Re: [Freesurfer] freeview -v file stuck loading at 99% in 7.2 but not 6.0.1

you might have that write to that subdir. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Drucker, Daniel Date: Tuesday, November 15, 2022 at 3:01 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] freeview -v file stuck loading at 99% in 7.2 but not 6.0.1 * External Email

[Freesurfer] freeview -v file stuck loading at 99% in 7.2 but not 6.0.1

Hi, If I do: $ freeview -v myfile.nii.gz If I'm pointed at my 6.0.1 freesurfer, this works fine. In 7.2, the freeview window pops up, the loading bar gets to 99%, then then nothing else happens. I'm not sure what to do to debug this further. -- Daniel M. Drucker, Ph.D. Director of IT

Re: [Freesurfer] Freeview on WSL in Windows 10

Hello Monica, The login page you display is not accessible to the public. We have information about how to get started with WSL on the public wiki pages, e.g., https://surfer.nmr.mgh.harvard.edu/fswiki/FS7_wslWe talk about installing WSL version 1 and WSL version 2, though it reads like

Re: [Freesurfer] Freeview: missing voxels in reconstructed surfaces

This appears to be a rendering artifact that happens sometimes with remote display. Are you viewing remotely from a Windows machine? Ruopeng On Oct 18, 2022, at 9:45 AM, Sarah Lavelle mailto:lavel...@tcd.ie>> wrote: External Email - Use Caution Dear Freesurfer, I have an issue when

Re: [Freesurfer] Freeview does not show images

External Email - Use Caution Did it say the driver was installed successfully? I’m wondering if the driver did not install because it does not support your machines hardware for some reason. But it should tell you if it cannot be installed. You can tell if the DCH driver is

Re: [Freesurfer] Freeview does not show images

External Email - Use Caution Hi Ruopeng, I tried to run the glxgears command in the WSL Ubuntu subsystem, but it doesn't show me the gears. I am having the same issue as this thread linked here:

Re: [Freesurfer] Freeview does not show images

Are you able to run glxgears command? Do you see spinning gears? Ruopeng On Oct 6, 2022, at 4:28 AM, Justina Lee mailto:justinale...@gmail.com>> wrote: External Email - Use Caution To whom this may concern and can help, I am currently trying to run Freeview under the Windows

Re: [Freesurfer] Freeview does not show images

External Email - Use Caution I don’t think you told us what you installed for freesurfer in WSL. The freesurfer installation should match the version of Ubuntu Linux that WSL installed. You can check the Ubuntu OS version in the Ubuntu terminal window with, $ cat

Re: [Freesurfer] Freeview does not display image

External Email - Use Caution With regards to WSL, there is probably something preventing the X-server from correctly displaying graphics. Instead of running freeview you could try a simpler command to test X-window graphics. One command is “xeyes” which you can look for and try

Re: [Freesurfer] Freeview does not display image

External Email - Use Caution Hello R, Sorry I wasn’t so clear on my part. I am using ubuntu linux on the windows subsystem linux (WSL). I followed these instructions at

Re: [Freesurfer] Freeview does not display image

External Email - Use Caution Hello Justina, We need to know what your setup is on Windows for running Linux in order to help with running freeview. It reads like you are not using VirtualBox to run the Linux Ubuntu OS, I do not have VirtualBox installed ... So it’s not clear to

[Freesurfer] Freeview does not display image

External Email - Use Caution To whom that can provide any insight, I am currently using Ubuntu on windows to open freeview to show some data. My issue at hand is that freeview does not show any images, despite changing the window levels (contrast and brightness). Using the

[Freesurfer] FreeView feature request

External Email - Use Caution I am looking set up freesurfer to do two things. If they are not currently possible then I would like to submit two feature requests for freeview. Here they are When making voxel edits, it would be useful to see all voxels the mouse is pointing to.

