Hi
i am trying to transform/morph a tract created with tracula into my cvs
template subject space, using v.5.0
i am thinking the bb register transformation i am using is not the correct one,
but it seems the logical choice,
but obviously not working good as forceps minor ends up wraped around t
sandra,
the two fsaverage's that you are using are the same. you can change one
of the links to point at the other if you prefer, or continue to use it
as-is. it will not affect the results.
n.
On Tue, 2012-01-10 at 15:10 -0500, swood...@nmr.mgh.harvard.edu wrote:
> Hi all,
>
> We are trying
Hi all,
We are trying to run exactly the same analysis, particularly the recon-all
command, from two different directories. We've found that both
directories have '/fsaverage' but that they are sourcing two different
links/paths. Why is this and is there a difference in how analysis will
be run/
Hi Zonglei, you should contact the FSL list as to exactly what there
requirements are and how to get your data to that point.
doug
Zhen Zonglei wrote:
>
> I use FEAT from FSL to do the fMRI analysis. But the data were
> unpacked with the Freesurfer unpacksdcmdir.
>
>
> Zonglei Zhen
>
>
>
> On
Thanks to both Donald and Michael for catching my mistake about
recommending sample-size weighting within the contrast (both responses
are below). Depending upon the hypothesis being tested it is ok, but
you're probably not going to be in a situation in which you will want to.
doug
--
malcolm,
i attempted to add openmp support a few years ago but couldnt get it
working across the build. in principle it would be great to get it
working with freesurfer, but in practice threading issues and validity
of results will consume an order of magnitude more time than that to get
openmp t
malcolm,
running 'make check' is one way to check the build. we run that nightly
on our three build platforms (linux 32b, 64b and mac leopard). a goal
of our linux centos build is to have it run on as many linux variants as
possible without people having to modify their local install, and to
tha
Hi Clare,
I just posted something you may want to try, detailing some flags/expert
options that we tried that yielded dramatically better temporal lobe
surfaces for us.
cheers,
-MH
On Tue, 2012-01-10 at 15:38 +, Gibbard, Clare wrote:
> Hi Bruce,
>
> Thank you for your quick reply. I instal
Hi: I understand that information on the accuracy of the entorhinal cortex
parcellation, for each subject, may be found in their
?h.entorhinal_exvivo.label file. I reviewed this file but could not tell which
column (if any) contains accuracy information. Could someone point me in the
right dire
Hi all,
I'm posting a follow-up to my thread from November regarding "anterior
temporal lobe problems", so that it can be captured in the FS archives.
Based on a suggestion from Bruce, we tried re-running (from scratch)
using the -mprage flag in recon-all (since ours were MPRAGE
acquisitions) as
Hi Bruce,
Thank you for your quick reply. I installed v5.1.0 from the website and that
name is what comes up when I open a terminal window. However, I tried typing
recon-all -version and got $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18
nicks Exp $. So I'm not sure if that means the versio
Hi Paolo,
I think you'll find this tutorial has what you are looking for:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion#ResamplingStructuralDataintheDiffusionSpace
Allison
On Tue, 10 Jan 2012, paolo wrote:
> Hi, i have a problem:
>
> i have a file aseg+aparc.mgz, generated by fre
After being able to build with GCC, I tried to add OpenMP support:
[root@login002 freesurfer-dev-20120106]# ./configure --enable-openmp -disable-
all-apps --with-mni-dir=/export/minc-1.4/ --with-vxl-dir=/export/vxl-1.13.0
--prefix=/scratch/mtobias/freesurfer-dev-gcc-openmp
...
(Note: Mac OS X d
Nick,
Everything is now building successfully. Thanks for your help!
What do you normally do to test a build? I tried running 'make check' which
seemed pretty extensive. While many tests passed:
[root@login002 freesurfer-dev-20120106]# grep PASS make.check.out | wc -l
407
I did have one fa
Hi Claire,
hmmm, that is odd. What version are you running? If you upload the
subject before and after we'll take a look
Bruce
On Tue, 10 Jan 2012, Gibbard,
Clare wrote:
Hi,
I ran recon-all -all -subjid subjectx on around 40 scans. The registrations
and skull strips look fine. However,
Hi, i have a problem:
i have a file aseg+aparc.mgz, generated by freesurfer, and i would like
to visualize it with trackvis (i mostly need the aparc part). the
problem is, that if i just convert it to nifti, it seems to be in a
different reference frame.
i tried to read the freesurfer coordinate
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