On 2 December 2016 at 09:38, Parzer, Peter
wrote:
> I just tried recon-all with the -use-gpu flag from the current development
> version of freesurfer (freesurfer-Linux-centos6_x86_64-dev-20161123-bb356e0),
> but it fail with the message that is cannot open libcudart.so.5.0.
>
> I have the curr
I was told its be an MNI structure... found in the dependency package
undercentos6-x86_64-packages/mni, and build from this source tarball:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mni.srcbuild.June2015.tgz
On 12/02/2016 05:45 PM, Melvin Robinson wrote:
>
> OK, this so
OK, this sounds good. Where is General_transform defined? I could try to find
a fix.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Z K
Sent: Friday, December 2, 2016 4:43 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Bu
My guess is its a compatibility issue with the dependency package and
Fedora 23. Although I would have guessed it would have worked, the build
instructions have only been tested on Ubuntu, Debian and CentOS distros.
I will install Fedora23 on laptop to see if I can properly diagnose the
issue,
Hello Freesurfer, I replaced wm.seg.mgz from freesurfer with white matter +lesion (called it wm.seg.mgz before replacing) from lesion explorer. Do I run recon-all -autorecon2-wm -autorecon3 -s fsdir ( I know -autorecon2 -wm is used when you make edits to wm.mgz) or should I just run recon-all -aut
Hi Sean
none of these things are easy to do. Unless you have a compelling reason
you are better off letting recon-all do it's thing. Otherwise you will
send lots more person time fixing things that it would have gotten right
if you had let it
cheers
Bruce
On Fri, 2 Dec 2016, Hatton, Sean wro
Hello,
We are just interested in generating the white and pial surfaces without
segmentation.
1. Are there additional switches for running mris_make_surfaces without aseg
(for -white section) or apar.annot (for -pial section)?
2. We would like to control intensity values - can we specify tissu
OK the OS is Fedora 23 and here is my configure line:
./configure --with-pkgs-dir=../dependencies/centos6-x86_64-packages
--disable-Werror
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Z K
Sent: Friday, December 2, 2016 4:21 PM
To: freesu
What operating system are you using and what is the exact configure command?
On 12/02/2016 04:49 PM, Melvin Robinson wrote:
> I'm having a small (?) build problem with freesurfer. My configure line
> merely points to the dependencies package and the--disable-Werror flag,
> but I get the following
I'm having a small (?) build problem with freesurfer. My configure line merely
points to the dependencies package and the--disable-Werror flag, but I get the
following error. Grepping through the source I cannot find where the structure
is defined.
gcc -DHAVE_CONFIG_H -I. -I.. -I../include
Hi FreeSurfer team,
I'm trying to create a base for 5 time points in freesurfer version 5.1 and
have run into issues with my job submission exiting in error. This is the
command I originally tried using:
runFreeSurferSinglePBS -N huey.sw -r "-all -base P040_2yr5tp -tp P040b_v0 -tp
P040_v6 -tp
Im not sure I follow what you mean when you say "the file convert into a
text file." The FREESURFER_HOME/mni/bin/nu_correct file is a text file
(its a script). Try making sure that it is still executable:
$> chmod a+x $FREESURFER_HOME/mni/bin/nu_correct
On 12/02/2016 02:31 PM, jean-simon.bo
Looks like a permissions issue. Either open the permissions on the
$FREESURFER_HOME/subjects directory. Or, try copying over the
sample-001.mgz file to somewhere where root permissions are not
required, then run the same command.
-Zeke
On 12/02/2016 01:08 PM, Brad Matushewski wrote:
> OK - I w
Hi Zeke,
I'm trying to make modification on the first line of nu_correct (perl file) and
when I do the modification the file convert into a text file. I've tried to run
freesurfer with the text file but I got a message of nu_correct command not
found at the begining of the process.
Do you hav
OK - I went with Ubuntu. I had trouble getting the license.txt file in place
due usr/local requiring authentication. I bypassed the password part by
leading using "sudo gedit" which obviously prompted me for a password but let
me edit / paste license text into file.
When I tried this:
$> cd
It will handle mosaics (as the mosaics that fMRI data will come in).
Hard to say what is going on without more specifics (command line,
terminal output)
On 12/02/2016 10:26 AM, Marianna Riello wrote:
>
> Dear all,
>
> I am wondering whether mri_convert can compute .mgz files for the
> reconstr
You can run it like that or with --osgm (instead of --fsgd and --C),
osgm = one sample group mean.
On 12/01/2016 07:13 PM, Foo Keat Mak wrote:
> Hi Doug,
> I have pasted the correspondences below. My question is, if I want to
> identify the PCs in a group for a single modality (PET), how should
Dear all,
I am wondering whether mri_convert can compute .mgz files for the
reconstructions with the 'Mosaic Format SIEMENS DICOM files'.
I have been computing .mgz with the enhanced format .dcm so far, and it always
worked.
I have used mri_convert to compute .mgz from .nii (I previously transfo
Hi,
I just tried recon-all with the -use-gpu flag from the current development
version of freesurfer (freesurfer-Linux-centos6_x86_64-dev-20161123-bb356e0),
but it fail with the message that is cannot open libcudart.so.5.0.
I have the current cuda version install (8.0).
Does freesurfer only w
Dear Sebastian,
I suspect that you might be using the version from late 2015.
Please download the recently released beta from here:
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall6.0-beta
Cheers,
/Eugenio
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
Uni
Ubuntu 14.04.5 LTS
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Z K
Sent: December 2, 2016 8:42 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Ubuntu or Centos?
Which version of Ubuntu are you trying to install? I ask beca
Which version of Ubuntu are you trying to install? I ask because I too had
issues when installing ubuntu14 on a new laptop with laptop with UEFI.
Try using Ubuntu16 instead if you haven't already. And more luck with that, and
here is a link to more information as setting up these dual boots has
Dear Eugenio,
thanks for your fast response.
I am using FS 6.0.0beta (ubuntu-xenial-amd64).
Best,
Sebastian
- Original Message -
From: "Iglesias Gonzalez, Eugenio"
To: "Freesurfer support list"
Sent: Friday, December 2, 2016 2:23:15 PM
Subject: Re: [Freesurfer] HC Subfields LongHippo
I have had some issues with Ubuntu (installation stops before completing). I
am currently trying to get a dual boot set up with Windows 10. Someone
mentioned I should try Centos instead of Ubuntu?
Thoughts?
Pros vs Cons?
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.e
Dear Sebastian,
Are you using a dev version? If you are using the 6.0 beta, the command should
definitely be there.
Can you please send me the exact version you’re using?
Cheers,
/Eugenio
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http:/
Dear Freesurfer Community,
I ran the Freesurfer longitudinal pipeline for my subjects (7T, T1_data, 2
timepoints each).
Now I want to continue with the longitudinal segmentation of hippocampal
subfields:
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields
However, when I
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