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 mailto:sahil.br...@gmail.c

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. mailto:znasiriavan...@mgh.harvard.ed

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 n

[Freesurfer] freeview slow/choppy

External Email - Use Caution Dear All, I recently changed from ubuntu 16.04 to 18.04 LTS, then reinstalled Freesurfer. As opposed to prior behavior, freeview image manipulation (mainly mouse-based rotations) are exceedingly choppy and slow. The screen briefly freezes after moving t

Re: [Freesurfer] Freeview Error

External Email - Use Caution 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

[Freesurfer] Freeview on debian

External Email - Use Caution Hi everyone, I have a problem with freeview. My university created for me a virtual machine in a small analysis cluster. Unfortunately, they installed Debian 4.19.98. I read that freeview has some problems with Debian, and in fact I am not able to open

Re: [Freesurfer] freeview 3.0

External Email - Use Caution Hello Xiaomin, It might help for you to send along an example freeview command and file that demonstrates this issue in the WSL environment. - R. On Jul 8, 2020, at 12:08, Xiaomin Yue wrote:External Email - Use Caution   

Re: [Freesurfer] freeview 3.0

@hotmail.com<mailto:yu...@hotmail.com> Subject: Re: [Freesurfer] freeview 3.0 External Email - Use Caution I don’t see freeview directly linking against libXm.so from Motif, though it does link against X windows libraries like libXmu.so and libX11..so. You can see this with the “l

Re: [Freesurfer] freeview 3.0

iaomin From: fsbuild<mailto:fsbu...@contbay.com> Sent: Thursday, July 9, 2020 10:20 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Cc: yu...@hotmail.com<mailto:yu...@hotmail.com> Subject: Re: [Freesurfer] freeview 3.0 External Email -

Re: [Freesurfer] freeview 3.0

freeview 2. Thanks, Xiaomin From: Wang, Ruopeng<mailto:rwa...@mgh.harvard.edu> Sent: Friday, July 10, 2020 9:08 AM To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] freeview 3.0 Hi Xiaomin, Freeview 2 was built against much older Qt and V

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., f

[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. - perm.th20.p

[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 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 messa

[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. Cu

[Freesurfer] Freeview quit unexpectedly

I am trying to use freeview to load a volume. I am using freesurfer 7.3.2 on the new M1 mac pro with ios ventura. Please view below the error report I am getting. Is there any work around it? I have tried different volumes but same issues Translated Report (Full Report Below) -

[Freesurfer] Freeview Installation Error

External Email - Use Caution Hi, I have been trying to install FreeSurfer and I went to test out the freeview command but received the following error. freeview: error while loading shared libraries: libGL.so.1: cannot open shared object file: No such file or directory I am unsu

Re: [Freesurfer] Freeview error

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

Re: [Freesurfer] Freeview error

: 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

Re: [Freesurfer] Freeview error

, March 15, 2023 at 20:17To: Freesurfer support list Subject: Re: [Freesurfer] Freeview errorHi, Can you check if the path is correct?  What does ‘ls -l /Users/results/sub-101/mri/T1.mgz’ show? If you do ‘mri_info /Users/results/sub-101/mri/T1.mgz’, does it report anything? Best, Yujing From: freesurfer

Re: [Freesurfer] Freeview error

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

Re: [Freesurfer] Freeview Overlay

Hi Maria, I've tested the files you sent me and were able to replicate the problem. Will work on it asap. Sorry about the delay. Ruopeng On 06/27/2011 12:13 PM, iac...@nmr.mgh.harvard.edu wrote: > Hi all, > > I haven't had any answer to my post, so I give another try. Hope it > doesn't bother

Re: [Freesurfer] Freeview Overlay

Hi Maria, The fix is done and should be available in tomorrow's dev build. Ruopeng On 06/27/2011 12:13 PM, iac...@nmr.mgh.harvard.edu wrote: > Hi all, > > I haven't had any answer to my post, so I give another try. Hope it > doesn't bother you. > > I am trying to overlay a map on a specific su

