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If you installed freesurfer using the .deb or .rpm installers on linux,
or the .pkg file on the Mac - then you should have a working Qt setup, e..g.,
to run freeview. In particular on linux, if you didn’t use the .rpm
or.deb freesurfer package ins
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Have you tried the latest Mac build of freeview? This has been fixed recently.
On Jul 30, 2023, at 11:02 AM, Ha Manh Luu
mailto:hal4...@med.cornell.edu>> wrote:
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From: Ha Manh Luu
Sent: Thursday, July 20, 2023
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Hello Gonzalo,
If you have not already done so, then I suggest installing the .deb
installer package for 7.3.2 from,
surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2/freesurfer_ubuntu18-7.3.2_amd64.deb
- by cd’ing to where you downloaded the abov
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Hi:
I have Ubuntu 18.04.4 LTS and freesurfer release
freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275. When I run
freeview, I got the error:
"This application failed to start because no Qt platform plugin could be
initialized. Reinstalling th
Sent: Wednesday, March 15, 2023 8:31 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freeview error
External Email - Use Caution
Hi Yujing,
It shows “-rw-rw-r-- 1 username staff 0 Mar 15 09:44 T1.mgz” and “error:
mghRead(/Users/results/sub-101/mri/T1.mgz, -1): read error”.
Best
-boun...@nmr.mgh.harvard.edu On Behalf Of tsengyuheng1...@gmail.comSent: Tuesday, March 14, 2023 11:05 PMTo: freesurfer@nmr.mgh.harvard.eduSubject: [Freesurfer] Freeview error External Email - Use CautionHi, I met some errors when showing recon -all results in Freeview. I could not
: Tuesday, March 14, 2023 11:05 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Freeview error
External Email - Use Caution
Hi,
I met some errors when showing recon -all results in Freeview. I could not open
the brainmask.mgz or the T1.mgz via the terminal or Freeview GUI. But they
External Email - Use CautionHi, I met some errors when showing recon -all results in Freeview. I could not open the brainmask.mgz or the T1.mgz via the terminal or Freeview GUI. But they worked well with MRIcron. Could you please give me some advice on it? The errors:error: mghRead(
ch 10, 2023 12:59 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Freeview error
External Email - Use Caution
Hi, I'm trying to open freeview in a linux node in my institution's computing
cluster and an error is coming up consistently - see below. Can you please
ad
External Email - Use Caution
Hi, I'm trying to open freeview in a linux node in my institution's
computing cluster and an error is coming up consistently - see below. Can
you please advise? Thank you.
agc01:~ moana004$ module list
> No Modulefiles Currently Loaded.
> agc01:~ moana
Would it be possible to send us the volume and the surface files so that we can
try to replicate the issue?
Thanks,
Ruopeng
On Mar 14, 2022, at 12:01 PM, Wen Wen
mailto:wenw2...@gmail.com>> wrote:
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Dear Freesurfer experts,
I’m running Freeview on a centos7
External Email - Use Caution
Dear Freesurfer experts,
I’m running Freeview on a centos7 computer and having the issue of loading
surface data and 1mm volume data. The error message is *Segmentation fault
(core dumped).* This issue remains no matter I work locally or remotely.
Howe
details in the attachment. What should I do to fix
it?Best Xiao-原始邮件-发件人:fsbuild
<fsbu...@contbay.com>发送时间:2021-11-18 03:05:29
(星期四)收件人: freesurfer@nmr.mgh.harvard.edu抄送: xux...@xii.ac.cn主题: Re:
[Freesurfer] freeview error after installation: Segmentation fault(core
dumped) /
freesurfer@nmr.mgh.harvard.edu抄送: xux...@xii.ac.cn主题: Re:
[Freesurfer] freeview error after installation: Segmentation fault(core
dumped) / free( ): invalid pointer, Aborted(core
dumped)External Email - Use
CautionHello Xuxiao, In a
terminal window in Ubuntu running under WSL, pleas
FS_LICENSE=$HOME/license.txt" >> $HOME/.bashrc". Do I need to create a
license file manually?
-原始邮件-
发件人:fsbuild
发送时间:2021-11-17 10:16:00 (星期三)
收件人: freesurfer@nmr.mgh.harvard.edu
抄送: xux...@xii.ac.cn
主题: Re: [Freesurfer] freeview error after installation: Segmentation
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Hello Xuxiao,
In a terminal window in Ubuntu running under WSL, please try just running a
simple X windows program like xeyes to test that your X-server is running on
Windows,
$ xeyes
(see attachment for what it should look like)
Keep an eye out f
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Hello Gian,
I suspect the freeview binary is not going to be able to run on Debian linux.
