for an individual subjects file.
Thanks,
Crystal
On 2/1/13 5:57 PM, "Douglas N Greve" wrote:
>You can run it with --help to get more info, let m
I would like to upsample the aseg.mgz to
Dimensions: 370X512X512
Spacing 0.5mm in x,y, and z.
Any suggestions?
-
Josh
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The informati
Hi Josh
do you have a volume with those dimensions? If so, you can use
-rl -rt nearest
cheers
Bruce
On Mon, 4 Feb 2013, Joshua Lee wrote:
> I would like to upsample the aseg.mgz to
>
> Dimensions: 370X512X512
> Spacing 0.5mm in x,y, and z.
>
> Any suggestions?
> -
> Josh
>
>
__
forgot to mention, this is to upsample Freesurfer Aseg to compare with
manually traced hipp volumes from original structural images.
-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805
On Mon, Feb 4, 2013 at 11:15 AM, Jos
I do indeed. Thank you very much!
-
Joshua Lee
Graduate Student
Center for Mind and Brain &
Department of Psychology
University of California, Davis
530.747.3805
On Mon, Feb 4, 2013 at 11:19 AM, Bruce Fischl wrote:
> Hi Josh
>
> do you have a volume with those dimensions? If so, you can use
>
>
Hi,
I am looking at functional group surface data analyzed with mri_glmfit in
tksurfer (using Freesurfer 4.1). I would like to threshold
using FDR - but only within a specified label - and then see the resulting
functional data map.
Once I have the functional dta loaded as an overlay, I have be
Hi list,
I'm running :recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject
$SUBJECTS_DIR/hptu_sub001In bold the error that I'm visualizing:
Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0Current Stamp:
freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0INFO: SUBJECTS_DIR is
/Appli
Hi,
I wonder how much graphic card memory is needed by the CUDA commands. We
have two Quadro NVS 295's with 256MB memory and the CUDA commands all
report "out of memory" errors. I know the cards are kind of outdated but I
want to make sure a new card would meet the task before purchasing.
A separ
Those are warnings, not errors, and you can ignore them. Looks like it is still
running
Bruce
On Feb 4, 2013, at 5:48 PM, wrote:
> Hi list,
>
> I'm running :
> recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject
> $SUBJECTS_DIR/hptu_sub001
> In bold the error that I'm visualizing:
>
> S
On Mon, Feb 4, 2013 at 5:50 PM, Zhongtian Dai wrote:
> I wonder how much graphic card memory is needed by the CUDA commands. We
> have two Quadro NVS 295's with 256MB memory and the CUDA commands all report
> "out of memory" errors. I know the cards are kind of outdated but I want to
> make sure
Hi Richard,
Thanks for the speedy response. I think we will go with GTX 660 Ti with 2GB
GPU RAM. We don't have a lot of subjects (as we hope to have) to analyze,
so maybe we will try splitting left and right hemispheres to two graphic
cards if our CPU RAM doesn't deplete. How do you designate the
On Mon, Feb 4, 2013 at 6:54 PM, Zhongtian Dai wrote:
> Thanks for the speedy response. I think we will go with GTX 660 Ti with 2GB
> GPU RAM. We don't have a lot of subjects (as we hope to have) to analyze, so
> maybe we will try splitting left and right hemispheres to two graphic cards
> if our
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