Re: [Freesurfer] Freeview quitted unexpectedly

External Email - Use Caution Hello Danesh, Try putting your license.txt file into your home directory and setting the environment variable FS_LICENSE to point to it. $ export FS_LICENSE=$HOME/license.txt$ cd $HOME$ cat $FS_LICENSE… you should see your email address used to

[Freesurfer] Freeview quitted unexpectedly

External Email - Use Caution Dear support team, After installing Freeview, I tried to load a volume, while checking how it works with samples, from the subject folder in the Freesurfer folder. Unfortunately after choosing the file, Freeview crashed out and popped up an error

Re: [Freesurfer] Freeview quits unexpectedly on macOS Big Sur

freesurfer@nmr.mgh.harvard.eduSubject:[Freesurfer] Freeview quits unexpectedly on macOS Big SurExternal Email - Use CautionHello,I have installed Freesurfer 7.3.2 on macOS Big Sur, Version 11.6.8. The installation was successful, but every time I need to open freeview, it quits unexpectedly.The

Re: [Freesurfer] Freeview quits unexpectedly on macOS Big Sur

rd.edu Subject: [Freesurfer] Freeview quits unexpectedly on macOS Big Sur External Email - Use Caution Hello, I have installed Freesurfer 7.3.2 on macOS Big Sur, Version 11.6.8. The installation was successful, but every time I need to open freeview, it quits unexpectedly. The envir

[Freesurfer] Freeview quits unexpectedly on macOS Big Sur

External Email - Use Caution Hello, I have installed Freesurfer 7.3.2 on macOS Big Sur, Version 11.6.8. The installation was successful, but every time I need to open freeview, it quits unexpectedly. The environment seems to be set up correctly and I have also downloaded my

Re: [Freesurfer] freeview crashes after new fs install

External Email - Use Caution The wiki information may be out of date. Having multiple versions of freesurfer installed on your system may cause running an application bundle like freeview.app to crash if the system is confused about which version of freesurfer is installed. So

[Freesurfer] freeview crashes after new fs install

External Email - Use Caution Hi, I recently installed the new FS on my mac. I renamed my old "freesurfer" folder as instructed on the wiki. However now freeview crashes. it opens but when i try to load volume it crashes. Below you will find the report. (this happens if I use

Re: [Freesurfer] Freeview Closes Unexpectedly

External Email - Use Caution You need to use the sudo command to modify something under /Applications, so you could do$ sudo cp ~/Downloads/license.txt /Applications/freesurfer You could also just set FS_LICENSE to point to license.txt% setenv FS_LICENSE~/Downloads/license.txt

Re: [Freesurfer] Freeview Closes Unexpectedly

External Email - Use Caution Thank you! When I try to copy the license.txt file I receive this: % cp ~/Downloads/license.txt /Applications/freesurfer cp: /Applications/freesurfer/license.txt: Permission denied How can this be resolved? On Fri, Jul 22, 2022 at 6:37 AM Wang,

Re: [Freesurfer] Freeview Closes Unexpectedly

External Email - Use Caution Hi, To make sure, can you send me the instructions on how to download the FS license file? On Fri, Jul 22, 2022 at 1:31 AM Wang, Ruopeng wrote: > Have you install the FS license file properly? Another thing to check is > to make sure you have

Re: [Freesurfer] Freeview Closes Unexpectedly

Have you install the FS license file properly? Another thing to check is to make sure you have granted freeview permission to access your disk files. You can check it in the system preferences. Ruopeng On Jul 21, 2022, at 12:31 PM, user2038...@gmail.com wrote:

[Freesurfer] Freeview Closes Unexpectedly

External Email - Use Caution Hi, When I try to open any files in Freeview on a MacBook, the application closes unexpectedly. I only receive a message from Apple that says "Freeview quit unexpectedly" but gives no reason. This happens after I open the application and try to load a

[Freesurfer] freeview and dmri_trk2trk

External Email - Use Caution Hello freesurfer experts, I have been using TRACULA to analyze my group of images and I have noticed a bug or not. But I would like to comment it so that you can help me to solve it. I embed the two files with the dmri_trk2trk function. -

Re: [Freesurfer] Freeview GUI overlay and registration

*Date: *Wednesday, June 8, 2022 at 11:15 AM *To: *freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Freeview GUI overlay and registration You will need an lta file that maps from the anatomical to the fmri. You can get this with something bbregister --mov template.nii.gz --s subject --t2

Re: [Freesurfer] Freeview GUI overlay and registration

You will need an lta file that maps from the anatomical to the fmri. You can get this with something bbregister --mov template.nii.gz --s subject --t2 --reg reg.lta where template.nii.gz is the fmri motion correction template or the mean fmri (I forgot what it is called in FSL) On 6/3/2022

