Hello,
I would like to download the latest version of FreeView so I could use the
Recon Edit option. I've downloaded the latest version of FreeSurfer (v5.3), but
it seems that I have an older version of FreeView (v1.0). Could someone please
assist me in updating FreeView - I can't find the
Hi,
I’m looking to do some DTI analysis with dt_recon. I have Philips acquired DTI
images in par/rec. I ran dcm2nii and have retrieved the associated *bval, *bvec
and *nii.gz files that come out.
In the tutorial it mentions the -i flag requiring a dcm image. Is it possible
to pass a *.nii.gz
Hi,
I am trying to create a command line for data checking the same participant
over multiple longitudinal timepoints in freeview. However at the moment I am
running into issues.
Can someone provide me an example of a freeview command to be used if I wanted
to overlay the scans?
Any help is
Hi,
Is anyone aware of any issues that arise from overclocking and using
Freesurfer? I was looking to see how much it would speed up recon-all with
OpenMP using a stable overclock.
___
Bryan Chiu
Undergraduate Research Assistant
Aging, Mobility, and
Hi,
I need to overlay some functional imaging data onto a structural scan to create
some figures. How would I do this?
I tried an older tutorial but it seems the files don't exist anymore in the
tutorial dataset
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization). However
(PHTH)
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all CUDA error
Hi again experts,
What version of CUDA was used to compile the *_cuda files, on the FS 5.3 stable
version? Was it CUDA 5.0 or higher?
/Jordi
2014-07-03 18:25 GMT+02:00 Chiu, Bryan (PHTH)
bryan.c
.
Have you taken at look at the CUDA Developer's Guide wiki on the Freesurfer
site?
- Bryan
From: Jordi Delgado [jordi...@pic.es]
Sent: Thursday, July 03, 2014 12:36 AM
To: Chiu, Bryan (PHTH)
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all CUDA
(PHTH) bryan.c...@ubc.ca
Subject: Re: [Freesurfer] recon-all CUDA error (Chiu, Bryan (PHTH))
To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Message-ID:
680d9b8d5feaaf40a1a5878265424ca44a594...@s-itsv-mbx06p.ead.ubc.ca
Content-Type: text/plain; charset=iso-8859-1
Hi all,
I
Hi Chris,
If you could get support for CUDA 5.5 it would be marvelous. I'm quite
inexperienced with the CUDA programming (consider me an enduser), you would
have my full support.
I also have a computer here to do any testing if needed. I have a PC with
CentOS 6.5, Freesurfer 5.3.0, i7 4770k,
on the test setup of
that study, we have implemented a scheduler to manage K simultaneous recon-all
executions.
Thank you,
2014-07-02 19:06 GMT+02:00 Chiu, Bryan (PHTH)
bryan.c...@ubc.camailto:bryan.c...@ubc.ca:
Hi,
Turns out if you rename libcudart.so.6.0 to the 5.0 in your respective lib64
this to work.
-Bryan
Date: Fri, 27 Jun 2014 17:59:37 +
From: Chiu, Bryan (PHTH) bryan.c...@ubc.ca
Subject: [Freesurfer] recon-all CUDA error
To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Message-ID:
680d9b8d5feaaf40a1a5878265424ca44a594...@s-itsv-mbx06p.ead.ubc.ca
Hi,
I'm fairly novice at Linux and I've been trying to setup CUDA for recon-all. I
get an error as follows:
[TLA@COGMOB-linuxPC ~]$ recon-all -s bert -use-gpu -openmp 8
Testing for CUDA device:
/usr/freesurfer/bin/mri_em_register_cuda: error while loading shared libraries:
libcudart.so.5.0:
The output brain is that which I see from freeview. I usually check their sulci
and gyri to confirm if a scan is good. I resolved the issue by rerunning my
PAR/REC files through the same dicom to nifiti converter for all of them. It
turns out the person before me used a different tool which
Hi,
I'm attempting to do some longitudinal processing on a set of data with
subjects with up to 4 timepoint scans: Baseline, Midpoint, Final, 12 months
after Final.
When visually checking over a subject in Freeview, I notice that all of my
Midpoint runs are left-right flipped, where the other
There of course is some variability in the analysis due to the way the
segmentation happens. Your results are certainly not out of the ordinary for
the volume you are viewing. On average you can expect a ~1% variance between
several scans of the same subject.
If you want to know more I
Bump. Having the same problem with a similar setup.
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Hi,
Wanted to check in about Mac OS X and any effects on recon-all that I may not
be aware of. A while back the Mac was updated to 10.9.2 from some other version
of 10.x.x. I ran half of my recon-all on 10.x.x, and am running my 2nd half on
10.9.2. The update was due to some IT person thinking
Hi,
Trying to build a CUDA enabled PC for the lab to do processing for a variety of
neuroimaging programs including Freesurfer and FSL. Want to know input from
others about the 'recommended' PC and what the 'standard' is based on the
current PC prices and technology.
Sample build is from NCIX
Hi Douglas,
I've looked at the original images in freeview and they follow the correct
talairach coordinates. I've run mri_convert again and the files follow the
correct talairach coordinates. It appears this may have been a 'one-off' issue.
Will update after I autorecon everything.
- Bryan
Hi,
I am working on a dataset using free surfer.
I have NIFTII files which I am converting using mri_convert. Upon completion of
mri_convert, the orientations of the files are wrong. This likely leads to an
incorrect talairach (I was getting errors but used -notal-check) and leads to
an
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