Tomorrow I'll post a tutorial.
It's quite simple
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
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2011/11/9
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
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,
No. This is for non GPU instances
-- iOS 5.0
Em 09/11/2011, às 22:28, Satrajit Ghosh escreveu:
hi pedro,
will this work with gpu instances as well?
cheers,
satra
2011/11/9 Pedro Paulo de Magalhães Oliveira Junior
> Some weeks ago I was asked about a public image (AMI) to run in the Amazon
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 "fsl_sub_se
hi pedro,
will this work with gpu instances as well?
cheers,
satra
2011/11/9 Pedro Paulo de Magalhães Oliveira Junior
> 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
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 re
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 hippocampus.sm1
Dear Freesurfer users and developers,
Yes, sorry... I should have specified this. I meant the mean curvature
('curv' in qdec). And considering that this index is being calculated by
formula: 1/radius - there must be an opposite interpretation (so, not a
flattening actually, but folding?)... How
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 t
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
c
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,
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
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 you so much, things are getting slowly
> clearer now
>
> I can try to explain better what i want to do, so that perhaps
> it will be easier for you t
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 whe
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 subjec
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,
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 solut
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
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.
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
>
>
> _
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 (230
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 'TextEdi
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:
>>
>> Af
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 "C
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
accept
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___
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Freesurfer@nmr.mgh.harvard.edu
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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 :
> If you run som
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