lt;pgt;Dear FS experts,lt;br /gt;I use qdec to do two group study. in QDEC,
it set Normal = 1 and Disease = 2, useamp;nbsp;AGE as covariateamp;nbsp;and
apply DODS model, after analyze group cortical thickness, it showed significant
negative T value (blue color) in some brain areas. I have two
Thanks a lot, it works.
just waiting 24 hours.
Best regards,
Carolina
2011/6/10 rspr...@nmr.mgh.harvard.edu
Hi Carolina,
Sorry My bad. I was inaccurate in my previous message.
-subject should work.
Assuming that the MPRAGE of your subject is under the following directory:
Do you mean your individual subject after running through FS has a file
called t1.mgz and not T1.mgz? Something is definitely wrong there. Can
you send the log file?
doug
t...@ms36.hinet.net wrote:
Dear FS experts,
I use FS5.1 and previous data run on other machine. When I try to
They are in our own coordinate system, documented on our wiki. Do a
search for coordinates to find the page.
doug
soft.join Huang wrote:
Hi all,
I have a question about the coords of vertex in ?h.white file.
I load the ?h.white file in Matlab and get a variable called
vertex_coords, and
That interpretation is correct. The MNI coords are MNI305. The last
field is to hold a statistic. If it is 0, it means that the field was
not filled with anything.
doug
ZhiLiangLong wrote:
Hello:
I use qdec to generate statistical significant areas and draw ROI and
map the ROI to each
Dear Tracula Users
I completed trac-all -prep -c without difficulty or errors. However, without
any changes to my director structure or my Tracula config file I am
receiving the following errors when running trac-all -bedp -c. I will copy
and past my config file contents below the error messages.
Hi Deryk,
Is bedpostx properly installed in your computer? Can you just type
bedpostx in your terminal to see if it gives this message?
Usage: bedpostx subject directory [options]
expects to find bvals and bvecs in
Hi Priti
Thank you for your quick replay. The following files / folders are listed in
my dmri.bedpostx directory:
**
/usr/local/freesurfer/subjects/C001/dmri.bedpostX$ ls
commands.txt diff_slices logs monitor xfms
Hi Priti
In addition, if I run bedpostx from the command line as follows:
bedpostx /usr/local/freesurfer/subjects/C001/dmri
it works just fine without errors.
Deryk
Deryk S. Beal, Ph.D., CCC-SLP, S-LP(C), Reg. CASLPO
Speech-Language Pathologist
C.I.H.R. Post Doctoral Research Fellow
Hello Freesurfers,
I have Brodmann Area binary masks in the ICBM MNI 152 space, that I acquired
using WFU_PickAtlas toolbox in SPM. These
masks are .nii files, and have a RAS orientation.
I am trying to resample these masks into the fsaverage MNI 305 space,
specifically with the dimensions
Hi Sorry for bothering you again, but I am not sure I understand.
I was running whole brain correlation analysis (voxel by voxel). BUT for
comparison purposes, I want to compute region by region correlation matrix.
So, I want to divide up the brain into freesurfer parcellated regions - i.e.
Hi Carolina,
Do you know how can I run Freesurfer just to get some Benchmark Numbers
and to Check GPU Performance using Cuda?
Thanks,
*Leo Souza*
On 06/13/2011 07:04 AM, Carolina Valencia wrote:
Thanks a lot, it works.
just waiting 24 hours.
Best regards,
Carolina
2011/6/10
When you run recon-all, it will create a recon-all-status file in the
scripts directory. This has the start times of all the processes, so you
can work out how long each took. This will be wall clock time, so take
that into account.
doug
Leo Souza wrote:
Hi Carolina,
Do you know how can I
Yes, I did that, but it doesn't actually uses the GPU to do that, only CPU.
GPU percentage is 0%. (you can check it by do running: nvidia-smi -q
-d UTILIZATION -l 3 if your'e using any recent drivers.
Thanks,
*Leo Souza*
On 06/13/2011 02:44 PM, Douglas N Greve wrote:
When you run
Sorry my typos, got a weird keyboard here.
Thanks,
*Leo Souza*
On 06/13/2011 03:27 PM, Leo Souza wrote:
Yes, I did that, but it doesn't actually uses the GPU to do that, only
CPU.
GPU percentage is 0%. (you can check it by do running: nvidia-smi -q
-d UTILIZATION -l 3 if youŕe using any
Try adding -use-cuda to recon-all
Leo Souza wrote:
Yes, I did that, but it doesn't actually uses the GPU to do that, only
CPU.
GPU percentage is 0%. (you can check it by do running: nvidia-smi -q
-d UTILIZATION -l 3 if your'e using any recent drivers.
Thanks,
*Leo Souza*
On
Hi Deryk - Trac-all doesn't call the version of bedpostx under the FSL dir
but a specially modified version in the freesurfer distribution (called
bedpostx_seychelles for historical reasons).
It's fine to run bedpostx directly since that works for you. You can also
upload the data set for
No, if usemaskanat = 1, then the diffusion mask that comes from applying
bet to the lowb volume will not be used for tractography. A dilated
version of aparc+aseg will be used as a mask instead, which is typically
more reliable than trying to find the right bet threshold.
On Fri, 10 Jun
-use-cuda is invalid I think, but I did -use-gpu and see what I get:
[root@cuda-final2 bin]# ./recon-all -use-gpu
Testing for CUDA device:
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2010 NVIDIA Corporation
Built on Thu_Nov__4_12:44:17_PDT_2010
Cuda compilation tools, release 3.2,
recon-all -s bert -all -use-gpu
-- iOS 4.3
Em 13/06/2011, às 21:30, Leo Souza lso...@nvidia.com escreveu:
/recon-all -use-gpu
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