Hello everybody,
I have searched the mailing list and I have found the same error I am facing
but unfortunately I haven't been able fo find the correct answer.
I am running Freesurfer 6.0 on Debian 8.0 (Neurodebian).
When I run recon-all I get the following output, which I also attach in a t
hmmm, it looks like most of the memory on your machine is in use by other
processes. Can you terminate them and try again?
cheers
Bruce
On Mon, 5 Mar 2018, Anna
Daniels wrote:
Dear FreeSurfer team,
we are trying to remove dura from the brainmask automatically as described in
the SkullStrip
Hi,
you might try supplying an additional command-line argument while
calling the 'lme_mass_fit_vw' function:
lhstats = lme_mass_fit_vw(X,[1 2],Y,ni,lhcortex,[],1)
This will tell Matlab to use only one worker. Further documentation on
this additional argument can be obtained by typing 'help
lme_
Thanks for the quick response Kersten.
I tried all the potential suggestions mentioned in your post but still no luck.
Here’s the summary:
lhstats = lme_mass_fit_vw(X,[1 2],Y,ni,lhcortex,[],1)
Undefined function or variable 'matlabpool'.
Error in lme_mass_fit (line 124)
if (matlabpool('si
it all depends on what surface you are looking at. I think tksurfer
reports coords for the ?h.orig
On 03/03/2018 02:19 PM, Yagmur Ozdemir 19 wrote:
> Thank you!
>
> Best
> Idil
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mg
Dear Free Surfer,
I was wondering if it was possible to analyse (surface-based morphometry and
SPM) NOT brain scans.
I am doing my PhD looking at how the shape of children's feet change as they
get older (2-7 years old).
I will use a 3D scanner which will provide me with a mesh of triangles of
Hi Matyas
it is possible, but will be a fair amount of work, probably including some
c coding since many of our tools are brain-specific
cheers
Bruce
On Mon, 5 Mar 2018, Matyas Varga wrote:
Dear Free Surfer,
I was wondering if it was possible to analyse (surface-based morphometry and
Dear Bruce,
Thank you for your quick reply. I think that whatever software I am going to
use, it will require some coding as most similar software are brain specific.
I use Matlab on a regular basis, and am happy to learn c in order to complete
this project. My ultimate aim is to create a soft
Hello Freesurfer Experts,
I am using freesurfer looking to get the cross-sectional area of the corpus
callosum using the midline plane. Could you please explain how to define
the midline plane in freesurfer so we can compute our cross-sectional area?
Thank you,
Ben
___
Hi Matyas
we have online tutorials on our wiki and data you can download. Not sure
how easy it will be though - a lot of what we do is brain specific
Bruce
On Mon, 5 Mar 2018, Matyas Varga wrote:
Dear Bruce,
Thank you for your quick reply. I think that whatever software I am going to
use
can you send the entire recon-all.log file?
On 02/27/2018 09:51 AM, shilin18 wrote:
>
> Hi all, very nice to find a place to ask all the fs giants a question.
>
> I run recon-all …-all -localGI, which always return this at the end.
> Can anyone help me find out what I need to do to evade this er
I'm not sure what you are trying to do. The 2nd tutorial below is for
FSFAST which is a comprehensive fMRI analysis package in which
mri_vol2surf is built-in. The 1st tutorial is if you were using some
other fMRI package and you wanted to interface with FreeSurfer.
On 02/26/2018 06:16 PM, Sar
Hi Ben
we don't write out the mid saggital plane image, although we do compute
it internally. mri_cc prints the transformation matrix, which you could
paste into a .lta file and apply that transform to the data I guess.
Actually, looking at the code there is an old diagnostic you can use. Do
s
Dear Sir/Madam,
I found that the QATools is still not updated for the Freesurfer v6.0
yet at https://surfer.nmr.mgh.harvard.edu/fswiki/QATools. Could you please
let me know what't the timeline for the update? or Do you know if anyone
can share the updated QATools with me?
Looking forward to h
Hi,
thanks for the additional information.
I believe that we are dealing with a version issue now.
Specifically, I have so far been testing with an LME toolbox from a
Freesurfer 6.0 version on Matlab R2016a. In that sense, there is no
need for a separate download of the LME scripts, since they a
The version string I have been using:
$Revision: 1.1.1.1 $ $Date: 2012/02/02 11:25:52 $
So, it appears that I do indeed have the older version.
I am running Matlab 2017a, which is a relatively newer version.
Before I proceed with using LME toolbox from a freesurfer 6.0, I would
appreciate your
No, you should be using the white surface. It does not matter what you
visualize it on.
On 03/02/2018 12:27 PM, Adam Mecca wrote:
> HelloFreeSurferDevelopers,
>
> I have run a glm on the left hemisphere to compare cortical thickness
> between 2 groups. After, I did a cluster-wise correction wit
Why did you remove the registration file? --srcreg below
On 02/28/2018 04:13 PM, srishti goel wrote:
> Hello,
>
> Thank you so much! I used the following command as you said and got an
> error : must specify a source registration file or --regheader
>
> mri_vol2surf --src negative_allsocial_avgn
It depends on how you do the transform back to native space. You can
view the roi on the volume in the native space to see whether it landed
in the right place and that the surface goes through it
doug
ps. Please remember to include previous correspondences
On 02/28/2018 07:29 PM, Albrecht, D
Hi list,
is it possible to avoid the clusters < 5 voxels using freeview for FS-FAST
results (mni.305) obtained after running mri_glmfit-sim --glmdir my-glm.wls
--grf?
Thanks
Kind regards
Stefano___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvar
Set --cwp 1. This will keep all clusters regardless of size. Then look
in the summary table and see where the cluster-wise p-value is for 5
voxels or less, then rerun with that cwp. FYI, this is not a good way to
correct for multple comparisson
On 03/05/2018 03:35 PM, std...@virgilio.it wrote
Hi Matt
no idea what that would happen. If you upload the dataset we will take a
look
cheers
Bruce
On Mon, 5 Mar 2018, Matthew Grecsek wrote:
Following your advice below, it was clearly apparent that the output from the
skull stripping step
was missing a lot. I tried adjusting the -wsthresh
Thanks, what's meaning FYI?
What do you advise?
>
> Il 5 marzo 2018 alle 21.42 Douglas N Greve ha
> scritto:
>
> Set --cwp 1. This will keep all clusters regardless of size. Then look
> in the summary table and see where the cluster-wise p-value is for 5
> voxels or less, the
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