Re: [Freesurfer] freeview command line options

External Email - Use Caution Dear Eli, could you add the command line you used and the FreeSurfer version (e.g., output of `cat ${FREESURFER_HOME}/VERSION`)? Thanks, Tim > On September 20, 2019 at 10:14 PM "Rockers, Elijah D." > wrote: > > > External Email - Use

Re: [Freesurfer] freeview command line options

Hi Eli, I can confirm this is a bug. We'll fix it very soon. Best, Ruopeng On 9/20/19 4:14 PM, Rockers, Elijah D. wrote: External Email - Use Caution Hello, it's possible I found a bug in freeview: I'm using the overlay_color option with freeview. Specifically I am trying to

[Freesurfer] freeview command line options

External Email - Use Caution Hello, it's possible I found a bug in freeview: I'm using the overlay_color option with freeview. Specifically I am trying to use both the "truncate" and "inverse" options in a command line call to freeview for a pipeline I am building. The

Re: [Freesurfer] Freeview error

Is your work disk full? On 9/17/19 10:22 AM, Miguel Ángel Rivas Fernández wrote: External Email - Use Caution I tried in the command window where I started freeview but nothing happened. This is the output miguel@miguel-VirtualBox:~$ ls

Re: [Freesurfer] Freeview error

External Email - Use Caution 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

Re: [Freesurfer] Freeview error

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

Re: [Freesurfer] Freeview error

External Email - Use Caution 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

[Freesurfer] Freeview 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

Re: [Freesurfer] freeview crash -- petsc error when opening volume

External Email - Use Caution In fact, I think I have narrowed the issue completely down to PETSC, irrespective of FreeSurfer/FreeView. In a Hail Mary attempt, I downloaded the PETSC source code and compiled it from scratch; I was going to try and replace the very out of date

Re: [Freesurfer] freeview crash -- petsc error when opening volume

: [Freesurfer] freeview crash -- petsc error when opening volume Hi Tristan, Would it be possible for you to try building against VTK 8.2 and Qt 5.12.x? Best, Ruopeng On 9/10/19 2:51 PM, TRISTAN J PAUTSCH wrote: External Email - Use Caution Thank you for the reply. Just to clarify, everything

Re: [Freesurfer] freeview crash -- petsc error when opening volume

the requested logs. Thank you! Tristan *From:* fsbuild *Sent:* Tuesday, September 10, 2019 1:19 PM *To:* freesurfer@nmr.mgh.harvard.edu *Cc:* TRISTAN J PAUTSCH *Subject:* Re: [Freesurfer] freeview crash -- petsc error when opening

Re: [Freesurfer] freeview crash -- petsc error when opening volume

ServerCPU: 4x Xeon Platinum 8164RAM: 512GB DDR4 ECC (16x32GB DIMMs)From:TRISTAN J PAUTSCH tpaut...@wisc.eduSent:Thursday, August 29, 2019 10:27 AMTo:fsbuild fsbu...@contbay.comCc:freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] freeview crash -- petsc error

Re: [Freesurfer] freeview crash -- petsc error when opening volume

(16x32GB DIMMs) From: TRISTAN J PAUTSCH Sent: Thursday, August 29, 2019 10:27 AM To: fsbuild Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume Thank you for the reply, I will try this when time permits

Re: [Freesurfer] FreeView : Tools : Volume Filter : Close

Hi Yar, close is a morphological close operation, which in the grayscale case is a max followed by a min I believe (in a 3x3x3 nbhd) cheers Bruce On Wed, 4 Sep 2019, Yasir Hadi wrote: External Email - Use Caution Hello FreeSurfer Developers, I just want to get the

Re: [Freesurfer] FreeView : Tools : Volume Filter : Close

Hi Ysr, I think it just uses a 3x3x3 kernel. Best, Ruopeng On 9/4/19 10:51 AM, Yasir Hadi wrote: External Email - Use Caution Hello FreeSurfer Developers, I just want to get the Information: which parameters are used as I apply the filter *Close* on the volume dataset using the

[Freesurfer] FreeView : Tools : Volume Filter : Close

External Email - Use Caution Hello FreeSurfer Developers, I just want to get the Information: which parameters are used as I apply the filter *Close* on the volume dataset using the FreeView Version 2.0 Builed Jan 18 2017 16:48:55. I've searched the list and the wiki and I

