Great. Thanks for the information.
-Zeke
On 08/22/2014 04:18 PM, dgw wrote:
> Just to add. If you are not using the CUDA options (which in my
> understanding aren't being updated anyway), I find that the gpu
> included in modern Intel cpus is more than sufficient for my
> FreeSurfer and MNE uses.
Just to add. If you are not using the CUDA options (which in my
understanding aren't being updated anyway), I find that the gpu
included in modern Intel cpus is more than sufficient for my
FreeSurfer and MNE uses.
HTH
D
On Fri, Aug 22, 2014 at 4:15 PM, Z K wrote:
> Tommi,
>
> Here at the Martin
I'm not entirely sure what you mean by that, but if you add
--no-resample to mri_vol2vol it will not change the pixels at all and
just update the geometry info in the header so that it shares an RAS
space with the anatomical
On 08/22/2014 04:04 PM, Jackie Lam wrote:
> Hello all,
>
> I’m trying
Tommi,
Here at the Martinos Center we use the proprietary drivers from NVIDIA.
We have no reasons to believe the Nouveau drivers would work better, but
that isnt to say one doesnt exist.
-Zeke
On 08/22/2014 03:23 PM, r...@nmr.mgh.harvard.edu wrote:
>
> Hi,
>
> Is there a FreeSurfer/MNE (maybe
Hello all,
I’m trying to register and transform a functional image to my high resolution
anatomical image. As I understand, it can be done with mri_vol2vol, but the
resulting functional image is resampled into 1x1x1 voxels (the resolution of my
high res anatomical). Is there a way to transform
Hi,
Is there a FreeSurfer/MNE (maybe even FSL, TrackVis) recommendation to use
the "noveau" drivers that come with CentOS 6.5 or would it be better to go
with the proprietary drivers from NVIDIA?
I would imagine that since FS 5.3 does not use GPU for analysis, this is
mainly relevant for visuali
These dicoms are run-length encoded, which FS does not read. What you
can do is the following
cd /place/where/dicoms/are
foreach dcm (*.dcm)
dcmdrle $dcm $dcm
end
then run mri_convert, like
mri_convert -it dicom IMG10.dcm ct.mgz
I did this and it converts, but the slice thickness looks w
Hi Freesurfers,
Apologies, I've never used this format before.
Here's the error:
FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0
Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
RedHat release: CentOS release 6.5 (Final)
Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_
Hello,
The latest version of mris_decimate for MacOS platform can be downloaded
using this the following link:
ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/Darwin_lion_x86_64/mris_decimate
-Zeke
On 08/21/2014 04:45 PM, Nicholas Heugel wrote:
> So I just redownloaded the r
Hi all,
I am getting an error that seems common for people running LGI where it
crashes due to a topological defect.
I have run mris_euler_number and everything looks fine. Plus, I went
through each slice and made sure the surfaces looked good.
Any advice on any other steps I can take? I have al
Hi Mia, please follow the instructions on the web site below for
submitting bug reports.
thanks
doug
On 08/22/2014 12:37 PM, Borzello, Mia wrote:
> Right, sorry. I was running a command with mri_convert in order to convert
> the ct dicoms to mgz format. The error I ran into was:
> UseSliceScale
Hmm, that means that 3dvolreg.afni that comes with FS does not run
properly on your system. Do you already have a full version of AFNI
installed on your system?
