Dear Freesurfer experts,
I am trying to perform the resting state fMRI analysis as in:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
I got stuck with the STEP8, when I tried to use my own fsgd file. I tried
to test for two group difference, no covariance as in:
Hi Bronwyn,
You raise a good point. You can consider creating a cortical mask using
aparc+aseg.mgz and use that to mask the networks.
However, another approach (which might be more accurate) is to take
cortical networks in fsaverage space and transform to your subject's
surface and then
Hello all,
I'm trying to make a patch and have run into the 'bad vertex' error. It's
come up a few times on the listserv, but I never saw a public resolution.
One possible source of errors is that I had to do a manual correction in
FreeView, including a 'remove intersections' in FreeView.
thanks Bruce - I had found that option for my fsaverage maps and it worked.
What about if I am importing probability maps formed as .mnc and creating
overlays from them? The percentages seem to be very odd for min and max
threshold.
Trisanna
--
Ph.D. Candidate
McGill University
Integrated
Hi Trisanna
if you are using mri_average you can give it -p as the first argument and
it will compute a percent at the end
Bruce
On Wed, 22 Jun 2016, Trisanna
Sprung-Much wrote:
Hi Bruce
Is there is a way to set the probability of an overlay between 0 and 1?
Would this have to be done
On 22 June 2016 at 19:32, Derek Pisner wrote:
> Thanks for the very quick reply. Good to know that someone has successfully
> compiled GPU binaries for newer CUDA versions. I took a quick look at the
> developer's guide for building the cuda binaries from
Hi Richards,
Thanks for the very quick reply. Good to know that someone has successfully
compiled GPU binaries for newer CUDA versions. I took a quick look at the
developer's guide for building the cuda binaries from source, but it seems like
a very involved process? Do your compiled
Hi Bruce
Is there is a way to set the probability of an overlay between 0 and 1?
Would this have to be done when creating the overlay using mri_vol2surf?
thanks
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
On Mon, Jun 20, 2016 at 12:11 PM, Bruce
On 22 June 2016 at 18:17, Derek Pisner wrote:
> Anyone manage to successfully configure recon-all to run with -use-gpu for
> recent cuda toolkit versions? I realize cuda support has ceased over the past
> few years for Freesurfer, but have there been any
Anyone manage to successfully configure recon-all to run with -use-gpu for
recent cuda toolkit versions? I realize cuda support has ceased over the past
few years for Freesurfer, but have there been any successful builds for CUDA
toolkit versions 6 and up? I am currently looking to configure
I should add that we're running tkmedit using xvfb since the process is
automated and runs without a physical screen.
Flavin
> On Jun 22, 2016, at 4:15 PM, Flavin, John wrote:
>
> Hi all,
>
> I run the pipelines for the CNDA and various other XNAT installations. We
>
Hi all,
I run the pipelines for the CNDA and various other XNAT installations. We
recently updated some of our packages, and our Freesurfer snapshots (generated
with tkmedit using a tcl script) have broken.
We're on Centos 6.8. The package that seems to cause the breakage is one of the
mesa
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Hi,
*After the command: *
asegstats2table --subjects AntonioMagnani -- meas volume --tablefile
TESTE.txt
This message:
[image: Imagem inline 1]
Thanks.
elias.
--
Atte.
Elias Vergílio Da Cás - Físico
UFES/HUCAM/EBSERH
___
Freesurfer mailing
Hi all,
I'll give some feedback about the two methods you've mentioned. I also
tried using a 0.5 T1 image and then:
*Changing the headers of the T1 and T2 images:*
It worked for the 0.7mm T1, however, in the 0.5mm the tailarach aligment
failed.
In both cases I had the warning
Brilliant - many thanks.
Kx
On 22 June 2016 at 14:57, Harms, Michael wrote:
>
> Yes on all fronts.
>
> --
> Michael Harms, Ph.D.
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University
Yes on all fronts.
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.
Tel:
Thank you Michael!
So - just to be super sure I'm on the same page here. If I've run a subject
using 5.3 I take that same subject directory (after backing it up
somewhere) and then run the dev version of recon-all with the -all flag.
After it's completed I (should - contingent on checking again
Hi,
You can simply rerun 'recon-all -all’ on top of your already processed/edited subject, and it will respect your previous edits. Of course, it is a good idea to still review/QC the results afterwards, to make sure that the outcome of those edits is satisfactory
under the new FS
Hi everyone,
I processed and edited 300 participants for our study using Freesurfer 5.3
and I'd like to move to using the dev version that's currently available
because we have a bunch more data that's been collected and I think it does
a better job. (This question also applies to moving to v 6
*Hello,*
*I’m trying to run recon-all -lgi - s Subjectname on my data but i am
getting this error!*
***
Error in dsearchn (line 79)
[d(i),t(i)] = min(sum((x-yi).^2,2));
Error in mesh_vertex_nearest (line 29)
nearestIndex =
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