Re: [Freesurfer] freeview crash

Hi Matt Could you please send information about what Freeview output before it crash. You could try to run strace freeview to se what is wrong. You could also add if you are using Linux or Mac Os X. Knut J On 08/08/2011 01:41 PM, Hoptman, Matthew wrote: > > Hi Ruopeg, > > No, glxgears doesn't cr

[Freesurfer] Freeview for Mac

Hi, I have a quick question: has freeview been compiled for an intel macbook pro? Thanks, Jon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Freeview on Mac

Hi Guys, Is it possible to get Freeview compiled for a Mac? Last time I check, it wasn't supported, but it would be of great help to me and at least a couple other members of my lab. Thanks. Best, Jon ___ Freesurfer mailing list Freesurfer@nmr.mgh.h

[Freesurfer] Freeview segmentation fault

External Email - Use Caution Hello, I am having some trouble using Freeview on my university cluster with my MacBook (macOS Monterey version 12.4). Freeview works fine from a Windows machine, but when I try to view images (using XQuartz on my Mac), I get "segmentation fault." It d

Re: [Freesurfer] freeview error....

External Email - Use Caution  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

[Freesurfer] Freeview sudden termination

External Email - Use Caution Hi, I am running freesurfer/7.3.2 and had an issue with freeview sudden termination. The error message is *sub-002/label/aparc.annot.ctabMRISreadAnnotationIntoArray: vertex index out of range: 538980362 i=2020300A, in_array_size=132205* *annot file:

Re: [Freesurfer] Freeview issue

External Email - Use Caution I have the same problem. I would greatly appreciate your help with this. Yunus Soleymani Ph.D. Candidate of Neuroimaging Tehran University of Medical Sciences soleymani.yu.

Re: [Freesurfer] Freeview issue

External Email - Use Caution  Wondering if you used the freesurfer_ubuntu22-7.4.1_amd64.deb installer package from the download page and installed it from your Downloads folder via, $ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.deb The link for that file on the downloads p

Re: [Freesurfer] Freeview issue

External Email - Use Caution I did the following codes respectively:> cd> wget  https://secure-web.cisco.com/1aP0_Kx1EvY11b0NT6IxCZDi6qJ8ESnNx0MiHNLpkaZPFkc2atT4gkCWc3WkByTuDOEIqIhM9LAHtdegpZGTzMy4IURh53TQgiuOLIyTWU05XwMo5HiW7OA6Gj_FcIXBLb1PLtrzw1mtmYjESjmRYre-WGHAz9AVyOuzR_oG9a9Oi

Re: [Freesurfer] Freeview issue

External Email - Use Caution   The Qt graphics libraries may need virtualGl over a remote X connection.  So try prefacing your freeview command with "vglrun".  See the introductory text about vglrun and the install commands on this page, https://secure-web.cisco.com/1_jeLuB9K3

Re: [Freesurfer] Freeview problems

Can you confirm where your license file is? Ruopeng On Apr 15, 2024, at 10:36 AM, Savoia, Alice (Stud. FPN) mailto:a.sav...@student.maastrichtuniversity.nl>> wrote: External Email - Use Caution To whom it may concern, I am using freesurfer package on a MacBook Pro (macOS Sonoma, Versi

Re: [Freesurfer] Freeview problems

External Email - Use Caution Is in the freesurfer directory From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Wang, Ruopeng Sent: Monday, April 15, 2024 4:40 PM To: Freesurfer support list Subject: Re: [Freesurfer] Freeview problems

Re: [Freesurfer] Freeview problems

ehalf of Wang, Ruopeng mailto:rwa...@mgh.harvard.edu>> Sent: Monday, April 15, 2024 4:40 PM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Freeview problems Can you confirm where your license file is? Ruopeng On Apr 15, 2024, at 10:36 AM, Savoi

Re: [Freesurfer] Freeview problems

Sent: Monday, April 15, 2024 4:44 PM To: Freesurfer support list Subject: Re: [Freesurfer] Freeview problems Can you try ‘mri_info --voxel 0 0 0’? Just wanted to make sure the license file is read properly. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of

Re: [Freesurfer] Freeview problems

Can you set the terminal output? From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Savoia, Alice (Stud. FPN) Sent: Monday, April 15, 2024 11:03 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freeview problems External Email - Use Caution I think is not reading it

Re: [Freesurfer] Freeview problems

l 15, 2024 4:44 PM To: Freesurfer support list Subject: Re: [Freesurfer] Freeview problems Can you try ‘mri_info --voxel 0 0 0’? Just wanted to make sure the license file is read properly. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Savoia, Alice (Stud.