Re: [Freesurfer] freeview crash -- petsc error when opening volume

External Email - Use Caution Thank you for the reply, I will try this when time permits! Tristan From: fsbuild Sent: Tuesday, August 27, 2019 4:25 PM To: TRISTAN J PAUTSCH Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] freeview

Re: [Freesurfer] freeview crash -- petsc error when opening volume

From: TRISTAN J PAUTSCH Sent: Friday, August 23, 2019 11:38 AM To: Freesurfer support list Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume Good morning Ruopeng, thank you for your continued assistance! Unfortunately, I get the same error using the CentOS6 dev

Re: [Freesurfer] freeview crash -- petsc error when opening volume

...@nmr.mgh.harvard.edu on behalf of Ruopeng Wang Sent: Thursday, August 22, 2019 5:00 PM To: Freesurfer support list Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume Hi Tristan, Thanks for the files. I have no problem loading them with the latest dev build and stable 6.0 build

Re: [Freesurfer] freeview crash -- petsc error when opening volume

s sequentially through the GUI. > > Thank you! > Tristan > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Ruopeng Wang > > Sent: Thursday, August 22, 2019 8:16 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] freeview crash -- petsc error

Re: [Freesurfer] freeview crash -- petsc error when opening volume

, August 22, 2019 8:16 AM To: Freesurfer support list Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume Hi Tristan, Would it be possible to send us the files and the command-line you run? Best, Ruopeng On Aug 21, 2019, at 12:18 PM, TRISTAN J PAUTSCH mailto:tpaut

Re: [Freesurfer] freeview crash -- petsc error when opening volume

Wang Sent: Thursday, August 22, 2019 8:16 AM To: Freesurfer support list Subject: Re: [Freesurfer] freeview crash -- petsc error when opening volume Hi Tristan, Would it be possible to send us the files and the command-line you run? Best, Ruopeng On Aug 21, 2019, at 12:18 PM, TRISTAN J PAUTSCH

Re: [Freesurfer] freeview crash -- petsc error when opening volume

Sent: Tuesday, August 20, 2019 2:35 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: [Freesurfer] freeview crash -- petsc error when opening volume > > External Email - Use Caution > Greetings all, I'll try to keep this succinct. > > I'm attempting to dep

Re: [Freesurfer] freeview crash -- petsc error when opening volume

? From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of TRISTAN J PAUTSCH Sent: Tuesday, August 20, 2019 2:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] freeview crash -- petsc error when opening volume External Email - Use Caution

[Freesurfer] freeview crash -- petsc error when opening volume

External Email - Use Caution Greetings all, I'll try to keep this succinct. I'm attempting to deploy FreeSurfer on Ubuntu 18.04 servers here at the lab. I used the stable 6.0/CentOS 6 download, in addition to the dev version of freeview per the .../fswiki/UpdateFreeview

Re: [Freesurfer] Freeview

External Email - Use Caution Hello JC, You can try installing the following, $ sudo apt-get install qt5-default qtcreator $ sudo apt-get install libqt5x11extras5-dev Are you working on Ubuntu 18 ? - R. On Jul 12, 2019, at 22:29, Juan Rivas jcr...@gmail.com wrote:External Email -

[Freesurfer] Freeview

External Email - Use Caution Hello, since yesterday i am trying to run freeview. I have followed the steps you asked to me, and today I updated freeview. I get this message again: *jcrn12@jcrn12-VirtualBox:~$ freeviewThis application failed to start because it could not find

[Freesurfer] freeview

External Email - Use Caution I try again with fortran, uploaded it again, and now I get this message: jcrn12@jcrn12-VirtualBox:~$ freeview This application failed to start because it could not find or load the Qt platform plugin "xcb" in "". Reinstalling the application may fix

Re: [Freesurfer] freeview

External Email - Use Caution Did you try, $ ldd /usr/local/freesurfer/bin/freeview | grep not ? - R. On Jul 12, 2019, at 08:42, Juan Rivas jcr...@gmail.com wrote:External Email - Use CautionIt looks like freeview is in: jcrn12@jcrn12-VirtualBox:~$

[Freesurfer] freeview

. -- Forwarded message - De: fsbuild Date: lun., 15 jul. 2019 a las 14:19 Subject: Re: [Freesurfer] Freeview To: Cc: Hello JC, Try this to see what libs are missing, $ ldd /usr/local/bin/freeview | grep not - R. ___ Freesurfer

