Hi Doug,
thanks a lot it worked for the eccen maps. I have now my eccen of interest...
Is there a command to make a intersection area between two labels? I
just found the command mri_mergelabels which merge two labels into a
bigger one.
cheers,
Erhan
2011/11/1 Douglas N Greve
Hi
Is there any way to get fwhm information from an mgh produced by mri_glmfit? I
have only the mgh file produce by mri_glmfit.
Knut J___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
Hi,
After editing a text file holding the b vecs to be supplied
as input to dt_recon this tool did not interpret the text
file correctly. It turned out that dt_recon did not recognise
the end-of line character in this file: this was decimal
code 13 (called CR). It seems that dt_recon only
accepts
On 11/9/11 07:59 , Ed Gronenschild wrote:
After editing a text file holding the b vecs to be supplied
as input to dt_recon this tool did not interpret the text
file correctly. It turned out that dt_recon did not recognise
the end-of line character in this file: this was decimal
code 13 (called
Hi Rudolph,
I used TextEdit. On a Mac with OS version earlier than OS10.6
this problem didn't occur. With TextEdit it is not possible to save
as UNIX format.
Thanks for the trick to use sed.
Ed
On 9 Nov 2011, at 15:27, Rudolph Pienaar wrote:
On 11/9/11 07:59 , Ed Gronenschild wrote:
After
On 11/9/11 09:36 , Ed Gronenschild wrote:
Hi Rudolph,
I used TextEdit. On a Mac with OS version earlier than OS10.6
this problem didn't occur. With TextEdit it is not possible to save
as UNIX format.
Thanks for the trick to use sed.
Ed
I'm not a great fan of the built in 'TextEdit'. That
On 11/9/11 09:49 , Rudolph Pienaar wrote:
sed 's/0xd/xoa/' file1.txt file2.txt
sed 's/0xd/x0a/' file1.txt file2.txt
Oops... critical typo.
--
Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301)
No, it is computed from the residuals.
doug
Knut J Bjuland wrote:
Hi
Is there any way to get fwhm information from an mgh produced by
mri_glmfit? I have only the mgh file produce by mri_glmfit.
Knut J
Nothing that is easy to do. You can try it in matlab. Another thing you
can do is to convert the label into a binary mask in a volume format
(eg, mgh or nifti) with mri_label2labe (using the --outmask option). Do
this for both of your labels, then use fscalc to compute an and of the
masks. You
Some weeks ago I was asked about a public image (AMI) to run in the Amazon
EC2 infrastructure
If you want to use FreeSurfer in the EC2 infrastructure you can use this
public AMI: *060244368407/FREESURFER51*
Just for your information this AMI can run a recon-all in 23 hours in an
Amazon AWS Small
Jeff,
While resize window does not work when invoked through a tcl flag there is a
manual way to bypass it. After you open tksurfer move back from the GUI to the
tksurfer terminal window and paste your tcl script there. Not nearly as
convenient as the tcl flag execution but it is the only
You can try running just recon-all -skullstrip first, if that doesn't fix
the problem, you can try changing the wsthresh and removing the
-no-wsgcaatlas flag (or add the flag if you didn't include it). Sometimes
that makes a difference.
-Khoa
On Wed, 9 Nov 2011, Julia Hill wrote:
Hi there,
Dear Freesurfer experts,
I opened the table (qdec.table.dat) in a text editor and add a line at the end
of the file. Then I tried to open the data table again. However, I received an
automatic error message again:
Number of columns: 286
fsid: column: 1
Number of factors: 285
Number of
Dear Freesurfer Expers
I have installed FS on the new mini Mac today, it can open bert with
tkmedit and tksurfer.
Using tkmedit for seeing my subject in /Users/nzadeh/freesurfer/subjects,
it says
cannot find subject N3237c in /Users/nzadeh/freesurfer/subjects or it is
not readable by you
but when
yes, use mri_vol2surf. You will need a proper registration file. If the
zstat space is the native functional subject space, then you should use
bbregister and specify the example_func as the template.
doug
kelsi wrote:
Hi all,
I would like to convert a nifti zstat file from post-processing
The tool to use is: track_transform
It should be distributed with the DTK / TrackVis tools.
-Lilla
On Wed, 9 Nov 2011, Douglas N Greve wrote:
Hi Paolo, I don't think we have have any tools to apply a matrix to a
trk file. Or maybe I'm wrong?
doug
paolo wrote:
Bruce, Doug, Thomas, thank
Hi, experts. We need to use FreeSurfer to process some analyze image data.
More specifically, we want to extract the hippocampus surfaces. We know
that FreeSurfer has done subcortical segmentation during -autorecon2 stage
in recon-all. We have checked the resulting aseg.mgz file and found that it
You can extract a binary mask for any structure with
mri_binarize --i aseg.mgz --match XX --o yourmask.mgh
where XX is a number from $FREESURFER_HOME/FreeSurferColorLUT.txt (eg,
17 = left hippo)
It is possible to generate hippo surfaces, but we cannot guarantee
accuracy. Let me know if you want
cd $SUBJECTS_DIR/subject/surf
mri_tesselate ../mri/aseg.mgz 17 lh.hippocampus; # this generates a
surface with jagged edges
mris_smooth -nw -n 10 lh.hippocampus lh.hippocampus.sm10; # smooths
surface 10 smoothing steps is just a guess
# Visusalize the surface
tksurfer subject lh
yes, that has the subcortical segmentation based on the automatic
algorithm and any changes that you might have made manually. The auto
is only the result from the automatic method.
doug
Jie Shi wrote:
Thanks a lot. Will try. Basically, is aseg.mgz the resulting file
which contains the
hi pedro,
will this work with gpu instances as well?
cheers,
satra
2011/11/9 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br
Some weeks ago I was asked about a public image (AMI) to run in the Amazon
EC2 infrastructure
If you want to use FreeSurfer in the EC2 infrastructure
Hi Anastasia,
It turns out that I was NOT able to run the original bedpostx on our
cluster, so thank you for pointing me in the right direction! In case other
users experience a similar problem, this is what we did to get the ball rolling
on our grid:
We found the
No. This is for non GPU instances
-- iOS 5.0
Em 09/11/2011, às 22:28, Satrajit Ghosh sa...@mit.edu escreveu:
hi pedro,
will this work with gpu instances as well?
cheers,
satra
2011/11/9 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br
Some weeks ago I was asked about a
Hi Shannon - Which version of FSL do you have? Older versions didn't use
to save the mean_dsamples.nii.gz, but that was a while ago.
How quickly it runs depends on the size of the brain mask, so I'd check
that that's ok too.
a.y
On Wed, 9 Nov 2011, Shannon Buckley wrote:
Hi Anastasia,
Pedro Paulo,
thanks for posting the info. i've added this to the Download wiki page,
and created a stub page for the Amazon Cloud:
https://surfer.nmr.mgh.harvard.edu/fswiki/AmazonCloud
i've never set one up so i have no idea how to do it. maybe someone can
flesh-out this page as using the ec2
Tomorrow I'll post a tutorial.
It's quite simple
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
2011/11/9
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