Re: [Freesurfer] Freeview problems

t on Mac https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration_Mac Also, which version of Freesurfer you are using? Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Savoia, Alice (Stud. FPN) Sent: Monday, April 15, 2024 11:12 AM To: Freesurfer support list Subject: Re: [Frees

Re: [Freesurfer] Freeview problems

ysg> From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Huang, Yujing Sent: Monday, April 15, 2024 5:27:35 PM To: Freesurfer support list Subject: Re: [Freesurfer] Freeview problems I don’t think you pass the arguments correctly to mri_info. You need to specify an input

Re: [Freesurfer] Freeview problems

External Email - Use Caution  You can check the post (quoted below) to verify the setup for the 7.4..1 release.   Instead of running the freeview command as listed in the post, you can run the mri_info command with no arguments to get the help info about the command line options

[Freesurfer] Freeview on Linux help

Hello, I am having trouble setting up FreeSurfer on Linux (SUSE 10 x84_64). I followed the installation and setup directions from the wiki, and that was all successful. When I attempt to test the installation though, it's clear something is not right. I tried opening freeview, and received the fo

Re: [Freesurfer] Freeview mountain lion

Hello Isabelle, Freeview has been undergoing many changes and you simply got unlucky and downloaded an unstable version of the program. I will be posting an updated version within the day and I will email you directly when it becomes available. -Zeke > Hi > there,I recently tried to update the F

Re: [Freesurfer] freeview read error

Hi Cat do those file exist? What does ls -l tell you for them? Bruce On Wed, 26 Aug 2015, Cat Chong wrote: Dear Experts,   I am trying to use Freeview to view volumes using the command listed on the website: http://freesurfer.net/fswiki/FsTutorial/OutputData_freeview but the only volume that l

Re: [Freesurfer] freeview read error

Hi Bruce, Yes, they exist.but this seems strange...-rwx--+ 1 mxx  MF\Domain Users         0 Aug 26 09:12 T1.mgz -rwx--+ 1 mxx  MF\Domain Users         0 Aug 26 09:12 wm.mgz -rwx--+ 1 mxx MF\Domain Users         0 Aug 26 09:12 brainmask.mgz On Wednesday, August 26, 2015 12:04 P

Re: [Freesurfer] freeview read error

they are empty (zero size). Maybe your disk filled up? On Wed, 26 Aug 2015, Cat Chong wrote: Hi Bruce, Yes, they exist. but this seems strange... -rwx--+ 1 mxx  MF\Domain Users         0 Aug 26 09:12 T1.mgz -rwx--+ 1 mxx  MF\Domain Users         0 Aug 26 09:12 wm.mgz -rwx--+ 1 mxx

Re: [Freesurfer] freeview read error

no, seems to be plenty left.. 240 TB On Wednesday, August 26, 2015 12:23 PM, Bruce Fischl wrote: they are empty (zero size). Maybe your disk filled up? On Wed, 26 Aug 2015, Cat Chong wrote: > Hi Bruce, > > Yes, they exist. > but this seems strange... > -rwx--+ 1 mxx  MF\Doma

Re: [Freesurfer] freeview read error

did you run recon-all? If so, check the recon-all.log for errors On Wed, 26 Aug 2015, Cat Chong wrote: no, seems to be plenty left.. 240 TB On Wednesday, August 26, 2015 12:23 PM, Bruce Fischl wrote: they are empty (zero size). Maybe your disk filled up? On Wed, 26 Aug 2015, Cat Chong

