After importing a subject's data (T1 single time point)
I run a script with these commands:
recon-all -s -autorecon1
recon-all -s -autorecon2
recon-all -s -autorecon3
I did this twice, once on each of two linux machines.
I am using the same exact input intensity T1 data and importing the data
Do you have permissions to the file? If so, rerun recon-all with -debug
as the first option, then send the terminal output to the list.
doug
ps. Please send emails to the list and not to us individually. thanks!
On 7/25/13 2:31 PM, Kyllo, Hannah M wrote:
yes
- Hannah Kyllo
Hi all,
I am doing cortical thickness and surface area analyses and had a few
questions regarding editing the borders.
1) Is it reasonable to edit every (big and small) error that I find?
Basically, how much a difference would it make in terms of the surface area
and cortical thickness values if
Hi Bruce,
OK, thanks.
I will try MRIcron.
Pom
On Thu, Jul 25, 2013 at 7:59 AM, Bruce Fischl wrote:
> Hi Pom
>
> are these the dicoms straight off your Philips scanner? We don't have a
> ton of experience with philips. Maybe you could use something else to
> convert them to NIFTI, like MRIcron,
Hi Pom
are these the dicoms straight off your Philips scanner? We don't have a ton
of experience with philips. Maybe you could use something else to convert
them to NIFTI, like MRIcron, then pass them to us?
cheers
Bruce
On Thu, 25 Jul 2013,
Pom Sailasuta wrote:
>
> Hello,
>
> I am resendi
Hi Haielom
have you read any of the documentation or tuturials? Look at the usage of
recon-all and start there. It's pretty simple to get started - just give
the recon-all script one file in a high-resolution T1-weighted dicom
series like an mprage.
cheers
Bruce
On Thu, 25 Jul 2013, Haielom E
Hi Team,
I have a question on making a group average of subjects for functional
connectivity.
In detail, I want to make a surface overlay that is the average correlation
(r-value) of a certain subject group. What commands would be used for this?
simply isxconcat-sess? I could not find much info on
Hello,
I am resending this post since there is no reply for 2 days, I really
appreciate your help.
thanks so much.
I have several errors using mri_convert to convert 3T Philips T1-wt, DTI
and fMRI images. The last one on T1-wt images tells me to send email to
freesurfer, so here is the error mes
Hi there,
I was trying to learn the freesurfer, I have hard time to download at the
beginning, later after that, I also have no knowledge of how to import images
and analyse them. I really need your help tremendously.
Thanks,
Haielom___
Freesurfer maili
Does subj001.nii.gz exist in the folder you ran recon-all from?
On 7/25/13 12:21 PM, Kyllo, Hannah M wrote:
Hello,
I've received the following error using Ubuntu 13.04:
"WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!
ERROR: cannot find subj001.nii.gz
Linux neuron 3.2.0-49-
look at $FREESURFER_HOME/build-stamp.txt
doug
On 7/25/13 11:45 AM, Rodrigo Perea wrote:
Is there any other way I can find the FreeSurfer version I am using?
According to
https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.HowdoIknowtheversionofFreeSurferI.27mrunning.3F
I
Hi Amirhossein - If your error happens when bbregister is run, then it's
not the error that the dmri_5.1_snow_leopard.tar.gz fix was meant to
address. In any case that fix is not relevant to you b/c you're using 5.3
and not 5.1. Can you please send your trac-all.log to establish where
exactly
Hello,
I've received the following error using Ubuntu 13.04:
"WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!
ERROR: cannot find subj001.nii.gz
Linux neuron 3.2.0-49-generic #75-Ubuntu SMP Tue Jun 18 17:39:32 UTC 2013
x86_64 x86_64 x86_64 GNU/Linux
recon-all -s exited with ER
Is there any other way I can find the FreeSurfer version I am using?
According to
https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.HowdoIknowtheversionofFreeSurferI.27mrunning.3F
I have to run: recon-all -version, but I get the output below. Now the stable
FreeSurfer Version is
Thank you for your reply!
I will try to run the new version, and also try to see what is the source
for such differences.
I guess the new release is the easiest solution.
clarissa
2013/7/25 Bruce Fischl
> yes, definitely for cortical surfaces
> Bruce
>
> On Thu, 25 Jul 2013, Watson, Christoph
yes, definitely for cortical surfaces
Bruce
On Thu, 25 Jul 2013, Watson,
Christopher wrote:
> I don't know, but I'm pretty sure the Freesurfer team will recommend you use
> v5.3.0. There are emails saying as much.
> Chris
>
> From: freesurfer-boun...@nmr.
Hi Clarissa
have you visually inspected them? Does one version look more accurate
than another to you? We do system tests on things like subcortical
volumes before releasing a version and our tests show that the accuracy
in these structures has not changed, so I'm not sure what the source of
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