Re: [Freesurfer] Freeview

External Email - Use Caution Hello JC, Try this to see what libs are missing, $ ldd /usr/local/bin/freeview | grep not - R. On Jul 12, 2019, at 06:19, Juan Rivas jcr...@gmail.com wrote:External Email - Use CautionHi, thank you for your help.I tried again and once again it did

[Freesurfer] Freeview

.g., CentOS 7, > Ubuntu 18, etc. > > - R. > > On Jul 15, 2019, at 12:39, Juan Rivas wrote: > > External Email - Use Caution > > > > -- Forwarded message - > De: Juan Rivas > Date: vie., 12 jul. 2019 a las 3:02 > Subject: Re:

[Freesurfer] Freeview

External Email - Use Caution -- Forwarded message - De: Juan Rivas Date: vie., 12 jul. 2019 a las 3:02 Subject: Re: [Freesurfer] Freeview To: fsbuild Hi, thank you for your answer. I did what you recommended to me, and I get this message: freeview: error while

Re: [Freesurfer] Freeview

External Email - Use Caution Hello JC, Your machine could be missing the qt5 libraries/files. On Ubuntu linux you can try installing them with,$sudo apt-get install qt5-default qtcreatorlibqt5x11extras5-dev On CentOS linux,$sudo yum install qt-create qt-config.x86_64$sudo yum

[Freesurfer] Freeview

External Email - Use Caution Hello, I am trying to use freeview, but everytime I try I get this message: freeview: error while loading shared libraries: libQt5Widgets.so.5: cannot open shared object file: No such file or directory. How can I fix it? Thanks a lot, JC.

Re: [Freesurfer] freeview parcellation error

Hi Ebru are you sure yo uare loading a label and not a color lut? What is the name of the file you are trying to load? cheers Bruce On Thu, 2 May 2019, Ebru Ayyürek wrote: External Email - Use Caution Hi FreeSurfer Developers, I'm attempting to perform a freeview

Re: [Freesurfer] Freeview update error

External Email - Use Caution Hi Kelly, you can try yum install qt5-qtbase-gui qt5-qtwebkit qt5-qtwebkit-devel And if it still doesn't work, you can try yum install harfbuzz On Mon, Apr 22, 2019 at 9:05 AM Kelly Vaughn wrote: > External Email - Use Caution > > Hello

Re: [Freesurfer] freeview and complex values

Hi Shahin, Freeview does not support color wheel colormap yet. We will add that option very soon. Best, Ruopeng On 4/22/19 2:52 PM, sha...@nmr.mgh.harvard.edu wrote: > Hi Surfers, > I am trying to use freeview to present retinotopy mapping in > subcortical regions. I need to show complex

[Freesurfer] freeview and complex values

Hi Surfers, I am trying to use freeview to present retinotopy mapping in subcortical regions. I need to show complex (real and imag) values generated by a retinotopy analysis in a 'color wheel' format (similar to what tksurfer does). Any hint? _ Shahin

Re: [Freesurfer] Freeview update error

External Email - Use Caution Hello FreeSurfer community, I believe I have installed both freetype and freetype-devel now. I now get a new error, that is similar, but may have a slightly different solution: Freeview:symbol lookup error:

Re: [Freesurfer] Freeview update error

External Email - Use Caution Thank you for your help! When I look within /usr/lib64 (using ls *libfreetype*) , I see: lib64/libfreetype.so.6 lib64/libfreetype.so.6.10.0 When I type: strings /usr/lib64/libfreetype.so.6 | grep -i ft_get_font_format I do not get any output. When

Re: [Freesurfer] Freeview update error

External Email - Use Caution ​Hello Kelly, Do you have libfreetype installed on your system (which defines that symbol)? $ strings /usr/lib64/libfreetype.so.6 | grep -i ft_get_font_format FT_Get_Font_Format If not, you can install it with, $ sudo yum install freetype.x86_64

[Freesurfer] Freeview update error

External Email - Use Caution Hello FreeSurfer Developers, I am having trouble opening the updated version of Freeview. I have followed the directions for Linux on the UpdateFreeview site ( http://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview), but when I get to the last step

Re: [Freesurfer] Freeview Scrolling through slices on a Mac

External Email - Use Caution Dear Chris, We're actually working on control points in our group as well - on Mac you have to press the 'fn' (very left bottom key) along with the up-down arrow keys. Hope that helps, Cheers, Barbara On 11/12/2018 18:36, Ruopeng Wang wrote: >