We don’t build or test on Debian linux, but freeview/freesurfer should be
fine on CentOS 6, CentOS7 and Ubuntu 18 for linux and also on Mac OS.
Maybe someone co
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Dear Freesurfer developers, I'm trying to use freeview but I'm having a lot
of problems. I'm not an expert in freesurfer neither in linux programming.
I followed all the instructions from the installation page of freesurfer,
unfortunately when I try to
Hello FreeSurfer Experts,
I'm attempting to install Freesurfer. I am trying to test my installation.
$>recon-all -i sample-001.nii.gz -s bert -all
$>recon-all -s bert finished without error at
Wed Mar 11 19:09:43 EDT 2020
done
However, after this I am getting an error message
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Hello Alek,
When you say you are running Ubuntu 14 via a Windows 10 PC, do you mean you are
running the add-on windows subsystem for linux (known as WSL) that allows you
run an Ubuntu shell on Windows 10? And then when you say you are
remotely vie
Is your work disk full?
On 9/17/19 10:22 AM, Miguel Ángel Rivas Fernández wrote:
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I tried in the command window where I started freeview but nothing
happened. This is the output
miguel@miguel-VirtualBox:~$ ls
/usr/local/freesurfer/subjects/4227/mri/brai
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I tried in the command window where I started freeview but nothing
happened. This is the output
miguel@miguel-VirtualBox:~$ ls
/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
El mar., 17 se
Can you run the command in the command window that you start freeview?
Ruopeng
> On Sep 16, 2019, at 5:11 PM, Miguel Ángel Rivas Fernández
> wrote:
>
> External Email - Use Caution
>
>
> Dear Ruopeng,
>
> I put that command in the freeview command console and this is the ou
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Dear Ruopeng,
I put that command in the freeview command console and this is the output
[FreeView] ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
This is not a shell. Only freeview commands are supported. Type '-h' for
all the available com
If you run:
ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
What does it show?
Ruopeng
On 9/16/19 4:29 PM, Miguel Ángel Rivas Fernández wrote:
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Dear Freesurfer devs,
I tried to open the brainmask.mgz file in freeview but I obtained this
error:
External Email - Use Caution
Dear Freesurfer devs,
I tried to open the brainmask.mgz file in freeview but I obtained this
error:
mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could
not open file
MRIread failed: Unable to read from
/usr/local/freesurfer/subj
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Hello freesurfer team,
How can ı fix the problem?
Ubuntu-brain:~$ freeview
Could not set locale
No such file or directory
This application failed to start because it could not find or load the Qt
platform plugin "xcb"
in "".
Reinstalling the applica
Hi, this should be fixed now in the OSX dev distribution.
best,
Andrew
From: on behalf of "Md. Mamun Al-Amin"
Reply-To: FS Help
Date: Saturday, September 22, 2018 at 1:15 AM
To: FS Help
Subject: [Freesurfer] Freeview error
External Email - Use Caution
Dear Experts
I
External Email - Use Caution
Dear Experts
I have been encountered a problem opening Freeview window in Mac Terminal.
Could you please help me troubleshooting this problem?
Here is the screenshot.
Thanks in advance.
--
Kind regards
Md. Mamun Al-Amin
Thanks that makes sense!
here is the text file and embedded just in case there is anything else to it
Thanks!
"Last login: Sat May 27 20:26:15 on ttys000
freesurfer-Darwin-lion-stable-pub-v5.3.0
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applicatio
The error message says it:
ERROR: MRISread: file
'/Users/schumman/Non-Inf_FS_5_3/0002_WIP_3DT1_SAG_SENSE_3_1.nii/surf/lh.area.pial'
has many more faces than vertices!
Probably trying to use a scalar data file as a surface!
You were not loading a correct surface file. lh.area.pial is a scalar da
actually the attachment doesn't have an extension, so I can't even look
at it. Can you just resend as text?
cheers
Bruce
On Sat, 27 May 2017, Schumman Resonance
wrote:
Attached is the full command line; as per a screen output Freeview quits.I
have not tested all surface files, but Freeview u
I'll take a look, but in the future can you just send this as text
embedded in the email instead of screen shots.
thanks
Bruce
On Sat, 27 May 2017, Schumman
Resonance wrote:
Attached is the full command line; as per a screen output Freeview quits.I
have not tested all surface files, but Fr
Attached is the full command line; as per a screen output Freeview quits.