Re: [Freesurfer] Freeview XDG_runtime_dir not set

This thread might be helpful: https://stackoverflow.com/questions/59790350/qstandardpaths-xdg-runtime-dir-not-set-defaulting-to-tmp-runtime-aadithyasb Ruopeng On Jun 5, 2022, at 9:29 PM, Manuela Dorado Novoa mailto:manue...@uw.edu>> wrote: External Email - Use Caution Hi Freesurfer

Re: [Freesurfer] Freeview XDG_runtime_dir not set

External Email - Use Caution I've seen XDG_RUNTIME not be set/recognized if you are logged in as root/admin user or prefacing your commands with sudo when you run them logged in as a normal or non-privileged user. It might help for us know what operating system you are on, what

[Freesurfer] Freeview XDG_runtime_dir not set

External Email - Use Caution Hi Freesurfer team, I am having issues launching freeview from my linux terminal. My freesurfer works fine but when I call freeview it opens but I can't load images, I get an error message in my terminal that says: "QStandardPaths: XDG_RUNTIME_DIR not

[Freesurfer] Freeview GUI overlay and registration

Hi Freesurfer experts, I am trying to use the Freeview GUI to load fMRI BOLD activation data (analyzed in FSL) and project on the inflated surface. I used the feature “Overlay/Load generic” and was prompted to select overlay file and/or apply registration. The selected overlay file didn’t seem

Re: [Freesurfer] [Freeview] View Flatmap

in freeview, runsomethiing like freeview -f rh.white:patch=rh.full.flat.patch.3d The rh.white is just there to give freeview a full surfce to load. You will only see your patch On 4/14/2022 4:30 AM, Morgenroth Elenor wrote: External Email - Use Caution Dear Freesurfer Experts, I

Re: [Freesurfer] freeview crashes

External Email - Use Caution Hello Stephen, I'll assume the VM is setup according to the online instructions, e.g., the VM is assigned 8G of RAM and 2 cores from the host machine. I'll also assume you are opening files with freeview from within the VM's virtual disk, e.g.,

Re: [Freesurfer] Freeview error on centos7

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: External Email - Use Caution Dear Freesurfer experts, I’m running Freeview on a

[Freesurfer] Freeview error on 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.

Re: [Freesurfer] Freeview problem - can't see surfaces, hidden behind volumes

-server-release-notes%2F%3Fsource%3DFastX3-3.2.34 From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Wang, Ruopeng Date: Saturday, 19 February 2022 at 1:28 am To: Freesurfer support list Subject: Re: [Freesurfer] Freeview problem - can't see surfaces, hidden behind volumes

Re: [Freesurfer] Freeview problem - can't see surfaces, hidden behind volumes

February 2022 8:25 AM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Freeview problem - can't see surfaces, hidden behind volumes It sounds like a remote display issue. Are you connecting from a Windows machine? If so what x-term software do y

Re: [Freesurfer] Freeview problem - can't see surfaces, hidden behind volumes

on my issue… Any help would be appreciated Thanks! Harriet p.s., I am using freesurfer/ freeview on a remote machine of my university. They inform me no updates have been performed CODE freeview -v mri/T1.mgz \ mri/brainmask.mgz \ mri/wm.mgz:vis

Re: [Freesurfer] Freeview Transform Volume tool - output nifti keeps rotations but loses translations

:* freesurfer-boun...@nmr.mgh.harvard.edu *On Behalf Of *Wang, Ruopeng *Sent:* Tuesday, December 14, 2021 6:12 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Freeview Transform Volume tool - output nifti keeps rotations but loses translations What version of Freesurfer are you

Re: [Freesurfer] Freeview Transform Volume tool - output nifti keeps rotations but loses translations

PanksFrom:freesurfer-boun...@nmr.mgh.harvard.edufreesurfer-boun...@nmr.mgh.harvard.eduOn Behalf OfWang, RuopengSent:Tuesday, December 14, 2021 6:12 PMTo:Freesurfer support list freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] Freeview Transform Volume tool - output nifti keeps rotations but loses

Re: [Freesurfer] Freeview Transform Volume tool - output nifti keeps rotations but loses translations

To: Freesurfer support list Subject: Re: [Freesurfer] Freeview Transform Volume tool - output nifti keeps rotations but loses translations What version of Freesurfer are you using? Would it be possible to send us the volume files before and after the rotation? Best, Ruopeng On Dec 14, 2021, at 6:10

Re: [Freesurfer] Freeview Transform Volume tool - output nifti keeps rotations but loses translations