[Freesurfer] freeview warning: invalid drawable

Dear freesurfer experts, I'm wondering why I get this warning message when I open up any surf template in either fsaverage or fsaverage_sym directory. FYI, I'm using freeview v1.0 if anybody know, please help. -Glen $ freeview -f lh.inflated 2013-03-20 16:03:05.801 freeview.bin[52449:907] invalid

[Freesurfer] freeview v5.3 reposition surface

Hi Freesurfer experts, I noticed that Freeview has gotten an upgrade from v5.1 to v5.3 and the reposition tool now has a GUI and it works! Dr. Fischl said in response to Dr. Pietro De Rossi on October 24th, 2012 that the pipeline for the reposition surface tool was not yet implemented and you sti

[Freesurfer] [FreeSurfer] Freeview: Invalid drawable

Dear Koen, Freeview returns 8 lines of the error message "invalid drawable" whenever executed. The messages are as follows 2013-06-24 14:24:57.930 Freeview[1937:303] invalid drawable 2013-06-24 14:24:57.931 Freeview[1937:303] invalid drawable 2013-06-24 14:24:57.944 Freeview[1937:303] invalid dra

Re: [Freesurfer] freeview save error

Hi Jason any chance you can figure out how to replicate this reliably? If so, we can track it down. Otherwise it's going to be hard thanks Bruce On Mon, 22 Jul 2013, Jason Tourville wrote: Hi there,Occassionally when using the "save volume" function from the gui to save edits made to the w

Re: [Freesurfer] freeview "invalid drawable"

You can just ignore this warning message on Mac. Best, Ruopeng On Oct 23, 2013, at 8:52 PM, Elissa McIntosh wrote: > Hi, When trying freeview command (see below) from the “Testing your > freesurfer installation” page using my own data, freesurfer opened, but I am > concerned about the “inval

Re: [Freesurfer] freeview error {Disarmed}

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

Re: [Freesurfer] Freeview not working

> saurabh@saurabh-Precision-WorkStation-T3500:/usr/local/freesurfer$ freeview > freeview.bin: error while loading shared libraries: libXss.so.1: cannot > open shared object file: No such file or directory > saurabh@saurabh-Precision

Re: [Freesurfer] Freeview not working

s) > on the command line? > > -Zeke > > On 02/10/2014 05:17 AM, Saurabh Thakur wrote: > > Hi all, > > > > My freeview is not working. > > > > //=// > > > > saurabh@saurabh-Precision

Re: [Freesurfer] Freeview crashes xterm

My apologies, I meant the X server crashes, not the xterm. Thanks. - Archana > -Original Message- > From: Venkataraman, Archana > Sent: Monday, March 3, 2014 1:19 PM > To: 'freesurfer@nmr.mgh.harvard.edu' > Subject: Freeview crashes xterm > > Hi, > > I am running freesurfer on a RedHa

Re: [Freesurfer] freeview display problem

Is there any other layer loaded? It looks like there is at least another overlay on top of the volume layer? Best, Ruopeng > On Jun 23, 2016, at 2:37 PM, Ramtilak Gattu wrote: > > Hello , > > I am having strange freeview display problem. The images doesnt appear in > gray scale anymore. Plea

Re: [Freesurfer] freeview display problem

That is just one layer the yellow contrast is from when we tune the contrast up or down. From: Ramtilak Gattu Sent: Thursday, June 23, 2016 2:37:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: freeview display problem Hello , I am having strange freeview dis

Re: [Freesurfer] freeview display problem

That’s indeed strange. I wonder if it is a graphics card issue. Does the blue tone appear all the time? on any volume? > On Jun 23, 2016, at 3:31 PM, Ramtilak Gattu wrote: > > That is just one layer the yellow contrast is from when we tune the contrast > up or down. > From: Ramtilak Gattu > S

Re: [Freesurfer] freeview display problem

This issue is only with freesurfer , images on fslview doesnt have this problem. From: Ramtilak Gattu Sent: Thursday, June 23, 2016 3:31:41 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: freeview display problem That is just one layer the yellow contrast is