Re: [Freesurfer] Freeview Scrolling through slices on a Mac

What version of freesurfer are you running? I think in 6.0, up/down arrow keys will scroll through slices. If not, the latest dev build should have it. You can get the latest freeview build here: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview Best, Ruopeng On 12/11/2018 01:23 PM,

[Freesurfer] Freeview Scrolling through slices on a Mac

External Email - Use Caution Maybe I am missing something, but how can I scroll through slices with keyboard or mouse in Freeview on a Mac? Nothing I’ve tried works thus far. Any typical key ( cmd, ctrl, shift ) with scroll just zooms. Up/down moves the image up and down …

Re: [Freesurfer] Freeview command not found {Disarmed}

External Email - Use Caution It should be OK to use qt4 on Ubuntu 16, though I think qt5 would work as well. Please test to see if you can freeview from where it was installed. Your output below says that FREESURFER_HOME is /usr/local/freesurfer, so you should have a

Re: [Freesurfer] Freeview command not found

External Email - Use Caution *Thanks so much!* *I installed the qt4 library but I received another error the* 'freeview: command not found error' *When I attempted it again, I received the following error:* freeview.bin $argv freeview.bin: error while loading shared libraries:

Re: [Freesurfer] Freeview command not found

External Email - Use Caution Hello Maeve, You can search for the package to install with apt-file, but you may need to install that first, so try, $ sudo apt install apt-file $ sudo apt update … now search for the package with that library name using apt-file $ sudo apt-file

[Freesurfer] Freeview command not found

External Email - Use Caution *Hello,* *I've been trying to resolve this issue but I haven't found a fix on the mailing lists. I downloaded and installed the most recent version of Freesurfer for Linux. I am running Ubuntu 16.04 LTS as guest on Virtualbox 5.2.22 on a windows 10

Re: [Freesurfer] freeview showing results in a strange manner

When you open it in freeview, you have to specify a surface (eg, fsaverage/surf/lh.white) and then load that file as an overlay to that surface On 11/21/2018 05:11 PM, 姜时泽 wrote: > > External Email - Use Caution > > Dear freesurfer experts, > I am using freesurfer to analyze my PET data

Re: [Freesurfer] freeview showing results in a strange manner

Hi Shize is lh.subj1.mgz a surface overlay? If so you display it as: freeview -f lh.inflated:overlay=lh.subj1.mgz cheers Bruce On Thu, 22 Nov 2018, 姜时泽 wrote: External Email - Use Caution Hi Ruopeng, my freeview command for this result is 'freeview -v lh.subj1.mgz'. I

Re: [Freesurfer] Freeview fly through frames

Hi Hervé I'm not sure what you want is supported, although Ruopeng could probably implement it pretty quickly. The movie frame utility is to make a flythrough of the volume, slice-by-slice, or a rotational move of the surface, not go go through frames of an overlay cheers Bruce On Thu, 22

Re: [Freesurfer] Freeview fly through frames

External Email - Use Caution Dear Freesurfer users, Any ideas? Does "frames" even refers to frames in the overlay? Best, Hervé LEMAITRE Faculté de Médecine Université Paris-Sud 63, rue Gabriel Péri 94276 Le Kremlin-Bicêtre - Mail original - De:

Re: [Freesurfer] freeview showing results in a strange manner

External Email - Use Caution Hi Ruopeng, my freeview command for this result is 'freeview -v lh.subj1.mgz'. I tried 'freeview -f lh.subj1.mgz' also, the message with in terminal said 'freadFloat: fread failed' Thank you Shize At 2018-11-22 06:38:29, "Ruopeng Wang" wrote:

Re: [Freesurfer] freeview showing results in a strange manner

What is your freeview command? Is there any message shown in the terminal? Ruopeng > On Nov 21, 2018, at 5:07 PM, 姜时泽 wrote: > > Dear freesurfer experts, > I am using freesurfer to analyze my PET data according to the tutorial > online. It works pretty well and I write the values of the

[Freesurfer] Freeview fly through frames

External Email - Use Caution Dear Freesurfer users, I want to use the "Save Movie Frames..." in freeview to go through 305 frames of an overlay on a pial surface. When a select: Fly through Frame Start number 0 End number 305 Step size 1 I click "write" and it writes only

