Freesurfer has a coordinate displacement between their surfaces and
volumes, which depends on the volume space that was used. That might be
part of the picture. However, this is purely a shift, no rotation or flip,
and I think is typically about half the brain size, so something else must
also
Hello,
I am a very new HCP Connectome WB user trying to import nifti and gifti files
into Brainstorm (Bst) for EEG modeling. I am having a strange problem and am
looking for some direction. In the past I was able to import T1.nii volume
files and lh.pial/rh.pial files from FreeSurfer with no
Hi Niels,
Indeed, I figured as much. I was just wondering if there’s cluster-specific
code or some other code in there that I need to alter to get it to work for me.
Regards,
Karthik
From: Niels Bergsland [mailto:npbergsl...@bnac.net]
Sent: Tuesday, January 31, 2017 12:41 PM
To:
Hi Karthik,
I unfortunately don't have any experience myself with torque. However,
taking a quick look again at the code, it looks like the idea is to copy
the updated files under ${FSLDIR}/overlay and then you update the PATH
variable with the overlay directory as the first entry. This way any of
Thanks Niels and Moises!
Niels, the documentation in the Github repo makes setting up the overlay look
pretty straight-forward. I did take a look at some of the code – it looks like
the fsl_sub script has been altered to use qsub for Torque. Do you suggest
deploying this overlay as-is? Or do
Hi Daniel,
Genotyping data on HCP subjects has not yet been released but should be
available sometime in March 2017 from dbGaP. When we announce the release on
the HCP-announce and HCP-Users email lists (if you aren't a member of
HCP-announce or HCP-users, sign up
Hi,
Just want to follow up with en earlier email thread about the availability
of the genotyping data. I was wondering whether the genotyping data has
been released. And if so, what would be the best way to access it?
Best,
Daniel
___
HCP-Users
Hi Karthik,
You may find this useful for getting FSL scripts adapted for torque:
https://github.com/octomike/fsl_overlay/
On Mon, Jan 30, 2017 at 11:30 PM, Gopalakrishnan, Karthik <
gkart...@gatech.edu> wrote:
> Hi Moises,
>
>
>
> Thanks for the reply!
>
>
>
> I also want to know a couple other
Hi Karthik,
You can use any queue system, but you will need to adapt the script that
submits the jobs to the queue, bedpostx.
bedpostx script uses fsl_sub to submit the jobs, which is another script
intended for SGE.
You can modify the lines that call to fsl_sub with qsub (Torque), but take
care