Re: [Freesurfer] freeview display problem

So it happens with freeview all the time? Freeview uses openGL as backend for rendering, which I believe is not the case for fslview. Would it be possible for you to update your graphics card driver? > On Jun 23, 2016, at 4:10 PM, Ramtilak Gattu wrote: > > This issue is only with freesurfer ,

Re: [Freesurfer] freeview display problem

May be thats the problem. I'll try to give it a shot to see if it fixes the problem. Thanks. From: Ramtilak Gattu Sent: Thursday, June 23, 2016 4:10:28 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: freeview display problem This issue is only with freesurf

Re: [Freesurfer] freeview display problem

I tried updating my Nvidia drivers. but now whenever I try to open freeview it says " aborted ( core dumped). please help. Thanks Regards Tilak From: Ramtilak Gattu Sent: Thursday, June 23, 2016 5:27:12 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: fre

Re: [Freesurfer] freeview display problem

Is that all? Are there any other error messages? On 06/24/2016 10:25 AM, Ramtilak Gattu wrote: I tried updating my Nvidia drivers. but now whenever I try to open freeview it says " aborted ( core dumped). please help. Thanks Regards Tilak --

Re: [Freesurfer] freeview display problem

That is all . No error messages at all. From: Ramtilak Gattu Sent: Friday, June 24, 2016 10:25:42 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: freeview display problem I tried updating my Nvidia drivers. but now whenever I try to open freeview it says " ab

[Freesurfer] Freeview nightly / dev / beta

Hello Freesurfer developers, I am looking for a version of Freeview that recognizes the -noquit flag. V 1.0 Build Aug 24 2015 14:50:08 allows this, but is no longer available from "ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev

Re: [Freesurfer] Freesurfer/Freeview help

, > I am trying to segment a MRI brain in order to create a mesh of the image > into finite elements, but I am very new with Freesurfer/Freeview and am not > familiar with the tools. So far, I have only uploaded brain.mgt from the > bert file that comes with the program. If I wanted to

Re: [Freesurfer] Freesurfer/Freeview help

u could mesh, but we don't > by default. > > cheers > Bruce > On Mon, 27 Jun 2016, Abbie McNulty wrote: > > > Hello, > > I am trying to segment a MRI brain in order to create a mesh of the image > > into finite elements, but I am very new with Freesurfer/Free

Re: [Freesurfer] Freesurfer/Freeview help

>> >> cheers >> Bruce >> On Mon, 27 Jun 2016, Abbie McNulty wrote: >> >> > Hello, >> > I am trying to segment a MRI brain in order to create a mesh of the >> image >> > into finite elements, but I am very new with Freesurfer/Freeview an

Re: [Freesurfer] Freesurfer/Freeview help

lty wrote: > > > Hello, > > I am trying to segment a MRI brain in order to create a mesh > of the image > > into finite elements, but I am very new with > Freesurfer/Freeview and am not > > familiar with the tools. So far, I have

Re: [Freesurfer] freeview display problem

Hey Ruopeng, I still couldnt figure out whats going on the freeview display. I updated the Nvidia drivers but still its not displaying in gray scale. please help. thanks Regards Tilak From: Ramtilak Gattu Sent: Friday, June 24, 2016 12:25:50 PM To: freesur

Re: [Freesurfer] freeview display problem

Do other colormaps (heat scale, jets, etc) look normal? > On Jun 28, 2016, at 2:01 PM, Ramtilak Gattu wrote: > > Hey Ruopeng, > > I still couldnt figure out whats going on the freeview display. I updated the > Nvidia drivers but still its not displaying in gray scale. > > please help. > > t

Re: [Freesurfer] freeview display problem

Nope they dont look normal they are being displayed in some other colors like heat is showing up as blue , jet as green etc. Even when the surfaces are loaded up the color of the surfaces doesnt look right. when the surface yellow is chosen are red it is being displayed as blue. Thanks Regard

Re: [Freesurfer] freeview display problem

This sounds very likely a video card/driver issue. Would it be possible for you any other program that uses OpenGL/vtk, such as 3D slicer, Paraview? How does glxgears command show? > On Jun 28, 2016, at 2:55 PM, Ramtilak Gattu wrote: > > Nope they dont look normal they are being displayed in