What version of Freesurfer are you using? Would it be possible to send us the volume files before and after the rotation? Best, Ruopeng On Dec 14, 2021, at 6:10 PM, Christopher Panks mailto:cpa...@uw.edu>> wrote: External Email - Use Caution I’m trying to get images of post-mortem

[Freesurfer] Freeview Transform Volume tool - output nifti keeps rotations but loses translations

External Email - Use Caution I'm trying to get images of post-mortem brains, some from cadavers, some excised, into standard space. I'm new to Freeview, so I'm not sure if I'm doing something wrong, or my expectations are wrong. I find the Transform Volume tool easy to use to

Re: [Freesurfer] Freeview grey matter, white matter and Tracula outputs

y, November 22, 2021 8:59 PM To: Freesurfer support list Subject: Re: [Freesurfer] Freeview grey matter, white matter and Tracula outputs External Email - Use Caution Hi Anastasia, I tried to visualize the RD.nii with the following steps, however, it doesn't represent well as fa.nii d

Re: [Freesurfer] Freeview grey matter, white matter and Tracula outputs

> RD = (L2+L3)/2 > > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi < > qi.z...@icahn.mssm.edu> > *Sent:* Monday, November 22, 2021 5:24 PM > *To:* Freesurfer

Re: [Freesurfer] Freeview grey matter, white matter and Tracula outputs

You can get the AD and RD from the other outputs: AD = L1 RD = (L2+L3)/2 From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Zeng, Qi Sent: Monday, November 22, 2021 5:24 PM To: Freesurfer support list Subject: [Freesurfer] Freeview grey matter, whit

[Freesurfer] Freeview grey matter, white matter and Tracula outputs

External Email - Use Caution Hi, If I want to freeview fully segmented grey matter, white matter, and Tracula outputs, are the following commands correct to the request? # to visualize the segmented cortical outputs freeview -v mri/aparc+aseg.mgz Question: why is one hemisphere

Re: [Freesurfer] freeview error after installation: Segmentation fault(core dumped) / free( ): invalid pointer, Aborted(core dumped)

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) / free( ): invalid pointer, Aborted(core dumped)External Email - Use CautionHello, Xuxiao,You need to go

Re: [Freesurfer] freeview error after installation: Segmentation fault(core dumped) / free( ): invalid pointer, Aborted(core dumped)

of freesurfer, or by the command "echo "export FS_LICENSE=$HOME/license.txt" $HOME/.bashrc". Do I need to create a license file manually?-原始邮件-发件人:fsbuild fsbu...@contbay.com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: [

Re: [Freesurfer] freeview error after installation: Segmentation fault(core dumped) / free( ): invalid pointer, Aborted(core dumped)

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

Re: [Freesurfer] freeview error after installation: Segmentation fault(core dumped) / free( ): invalid pointer, Aborted(core dumped)

External Email - Use Caution 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

Re: [Freesurfer] freeview segmentation fault: 11 on MacOS 10.15.7

External Email - Use Caution Hello Emmanuel, You could try the suggestions in this post from last month,

Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number

Great! Thanks!! From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Tuesday, September 7, 2021 9:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number yes, in the process now of upgrading. We'll use dcm2niix

Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number

support list *Subject:* Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number Yes! Thanks! dmc2niix did the trick. I wonder why mri_convert failed. Thanks! Noam *From:* freesurfer-boun...@nmr.mgh.harvard.edu <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesu

Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number

Our dicom reader is probably too old Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Peled, Noam Sent: Tuesday, September 7, 2021 2:56 PM To: Freesurfer support list Subject: Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number Yes! Thanks! dmc2niix did the trick. I

Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number

Yes! Thanks! dmc2niix did the trick. I wonder why mri_convert failed. Thanks! Noam From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Fischl, Bruce Sent: Thursday, September 2, 2021 12:44 PM To: Freesurfer support list Subject: Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd

Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number

: Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number Unfortunately, it’s patient data from another hospital, and I also can’t access the files. I’m just helping them to use FreeSurfer. Is there a debug version that outputs more information? The temp file

Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number

...@nmr.mgh.harvard.edu On Behalf Of Wang, Ruopeng Sent: Thursday, September 2, 2021 10:00 AM To: Freesurfer support list Subject: Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number Would it be possible to send me the dicom files? Ruopeng On Sep 1, 2021, at 1:14 PM, Peled, Noam

Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number

rfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Wang, Ruopeng Sent: Wednesday, September 1, 2021 12:57 PM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd

Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number

The same error. Also, when trying to run recon-all on these files. Thanks, Noam From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Wang, Ruopeng Sent: Wednesday, September 1, 2021 12:57 PM To: Freesurfer support list Subject: Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd

Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number

What if you use mri_convert to convert them to a mgz or nii volume? Do you get the same error? Ruopeng On Sep 1, 2021, at 10:52 AM, Peled, Noam mailto:npe...@mgh.harvard.edu>> wrote: Hello! I’m trying to use freeview to visualize FSPGR dicoms files. I’m using ubuntu 18.04 with tcsh shell.