Re: [Freesurfer] Freeview volume measurements on newly created VOIs

mri_segstats using your VOI as the arg to --seg. Also include --excludeid 0 On 11/14/2018 06:14 PM, Kim, Jisoo,M.D. wrote: > > Hello Freesurfer developers, > > > I am trying to get volume measurements (mm^3) on VOIs (volume of > interest) that I created on Freeview. All I can do is to export the

[Freesurfer] Freeview volume measurements on newly created VOIs

Hello Freesurfer developers, I am trying to get volume measurements (mm^3) on VOIs (volume of interest) that I created on Freeview. All I can do is to export the VOI as an .mgz file. Do you know of an easy way to get the stats in .txt or any other formats? 1) Freesurfer version:

Re: [Freesurfer] freeview crash when launch in ubuntu 18.04 {Disarmed}

External Email - Use Caution ​Hello Knut, You might be better off using the gcc 4.8 compilers on Ubuntu 18 which you can install with$ sudo apt-get install gcc-4..8 g++-4.8 gfortran-4.8 Then on your cmake command line you could set those before the actual cmake command. I've

[Freesurfer] freeview crash when launch in ubuntu 18.04

External Email - Use Caution Dear Freesurfer exports, I am unable to launch freeview. I have uncommented qt_setup to be able to start freeview but now it does not start at all. I am sending output from a session where I started it using gdb. Please look below. I am using the

Re: [Freesurfer] Freeview xcb error

Hi Emily, we’re working on this now and a fix will be released within the next couple days. best, Andrew From: on behalf of Emily Levin Reply-To: FS Help Date: Friday, November 2, 2018 at 11:49 AM To: FS Help Cc: Maximilian King Subject: [Freesurfer] Freeview xcb error External

[Freesurfer] Freeview xcb error

External Email - Use Caution Hi Freesurfer experts, I'm using redhat 7 so I installed the development centos7 version of freesurfer: *https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ * I followed the

Re: [Freesurfer] freeview libpng12.so.0 error

External Email - Use Caution ​Hello Ashesh, You need to install the "gdebi" command on your Ubuntu machine. Then download and install the libpng12 package from, http://se.archive.ubuntu.com/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1ubuntu1_amd64.deb Then install that

[Freesurfer] freeview libpng12.so.0 error

External Email - Use Caution Dear FreeSurfer Team, I'm running FreeSurfer on a 64-bit Linux machine running Ubuntu 18.04 LTS. Here is my config: ashesh@ashesh-gpu:~$ source $FREESURFER_HOME/SetUpFreeSurfer.sh freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Re: [Freesurfer] Freeview coordinates

openg Wang" À: freesurfer@nmr.mgh.harvard.edu Envoyé: Vendredi 26 Octobre 2018 19:08:28 Objet: Re: [Freesurfer] Freeview coordinates Hi Florent, I'm not sure how you got -152, 73, -66. If you apply the matrix to (152, 66, 73, 1), you should get -24, -55, 62 Which matches what is shown i

Re: [Freesurfer] Freeview coordinates

endredi 26 Octobre 2018 19:08:28 Objet: Re: [Freesurfer] Freeview coordinates Hi Florent, I'm not sure how you got -152, 73, -66. If you apply the matrix to (152, 66, 73, 1), you should get -24, -55, 62 Which matches what is shown in freeview. Best, Ruopeng On 10/26/2018 12

Re: [Freesurfer] Freeview coordinates

Hi Florent, I'm not sure how you got -152, 73, -66. If you apply the matrix to (152, 66, 73, 1), you should get -24, -55, 62 Which matches what is shown in freeview. Best, Ruopeng On 10/26/2018 12:06 PM, k3...@free.fr wrote: External Email - Use Caution Hi Bruce, Thanks for

Re: [Freesurfer] Freeview coordinates

External Email - Use CautionHi Bruce,Thanks for the tip.When I run the command on 'lh.white' surface for example, I don't get an affine transform but a simpler one:vox2ras-tk:-1  0 0  128 0  0 1 -128 0 -1 0  128 0  0 0  1So when I apply this transform to a pixel position (152, 66,

Re: [Freesurfer] Freeview coordinates

Hi Florent if you run mris_info on the surface of interest it will print out the vox2ras-tkr matrix that you can use for this conversion. cheers Bruce On Fri, 26 Oct 2018, k3...@free.fr wrote: >External Email - Use Caution > > Hi Freesurfer team, > > Sorry to ask a new question about