Re: [Freesurfer] freeview display problem

glxgears shows up a screen with three gear wheels in blue, pink and green and frame information rate being printed out on the command window. From: Ramtilak Gattu Sent: Tuesday, June 28, 2016 2:55:32 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: freeview disp

Re: [Freesurfer] freeview display problem

Hi Tilak, Do the colors match this: https://en.wikipedia.org/wiki/GLX#/media/File:Xf86_glxgears.png ? hth d On 6/28/16 3:46 PM, Ramtilak Gattu wrote: > glxgears shows up a screen with three gear wheels in blue, pink and > green and frame information rate being printed out on the command window

Re: [Freesurfer] freeview display problem

The color should be red, blue and green. It is your graphics card or graphics driver issue. Best, Ruopeng > On Jun 28, 2016, at 3:46 PM, Ramtilak Gattu wrote: > > glxgears shows up a screen with three gear wheels in blue, pink and green and > frame information rate being printed out on the co

Re: [Freesurfer] freeview display problem

Ok, you should try updating your graphics card driver. There is also chance that your graphics card is broken. Unfortunately we are not able to diagnose that for you. Sorry. Best, Ruopeng > On Jun 28, 2016, at 4:17 PM, Ramtilak Gattu wrote: > > Attached is the screen shot comparison side by s

Re: [Freesurfer] Freeview recon button

Hi Walid Recon editing mode is in the upcoming v6. Our recent hardware woes slowed things down a bit, but we are still hoping to get It out soon What was the gyrification question? Cheers Bruce > On Jun 30, 2016, at 10:39 PM, Walid Yassin wrote: > > Hello freesurfers, > > I downloaded freesur

Re: [Freesurfer] Freeview recon button

Thanks a lot Bruce! I will wait for v6 and check freeview then. for the gyrification question i added a link. Here it is: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47883.html Thank you again! Best, Walid On Fri, Jul 1, 2016 at 12:08 PM, Bruce Fischl wrote: > Hi Walid >

Re: [Freesurfer] Freesurfer/Freeview help

..@nmr.mgh.harvard.edu> >> > wrote: >> > Hi Abbie >> > >> > what are you trying to create a mesh of? We supply meshes for >> > the >> > gray/white interface and for the pial surface. We supply voxel >> > segmen

Re: [Freesurfer] Freesurfer/Freeview help

   > Hello, >       > I am trying to segment a MRI brain in order to create a mesh >       of the image >       > into finite elements, but I am very new with >       Freesurfer/Freeview and am not >       > familiar with the t

Re: [Freesurfer] Freeview quits unexpectedly

Are you running FS 5.3 or the latest 6.0 beta? If former would it be possible for you to try 6.0 beta? Best, Ruopeng > On Aug 19, 2016, at 1:27 PM, Corriveau-Lecavalier Nick > wrote: > > Hello FreeSurfer developers, > > > I am trying to load a thickness file (ex: lh.long.thickness-avg.fwhm

Re: [Freesurfer] Freeview quits unexpectedly

BTW, what is the command you ran? > On Aug 19, 2016, at 2:20 PM, Ruopeng Wang wrote: > > Are you running FS 5.3 or the latest 6.0 beta? If former would it be possible > for you to try 6.0 beta? > > Best, > Ruopeng > > >> On Aug 19, 2016, at 1:27 PM, Corriveau-Lecavalier Nick >> wrote: >>

Re: [Freesurfer] freeview display problem

Is there any error message on the terminal? What happens if you run “glxgears” command? Does it run? Best, Ruopeng > On Sep 23, 2016, at 4:35 PM, KALEY E ELLIS wrote: > > Hello FreeSurfer Developers, > > I am attempting to open freeview to view the brainmask on a subject in our > study. Ever

Re: [Freesurfer] Freeview Loading Volumes

Hi Bob, I think freeview by default automatically locates to the default mri directory under the current subject. It is convenient in some use case but apparently not so much in your case. I will make that optional or figure out a better way to handle this. Best, Ruopeng On 9/25/2016 9:46 AM

