Hi and thank you very much for your availability. Now, I'm running tracula as
following:
trac-all -prep -c /Applications/freesurfer/subjects/subject_prova/CON_01
my CON_01 forder contains: data.nii.gz (DWI), bvals and bvecs (as used in
previous FSL analysis) and T1-images.nii.gz. File.niii.gz
Hi and thank you very much for your availability.
Now, I'm running tracula as following:
trac-all -prep -c /Applications/freesurfer/subjects/subject_prova/CON_01
my CON_01 forder contains: data.nii.gz (DWI), bvals and bvecs (as used in
previous FSL analysis) and T1-images.nii.gz. File.niii.gz
Hi Stefano - The argument of the -c option is a configuration file, not a
directory. For more info on trac-all and setting up the configuration
file, please see the trac-all wiki page:
http://www.freesurfer.net/fswiki/trac-all
and tracula tutorials:
The second command is probably failing because the first command is
failing. The 1st is failing because you don't have GLIBC 2.4. I'll have
to leave that one for Nick or Zeke.
doug
On 01/26/2013 03:21 PM, Gabriel Gonzalez Escamilla wrote:
Well there is actually two kinds of error:
1) when I
Thanks Doug for your answerBut, always the first one ends properlysurfreg --s c_003 --t fsaverage_sym --lhit's the second one that have two different errors:surfreg --s c_003 --t fsaverage_sym --lh --xhemiAnd yes you are right, it says that it's because of the library but, the original mri_convert
Dear Nick,
I was wondering whether you (or indeed anyone else reading this!) know
where the error that I report earlier in this thread might be coming from.
Many thanks in advance!
Tudor
On 20 December 2012 05:27, Douglas Greve gr...@nmr.mgh.harvard.edu wrote:
Hi Tudor, I don't know how to
Tudor, Greg, and Petr,
I'm currently attempting to replicate this problem. In the meantime,
can you tell me which Windows and which VirtualBox version you are
running this on? I'm at a loss as to why this build no longer works.
Nick
On Mon, 2013-01-28 at 18:19 +, Tudor Popescu wrote:
Thank you very much for you kindness Anastasia.
The folder that contains .nii.gz file is correct?I'm looking the recommended
trac-all update. Where can I put it?
Stefano
Messaggio originale
Da: ayend...@nmr.mgh.harvard.edu
Data: 28-gen-2013 16.45
A: std...@virgilio.it
Cc:
Hi Nick,
Thanks for your help, I'm on Windows XP SP3 VirtualBox 4.2.4
Tudor
On 28 January 2013 18:30, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote:
Tudor, Greg, and Petr,
I'm currently attempting to replicate this problem. In the meantime,
can you tell me which Windows and which
Hi Stefano - Type which trac-all to find out where trac-all lives on
your computer, then copy the updated version over it.
a.y
On Mon, 28 Jan 2013, std...@virgilio.it wrote:
Thank you very much for you kindness Anastasia.
The folder that contains .nii.gz file is correct?
I'm looking the
Dear all,
I am currently working on a 1.5T SPGR 1.5mm MRI longitudinal dataset, and I
would like to know if one is expected to manually skull strip the images before
de recon -all procedure. I am aware that the image quality may be a limiting
factor for the freesurfer processing.
Regards,
Pedro
How many vertices are on the surface? For nifti you have to reshape the
size of the image so that it fits in the nifti format (requires each dim
be less than 32k). If the number of vertices has a prime factor that is
more than 32k, then you cannot convert it to nifti and use it in another
Hi Pedro, you should run it through recon-all and see how the automatic
skull stripping does, then correct it if necessary.
doug
On 01/28/2013 02:08 PM, Pedro Rosa wrote:
Dear all,
I am currently working on a 1.5T SPGR 1.5mm MRI longitudinal dataset, and I
would like to know if one is
hello all,
Just for reference, we were having an issue with recon-all v 5.2 exiting with
errors due to issues with the perirhinal cortex. We were able to simply
commented out the parts of the script dealing with the perirhinal cortex. Just
an FYI to those who may be having a similar problem.
Hi Jon
what were the errors? We will want to fix them prior to official release.
thanks
Bruce
On
Mon, 28 Jan 2013, Jonathan Holt wrote:
hello all,
Just for reference, we were having an issue with recon-all v 5.2 exiting with
errors due to issues with the perirhinal cortex. We were able to
Jon,
If the error is where the perirhinal labels cannot be found in the
fsaverage that sits in your subjects dir, then that issue was fixed on a
more recent beta 5.2. recon-all now checks if the perirhinal labels
exist in the fsaverage found in the subjects dir (which might not be the
case if
Also, could I have a link for the centos4 of this updated version of 5.2? And
is there a working 5.2 for Mac OS X, 10.7 or 10.8 specifically?
jon
On Jan 28, 2013, at 3:19 PM, Jonathan Holt wrote:
Nick,
it was in fact an error with missing perirhinal cortex labels in fsaverage.
It did not
Nick,
it was in fact an error with missing perirhinal cortex labels in fsaverage. It
did not exist, and then the process exited. Good to know it's been fixed.
jon
On Jan 28, 2013, at 2:48 PM, Jonathan Holt wrote:
hello all,
Just for reference, we were having an issue with recon-all v 5.2
updated 5.2 versions for centos4_x86_64 and macos lion are here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/
an updated centos4 build (32b) will not be ready until tomorrow.
n.
On Mon, 2013-01-28 at 15:29 -0500, Jonathan Holt wrote:
Also, could I have a link for the
Hi Anastasia,
I have prepared this configuration file:
## Set locations of diffusion DICOMs, diffusion output, FreeSurfer recons##
This file contains commands that will be run by trac-all before an analysis.#
It is used to set all parameters needed for the analysis.## Remove a parameter
from
Hi Stefano - The file that you defined as your gradient vector file (set
bvecfile = ...) doesn't exist. This file has to exist.
Hope this helps,
a.y
On Tue, 29 Jan 2013, std...@virgilio.it wrote:
Hi Anastasia,
I have prepared this configuration file:
#
# Set locations of diffusion
I was able to verify that 'recon-all -s bert -nuintensitycor' works on
the windows virtualbox instance of fs5.1. bert is the sample data that
comes with the distribution, and nuintensitycor is the stage that runs
nu_correct.
I noticed in your recon-all.log file this line:
total
Dear All,
I ran a test subject on VM and the process took 20 hrs to complete.But
the same images on Mc pro took 58 hours.VM is 8GB and Mpro is 16 GB.I
have noticed this delay happening in the past as well,where VM takes
20-24 for a single patient and Mc takes 24-30 for the
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