doug
On 08/22/2014 05:00 AM, Milde, Christopher wrote:
> Dear Freesurfer Experts,
>
> I'm struggling with running only motion correct
Right, sorry. I was running a command with mri_convert in order to convert the
ct dicoms to mgz format. The error I ran into was:
UseSliceScaleFactor 0 (slice 0: 1)
Segmentation fault (core dumped)
Thanks,
m
From: freesurfer-boun...@nmr.mgh.harvard.edu
[
Looks like your fsgd file was created under a windows machine or old
macos, try converting the fsgd like this
cat old.fsgd | sed 's/\\r/\\n/g' > new.fsgd
On 08/22/2014 02:51 AM, Jürgen Hänggi wrote:
> Dear FS experts
>
> We run mri_glmfit and encountered the following error:
>
> INFO: gd2mtx
Hi Mia, do you realize that your description of the problem is too vague
for us to help you? If you want help in a timely fashion, please include
more detail like the problem you ran, the command-line arguments, the
terminal output, etc. Please see the following web page for the types
informa
Can you include the previous correspondence? I've already forgotten the
details of the previous email
doug
On 08/22/2014 12:05 PM, Meryem Ayse Yucel wrote:
> Hi Doug,
>
> I used mkheadsurf function.
>
> Meryem
>
>
> ___
> Freesurfer mailing list
> Free
Hi Freesurfers,
I'm in the process of creating the ct.mgz file, but it is erroring and saying
there is a "segmentation fault (core dumped)."
What can I do to remedy this?
Thanks,
m
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https://mai
Hello Nicholas
I can verify that mris_decimate was not included in the Lion Freesurfer
v5.3 release. I am not exactly sure why, but I suspect it has to do with
compatibility issues with some of the 3rd party libs required to
successfully build on the OSX platform.
I am working on building mris
Hi Doug,
I used mkheadsurf function.
Meryem
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The information in this e-mail is intended only for the person to whom it is
addresse
Hello,
I was just looking for some suggestions for the best way to manually edit
an image such as the one attached. As you can see, there is both white and
gray matter excluded from the pial surface on the medial aspect of the
right hemisphere. Is this best corrected by adding voxels to the
brainm
VirchowRobin spaces is another name for those (they are normal in small
amounts, not old strokes, and filled with CSF-like fluid).
Peace,
Matt.
On 8/21/14, 9:23 AM, "Bruce Fischl" wrote:
>Hi Mohammed
>
>these are dark regions, usually in inferior pallidum/putamen. There
>intensity is differen
Thank you.
Mohammed
On Thu, Aug 21, 2014 at 10:23 AM, Bruce Fischl
wrote:
> Hi Mohammed
>
> these are dark regions, usually in inferior pallidum/putamen. There
> intensity is different enough from gray matter that having it be a separate
> class helps us label them more accurately. They could
Hi
I have a very minor question about the naming scheme for tracula output.
I have the folders anat and anatorig in the dlabel folder. Am I right that:
anatorig is the T1 image in "freesurfer space" (256 x 256 x 256; LIA)
anat is a rotated version of the T1 image in freesurfer space that lines up
Dear Freesurfer Experts,
I'm struggling with running only motion correction.
After running mktemplate-sess which ran well, the mc-sess terminates with the
following error.
The terminal otput is attached:
"3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr
ERROR: 3dv
Hi Francesco
if you upload one of the dicom series that causes the problems we will
take a look. If you can also send us the rawavg.mgz after your successful
recon-all from the .nii that would also help
cheers
Bruce
On Wed, 20 Aug 2014, Francesco
Deleo wrote:
Hi all!
Sorry for my late ans
See if this helps:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 8/20/14 7:07 AM, Alejandra Machado wrote:
Hello,
I was wondering if FS has an output mask (labelled volume) for each
tissue types (gm+wm+venctricular_csf) that I can then turn into each
subject's native spa
Hmmm, sounds like a job for Ruopeng ...
On 8/20/14 2:04 PM, C.P. Frost wrote:
Thanks for the reply, Doug.
The main problem is that areas not included in my custom table appear
colored in freeview. These areas' numbers correctly correspond to
their indices on the default FreeSurferColorLUT,
So I just redownloaded the recent version of Freesurfer for Mac, Lion
operating system, making sure to grab the most recent version. I need to
use the tool mris_decimate but it is not in any of the files I downloaded,
nor was it in any of the files I had previously. Where can I get
mris_decimate,
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