Re: [Freesurfer] Freeview display problems

Its possible that XQuartz updated (Application -> Utilities -> XQuartz), what version are you running? You could try uninistalling and uninstalling older versions. On 11/16/2016 12:14 PM, Robert Kraft wrote: > I am running Freeview Version 1.0 Build May 26 2016 remotely from my Mac OS > 10.11.6

[Freesurfer] freeview command line options

Dear Freesurfer experts, When I use Freeview GUI to show overlays on a surface, I can click on the button "Configure", and then check the box "Enable" in the smooth section (upper right of the pop-out window), to smooth it. Is there any options to do similar stuff in the command line of freeview?

Re: [Freesurfer] freeview and ?h.cortex.patch.flat

Hi Xiaomin, At this time, viewing the ?h.cortex.patch.flat isn't possible in freeview. You can load it using tksurfer by loading your subject's inflated surface, then going to File -> Patch -> LoadPatch and choosing the correct patch.flat file. These instructions are detailed here: https://

Re: [Freesurfer] freeview and ?h.cortex.patch.flat

Thanks Xiaomin On Tue, Oct 6, 2015 at 11:35 AM -0700, "Lee Tirrell" wrote: Hi Xiaomin, At this time, viewing the ?h.cortex.patch.flat isn't possible in freeview. You can load it using tksurfer by loading your subject's inflated surface, then going to File -> Patch -> LoadPatch and choosing

Re: [Freesurfer] Freeview PETSC Error

Hello, I think that link pointed you to the centos6 version of freeview.bin, but you would want the centos4 version. You can download the correct version using the following link: ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/freeview/linux_centos4_x86_64/freeview.bin Hope this help

[Freesurfer] freeview, tkmedit won't start

Dear all I installed freesurfer as supposed for linux (ubuntu). When I tried to run freeview an error for tcsh occured. Apparenty I fixed that one but still freeview doesn't start. Typing the command: "freeview" nothing happens (I did export and source freesurfer correctly). Further trying to run

Re: [Freesurfer] FreeView Gave Errors

can you send us your command line? And does this happen right away, or after you do something in the interface? cheers Bruce On Thu, 8 Dec 2011, Xinian Zuo wrote: > Freesurfers, > > Anyone saw some errors below from FreeView? > -error > mess

Re: [Freesurfer] freeview: segmentation fault

Does it happen with just that file or with other files as well? Would it be possible to send us that volume file? Ruopeng On 12/08/2011 02:03 PM, Xin Zheng wrote: > Hi, > > We are trying to open something using freeview (ie. freeview -v > SubjectID_template/mri/norm.mgz) and would get a segmenta

Re: [Freesurfer] freeview: segmentation fault

can you open it in tkmedit? Sounds like something is wrong with the file On Thu, 8 Dec 2011, Xin Zheng wrote: > Hi, > > We are trying to open something using freeview (ie. freeview -v > SubjectID_template/mri/norm.mgz) and would get a segmentation fault. > When we tried to open it directly from t

Re: [Freesurfer] freeview: segmentation fault

I have no problem loading this file in freeview, in both old and new versions. Have you used freeview before on the same system? Did it work? Ruopeng On 12/08/2011 02:33 PM, Xin Zheng wrote: > Hi Ruopeng, > > It seems to be with all files. Attached is one of them. > > Thanks! > Xin > > On Thu, D

Re: [Freesurfer] freeview: segmentation fault

Hi, I have not used freeview before in any version. The images open in tkmedit. What can we do to diagnose this problem? Xin On Thu, Dec 8, 2011 at 3:16 PM, Ruopeng Wang wrote: > I have no problem loading this file in freeview, in both old and new > versions. Have you used freeview before on th

Re: [Freesurfer] freeview: segmentation fault

Would be hard for us to diagnose if we can't replicate the issue. Is there any core dump file or some kind of log file that may provide any hint? From what you described, it seems freeview crashes right when it is about to render the loaded image. that's about as far as I can guess now. Is that

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