I have not tested all surface files, but Freeview uploads fine pial, white,
inflated, orig, and sphere.
Thanks!
On Sat, May 27, 2017 at 8:46 PM, Bruce Fischl
wrote:
> Can you send us the full command line and screen output
Can you send us the full command line and screen output?
Cheers
Bruce
> On May 27, 2017, at 11:45 PM, Schumman Resonance wrote:
>
> Hi,
>
> Newbie question.
>
> When I try to upload a surface to Freview I get the following error:
>
>
> [0]PETSC ERROR:
>
Hi,
Newbie question.
When I try to upload a surface to Freview I get the following error:
[0]PETSC ERROR:
[0]PETSC ERROR: User provided function() line 0 in unknown directory
unknown file
[unset]: aborting job:
applicat
Hello all!
I know there are issues with freeview use on Ubuntu, but I hit a wall in fixing
them.
I am currently getting this error when typing "freeview" into the command
prompt:
"freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open
shared object file: No such file o
Hi Claudia
you need to send us your full command line and the various other
information we ask for when reporting issues (operating system, etc..)
thanks
Bruce
On
Tue, 20 Sep 2016, Claudia Dacquino wrote:
Hi all, after doing GLM analysis I'm trying to run freeview to see results,
but I get
Hi all,
after doing GLM analysis I'm trying to run freeview to see results, but I
get this warning:
Surface does not contain valid volume geometry information. It may not
align with volumes and other surfaces.
What's wrong?
I'm using 5.1 version.
Thanks to all.
Claudia
--
Dott.ssa Claudia D
Hi FreeSurfer Team,
I am trying to edit longitudinal data using FreeView. The original timepoints
were processed and edited using FreeSurfer 5.1. The longitudinal data was also
ran using FreeSurfer 5.1. I am currently trying to edit the longitudinal data
using FreeView, however FreeView seems
Dear all
I installed freesurfer as supposed for linux of centos 7.
I have a problem with freeview error.
After install was copleteted, Tying the command : "freeview"
-> freeview.bin: error while loading shared libraries: libXss.so.1: cannot
open shared object file: No such file or directory
So
What if you just load one surface:
freeview -f good_output/surf/lh.pial
Does it load?
Best,
Ruopeng
On 01/06/2015 03:23 PM, Hirsch, Gabriella wrote:
Hi,
I am trying to view surfaces in 3D using Freeview on my own subject
data via this command (replacing the subject name);
freeview -f
go
Hi,
I am trying to view surfaces in 3D using Freeview on my own subject data via
this command (replacing the subject name);
freeview -f
good_output/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \
good_output/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflate
Hi All,
I was hoping that someone might be able to help me.
When I load a surface into freeview (e.g.
/Applications/freesurfer/subjects/fsaverage/surf/lh.inflated), I get an error
in my terminal:
Did not find any volume geometry information in the surface
When I go on to load in my multiple co
Dear doug, bruce and others,
Previously I could not view "
freeview -f
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.negative.sig.ocn.annot
Dear Ruopeng,
Thanks for your help, Ruopeng.I learned the groupanalysis by manu
ofhttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis. I ran this
command on your tutorial data (buckner data). Would you please tell me where my
hardware setup is inappropriate?
Thanks.
All the best.
R
Dear Ruopeng,
Thanks for your help, Ruopeng.I learned the groupanalysis by manu
ofhttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis. I ran this
command on your tutorial data (buckner data). Would you please tell me where my
hardware setup is inappropriate?
Thanks.
All the best.
Hi Bruce and others,
Thanks Bruce. I had installed the centos6.5 x86_64 in my computer, and
setup the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz,
and I setup the nvidia drivers completely. Then I tried to run this
command:
freeview -f
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=
Hi Bruce and others,
Thanks Bruce. I had installed the centos6.5 x86_64 in my computer, and setup
the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz, and I setup the
nvidia drivers completely. Then I tried to run this command:
freeview -f
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overla
Hi Bruce and others,
Thanks Bruce. I had installed the centos6.5 x86_64 in my computer, and setup
the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz, and I setup the
nvidia drivers completely. Then I tried to run this command:
freeview -f
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overla
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