[Freesurfer] freeview: sh: 1: Syntax error: Bad fd number

Hello! I'm trying to use freeview to visualize FSPGR dicoms files. I'm using ubuntu 18.04 with tcsh shell. I'm getting the following error: sh: 1: Syntax error: Bad fd number Here is the full error message: Starting DICOMRead2() dcmfile =~/Desktop/04254335/05641194 dcmdir =

Re: [Freesurfer] Freeview question

Great! Thanks so much! Mona Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry | MGH/HMS 149 13th Street, 149-2615 Boston, MA, USA, 02129 On Jul 22, 2021, at 4:54 PM, Wang, Ruopeng mailto:rwa...@mgh.harvard.edu>> wrote: Hi Mona, The neg.label file has all

Re: [Freesurfer] Freeview question

Hi Mona, The neg.label file has all negative scalar values in it, where the default threshold for the label is set to 0. If you set the threshold to a big negative number it will show up. Best, Ruopeng On Jul 22, 2021, at 3:35 PM, Nasiriavanaki, Zahra,M.D.

[Freesurfer] Freeview question

Hello experts, I am trying to load two types of labels on left hemisphere of a single subject. In tksurfer, both labels load without an issue, but in Freeview, one type of labels (neg.label) don’t show up. There is no error in the terminal, so I’m not sure what’s going on. I copied the labels

Re: [Freesurfer] FreeView issue!

Can you try resetting freeview’s preferences. You can do it in a terminal with the following command: rm ~/Library/Preferences/edu.harvard.mgh.nmr.FreeView.plist Wait for a few seconds and try starting freeview again. Ruopeng On Jul 21, 2021, at 1:49 PM, Sahil Bajaj

Re: [Freesurfer] FreeView issue!

External Email - Use Caution Hi, I reinstalled FreeSurfer and now the latest version i.e., 7.2.0, but somehow I am still getting the same error message, please see below. I am still unsure how can I fix this issue? Last login: Wed Jul 21 12:43:52 on ttys003

Re: [Freesurfer] FreeView issue!

External Email - Use Caution There are some reports of running Qt 5.12 on MacOS BigSur (your version is 11.4), that setting the environment variable below in your (e.g.., bash) shell can help the main application window start. No need to send another crash report if freeview

Re: [Freesurfer] FreeView issue!

External Email - Use Caution Just wondering if you already tried using bash to setup the environment. - R. %]bashbash-3.2$ export FREESURFER_HOME=/Applications/freesurfer/7.1.1bash-3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh Setting up environment for FreeSurfer/FS-FAST

Re: [Freesurfer] FreeView issue!

External Email - Use Caution Hi Ruopeng Thanks for your quick response. If I use that I still get the similar error: BT136080:~ bajsah$ $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview Segmentation fault: 11Segmentation fault: 11 Sahil On Fri, Jul 16, 2021 at 1:23 PM

Re: [Freesurfer] FreeView issue!

What if you run: $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview -f fsaverage/surf/lh.inflated > On Jul 16, 2021, at 1:07 PM, Sahil Bajaj wrote: > > External Email - Use Caution > > > Hi everyone, > > I am having following error while opening freeview in terminal: >

[Freesurfer] FreeView issue!

