Hi Folks,
I would like to use the -nuintensitycor-3T flag as listed in the release
notes (http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes)
I had two questions about this new option:
1. Can I just use this as follows: recon-all -s bert -autorecon1 -autorecon2
-nuintensitycor-3T (then run -aut
Hi Alan
we produce lots of curvature measures. Which one do you mean? Which file
are you reading it from?
Bruce
On Tue, 17 Aug
2010, Alan Francis wrote:
> Hi Bruce:
>
> As you know - along with Volume, Thickness and SA, FS also gives curvature
> numbers for the 5 subregions of the CC. In my
Hi Fernanda,
do you have a linux machine you could try it on?
Bruce
On Tue, 17 Aug 2010, Fernanda Palhano wrote:
> Hello,
>
> When trying running recon-all I am getting the following error:
>
> #...@# Fix Topology rh Sat Aug 14 04:15:31 BRT 2010
>
> ERROR: _FindFacePath: could not find path!
>
no problem, eventually we'll have a help page once we gather all the new
issues with this new gpu stuff.
what kind of card do you have? is it one of these:
http://www.nvidia.com/object/cuda_gpus.html
make sure your driver is the one from the site. the driver name
'nvidia-gfxG02-kmp-desktop' doe
Hi Bruce:
As you know - along with Volume, Thickness and SA, FS also gives curvature
numbers for the 5 subregions of the CC. In my dataset, which is comparing
High risk offsping of SZ subjects and healthy controls, the curvature
numbers show a siginficant difference (p < 0.03) between the groups.
Sorry to be a PITA but I'm still having issues. I pointed at cuda-64 and
now I get:
mri_em_register_cuda -skull nu.mgz
> /usr/freesurfer/average/RB_all_withskull_2008-03-26.gca
> transforms/talairach_with_skull.lta
>
> Acquiring CUDA device
> Using default device
> CUDA Error in file 'devicemanag
make sure your LD_LIBRARY_PATH is pointing at:
/usr/local/cuda/lib64
which has the 64b libcudart, and not:
/usr/local/cuda/lib
which has the 32b.
n.
On Tue, 2010-08-17 at 12:17 -0500, joel bruss wrote:
> Nick-
>
> I Dl'ed the tarball, unpacked, and re-ran. I received the following
> error
Nick-
I Dl'ed the tarball, unpacked, and re-ran. I received the following error
message:
/lcn2/lesion_warp.dir/MAP3_Nifti/freesurfer_subs.dir/PC/mri
>
> mri_em_register_cuda -skull nu.mgz
> /usr/freesurfer/average/RB_all_withskull_2008-03-26.gca
> transforms/talairach_with_skull.lta
>
> mri_em_
Thx. Nick. Will give it a shot. BTW, is there also a plan for using OPENMP, MKL
or ATLAS to speed it up a bit? A lot of off the shelf rack mounted servers
cannot put those cards in.
Gen
On 8/17/10 10:03 AM, "Nick Schmansky" wrote:
i forgot to add: make sure you have the latest nvidia driver,
i forgot to add: make sure you have the latest nvidia driver, which has
support for cuda 3.
n.
On Tue, 2010-08-17 at 13:00 -0400, Nick Schmansky wrote:
> currently the _cuda binaries are distributed only in the centos4 and
> centos4_x86_64 distributions. however, those should work in centos5,
>
currently the _cuda binaries are distributed only in the centos4 and
centos4_x86_64 distributions. however, those should work in centos5,
and i've made a tarball of the _cuda binaries downloadable from here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc
look for the file 'fscudabins-
Not to hijack your question, but I have similar questions. I have CUDA
toolkit 3.1 installed, "cudadetect" returns: "Detecting CUDA... 32767 CUDA
enabled device(s) detected." but, when I run recon-all, e.g.:
recon-all -subjid PC -all -use-gpu
I get the following errors at the mri_em_register_c
Carl,
Looks like you only use relative path. You need to put in absolute path.
Something like
setenv FREESURFER_HOME /home/carl/Desktop/freesurfer
Gen
On 8/17/10 9:14 AM, "Carl Dambkowski" wrote:
Hi, again (I've emailed once before),
I am trying to test my freesurfer installation and everyt
Hi, again (I've emailed once before),
I am trying to test my freesurfer installation and everything goes fine
(tksurfer, qdec, etc). However, once I get to:
recon-all -s bert -autoreco1
i get:
FREESURFER_HOME: Undefined variable.
However, I believe I've set it up properly with:
setenv FREESU
Hi!
I will like to try the beta CUDA support in 5.0. And I have some questions here
1. Are all needed libraries bundled in the release? Or I need to go to CUDA's
site to get those dependency? And if I need to, what are those dependency I
need to grab and install?
2. I have RH 5 64 bit lin
I've looked briefly at this with out data and cannot find any such bias
to one side or another. Do you have reason to believe that it actually
exists in your patient population? Do the images have any strong
intensity gradients from right to left? Another option is to take one or
two of your su
Hi all,
The total rh surface is always bigger than the lh surface (I've checked also
the cerebral cortex volumes and the rh are also bigger than the lh volumes).
I have the rh_medialorbitofrontal area bigger in 30 of my 32 subjects, but when
I compare the lateralorbitofrontalareas, these appear
Hello,
When trying running recon-all I am getting the following error:
#...@# Fix Topology rh Sat Aug 14 04:15:31 BRT 2010
ERROR: _FindFacePath: could not find path!
Darwin Fernanda-Palhanos-Mac-Pro.local 10.4.0 Darwin Kernel Version 10.4.0:
Fri Apr 23 18:28:53 PDT 2010; root:xnu-1504.7.4~1/RELE
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