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
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:/
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 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
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
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
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
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 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
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
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
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
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
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
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
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
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
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
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
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
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 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
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,
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
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
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
26 matches
Mail list logo