External Email - Use Caution Hi everyone, I am having following error while opening freeview in terminal: BT136080:01_Project_FreeSurfer bajsah$ freeview -f fsaverage/surf/lh.inflated /Applications/freesurfer/7.1.1/bin/freeview: line 2: 27046 Segmentation fault: 11

Re: [Freesurfer] Freeview filled in labels along with their outlines

It is possible to show outline only but not combined with filled ones. Ruopeng On Jul 8, 2021, at 5:02 PM, Pradyumna Bharadwaj mailto:p...@email.arizona.edu>> wrote: External Email - Use Caution Hi, In freeview, is it possible to view a collection of labels with different filled in

[Freesurfer] Freeview filled in labels along with their outlines

External Email - Use Caution Hi, In freeview, is it possible to view a collection of labels with different filled in colors, as well as their outlines? So, a combination of the filled in and outline only modes? Best, Prad ___

[Freesurfer] Freeview mghRead error

External Email - Use Caution Dear Freesurfer Developers, I have recently switched to a Mac for ease of use and have encountered an error upon trying to view output files from a previous data cohort which were processed on a remote computing server and copied to this Mac's local

Re: [Freesurfer] Freeview Update using MAC

arvard.edu on behalf of Erika Nolan Date: Tuesday, May 18, 2021 at 2:57 PM To: Freesurfer support list Subject: Re: [Freesurfer] Freeview Update using MAC External Email - Use Caution External Email - Use Caution Hi Ruopeng, Thank you for the quick reply. When I attempt to unta

Re: [Freesurfer] Freeview Update using MAC

Would it be possible to send me the gii file? From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Erika Nolan Sent: Tuesday, May 18, 2021 2:56:53 PM To: Freesurfer support list Subject: Re: [Freesurfer] Freeview Update using MAC External

Re: [Freesurfer] Freeview Update using MAC

Hi Erika, What error message do you get when you launch Freeview on your macOS 10.12? Ruopeng On May 18, 2021, at 1:57 PM, Erika Nolan mailto:erika.no...@mail.mcgill.ca>> wrote: External Email - Use Caution External Email - Use Caution Good afternoon, I downloaded

[Freesurfer] Freeview Update using MAC

External Email - Use Caution Good afternoon, I downloaded Freesurfer 7.1.1 and am trying to open HCP .gii files in Freeview. I tried updating Freeview

Re: [Freesurfer] Freeview slow on CentOS 8 Stream

External Email - Use Caution Hi Ruopeng He did. " On 2021-05-05 13:31, Torkil Svensgaard wrote: > Perfect, thanks. Did it go stall slow while capturing, or just a bit > slow from valgrind overhead? I would say it was 90% of the worst I've seen. Didn't want to push more, was

Re: [Freesurfer] Freeview slow on CentOS 8 Stream

Thanks for the file. Did the user experience slow-down while generating the profile (other than the slow-down by valgrind)? Ruopeng On May 5, 2021, at 7:40 AM, Torkil Svensgaard mailto:tor...@drcmr.dk>> wrote: External Email - Use Caution Hi Ruopeng All the boxes are fully upgraded.

Re: [Freesurfer] Freeview slow on CentOS 8 Stream

External Email - Use Caution Hi Ruopeng All the boxes are fully upgraded. Some of them have an Nvidia GPU and some of them only have onboard video, but the problem is the same on all of them, so probably not that. I sent you a callgrind file from one of my users, I hope that

Re: [Freesurfer] Freeview slow on CentOS 8 Stream

Hi Torkil, I just sent you a freeview build for profiling via secure file transferl. Can you run it through valgrind? First please copy it to your freesurfer bin folder $FREESURFER_HOME/bin. Then run this command: valgrind --tool=callgrind --dump-instr=yes $FREESURFER_HOME/bin/freeview_prof

Re: [Freesurfer] Freeview slow on CentOS 8 Stream

HI Torkil, We tested on our CentOS 8 machines as well as CentOS 8 VM but did not notice any slow-down. I personally run freeview remotely on a CentOS 8 machine occasionally and have never experience such an issue. I’m at a loss, too. :( I’m just shooting in the dark now - as I mentioned

Re: [Freesurfer] Freeview slow on CentOS 8 Stream

External Email - Use Caution Hi again Also the same when run via X11 from a beastly compute node. As it runs just fine on Ubuntu 16.04 with the very same NFS storage backend we are at a loss, but the finger points at something with CentOS Stream I guess. Anyone using it on

Re: [Freesurfer] Freeview slow on CentOS 8 Stream

External Email - Use Caution Hi It the same on every login server. Running locally inside at Thinlinc session. Mvh. Torkil On 29/04/2021 15.05, Wang, Ruopeng wrote: > So did all the issues happen on the same machine? Did your team run freeview > locally on the machine or via

Re: [Freesurfer] Freeview slow on CentOS 8 Stream

So did all the issues happen on the same machine? Did your team run freeview locally on the machine or via remote X display? Ruopeng > On Apr 29, 2021, at 8:49 AM, Torkil Svensgaard wrote: > >External Email - Use Caution > > Hi again > > The user reports freeview being

Re: [Freesurfer] Freeview slow on CentOS 8 Stream

External Email - Use Caution Hi again The user reports freeview being unusable right off the bat this morning. He left it running in that state, is there anything I can do to capture something that might provide insights? Mvh. Torkil On 28/04/2021 21.24, Torkil Svensgaard

Re: [Freesurfer] Freeview slow on CentOS 8 Stream

External Email - Use Caution Hi We've moved to an environment modules setup for the new HPC installation and I've made modules for 5.3.0, 6.0.0 and 7.1.1, which all exhibit the same symptom. I installed a dev build this morning and one heavy user reports the following from

Re: [Freesurfer] Freeview slow on CentOS 8 Stream

External Email - Use Caution Hello Torkil, Not sure what version of Freesurfer you are using, but if it’s an older release, it could be interesting to compare the performance with one of the latest development builds (not a release)

Re: [Freesurfer] Freeview slow on CentOS 8 Stream

External Email - Use Caution Hi Ruopeng The users all agree it is GUI responsiveness. Everything else can run just stellar on the very same desktop, matlab etc, at the same time as freeview stalls. Mvh. Torkil On 26/04/2021 19.16, Wang, Ruopeng wrote: > Hi Torkil, > > Can

Re: [Freesurfer] Freeview issues with surfaces

Wang, Ruopeng Sendt: 26. april 2021 16:05 Til: Freesurfer support list Emne: Re: [Freesurfer] Freeview issues with surfaces There is a ‘Overlay’ drop down box on the left pane, where you can load overlay after loading a surface. Ruopeng On Apr 26, 2021, at 9:49 AM, Pål Gunnar Larsson mailto:p

Re: [Freesurfer] Freeview issues with surfaces

Sendt: 26. april 2021 15:42 Til: Freesurfer support list Emne: Re: [Freesurfer] Freeview issues with surfaces Hi Pål, lh.area and lh.thickness are not surface files. They can be loaded as a surface overlay like this: freeview -f lh.pial:overlay=lh.thickness Best, Ruopeng On Apr 26, 2021, at 9

[Freesurfer] Freeview issues with surfaces

External Email - Use Caution I have made a new install of everything, now running Ubuntu 20.04 with Virtualbox 6.0 and Freesurfer 7.1. Freesurfer crashes with : "nquads=10158084, nvertices=529 terminate called after throwing an instance of 'int' Aborted (core dumped)" If I try

Re: [Freesurfer] Freeview slow on CentOS 8 Stream

Hi Torkil, Can you tell what part of the program slows down the most? Data loading? GUI responsiveness? Image/3D rendering? Or just in general? If it is the rendering, maybe try updating the graphics card driver to the latest? Best, Ruopeng > On Apr 26, 2021, at 6:06 AM, Torkil Svensgaard

Re: [Freesurfer] Freeview issues with surfaces

' Subject: Re: [Freesurfer] Freeview issues with surfaces External Email - Use Caution Thank you. In version 5 I could load an overlay with e.g. thickness. I don’t see that alternative in Freeview? Pål not sensitive Fra: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun

Re: [Freesurfer] Freeview issues with surfaces

rt list Emne: Re: [Freesurfer] Freeview issues with surfaces Hi Pål, lh.area and lh.thickness are not surface files. They can be loaded as a surface overlay like this: freeview -f lh.pial:overlay=lh.thickness Best, Ruopeng On Apr 26, 2021, at 9:36 AM, Pål Gunnar Larsson mailto:p...@ous-h

Re: [Freesurfer] Freeview issues with surfaces

Hi Pål, lh.area and lh.thickness are not surface files. They can be loaded as a surface overlay like this: freeview -f lh.pial:overlay=lh.thickness Best, Ruopeng On Apr 26, 2021, at 9:36 AM, Pål Gunnar Larsson mailto:p...@ous-hf.no>> wrote: External Email - Use Caution I have made

[Freesurfer] Freeview slow on CentOS 8 Stream

External Email - Use Caution Hi We have an older Ubuntu 16.04 HPC installation on which Freeview runs just fine. We also have a brand new CentOS 8 Stream HPC installation with much better hardware on which Freeview slows to a crawl after a bit of use. There's no error as

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