[Freesurfer] Freeview coordinates

External Email - Use Caution Hi Freesurfer team, Sorry to ask a new question about FreeSurfer coordinates (I know it has been debated multiple times reading old messages) but I am still confused with all these spaces. I have a very simple use case in Freeview, when I load the

[Freesurfer] freeview error

External Email - Use Caution 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

Re: [Freesurfer] freeview problem on Linux RHEL 7-4 libGLU.so.1

External Email - Use Caution Dear Avner and fellow freesurfer users, I've just came across the same issue testing QDEC after the installation of Freesurfer 6.0 using FEDORA 28 “qdec.bin: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No such

Re: [Freesurfer] Freeview error

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

[Freesurfer] Freeview error

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

[Freesurfer] freeview automated screenshots using color wheel scale & qt library issues

External Email - Use Caution Hi, I am attempting to generate automated screenshots with freeview version 3.July 2018 and I noticed that when applying the color wheel option for a surface overlay the coloring would be wrongly applied and I would need to enter the configuration

Re: [Freesurfer] Freeview: Load multiples overlays for one surface

External Email - Use Caution It's works! Thanks a lot! El vie., 7 sept. 2018 a las 16:46, Ruopeng Wang () escribió: > Yes, it is possible. But you should use ':' as separator like this: > > -f > surf/lh.inflated:overlay=surf/lh.sulc:overlay=surf/lh.thickness:overlay_threshold=1,5

Re: [Freesurfer] Freeview: Load multiples overlays for one surface

Yes, it is possible. But you should use ':' as separator like this: -f surf/lh.inflated:overlay=surf/lh.sulc:overlay=surf/lh.thickness:overlay_threshold=1,5 Ruopeng On 09/07/2018 03:11 PM, Emanuel Alvaredo wrote: External Email - Use Caution Hi! I would like from command line to

[Freesurfer] Freeview: Load multiples overlays for one surface

External Email - Use Caution Hi! I would like from command line to open one surface with multiple ovelays. For example, intead of this ..-f surf/lh.inflated:overlay=surf/lh.sulc surf/lh.inflated:overlay=surf/lh.thickness:overlay_threshold=1,5 I would like to do something

[Freesurfer] Freeview heat map

External Email - Use Caution Dear Freesurfer developers, I analyzed some data in Freesurfer. At the end, I used "mri_segstats" to measure a parameter of interest for every ROI in DKT atlas. I would like to load the mean values of this parameter to Freeview (every ROI in DKT has

Re: [Freesurfer] Freeview modalSession has been exited prematurely - check for a reentrant call to endModalSession:

do you have read permissions? Can you run ls -l on one of them? And mri_info? On Sat, 14 Jul 2018, Renew Andrade wrote: External Email - Use Caution Hello:I attach here the command output of an error that I have while using Freeview. It doesn’t allows me to read any file. 

[Freesurfer] Freeview modalSession has been exited prematurely - check for a reentrant call to endModalSession:

External Email - Use Caution Hello: I attach here the command output of an error that I have while using Freeview. It doesn’t allows me to read any file. sh-3.2# freeview -v \ > good_output/mri/T1.mgz \ > good_output/mri/wm.mgz \ > good_output/mri/brainmask.mgz \ >

Re: [Freesurfer] Freeview not showing images

r-boun...@nmr.mgh.harvard.edu On Behalf Of Ruopeng Wang Sent: Friday, June 29, 2018 10:43 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freeview not showing images What if you run 'glxgears'? Does it render properly? Ruopeng On 06/29/2018 09:50 AM, Mark Wagshul wrote: Yes, I’m r

Re: [Freesurfer] Freeview not showing images

ddress above, delete this email from your computer, and destroy any copies in any form immediately. *From:* freesurfer-boun...@nmr.mgh.harvard.edu *On Behalf Of *Ruopeng Wang *Sent:* Friday, June 29, 2018 8:39 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Freeview not showing

Re: [Freesurfer] Freeview not showing images

oy any copies in any form immediately. From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Ruopeng Wang Sent: Friday, June 29, 2018 8:39 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freeview not showing images This looks like a display artifact. Are you running freeview via som

Re: [Freesurfer] Freeview not showing images

This looks like a display artifact. Are you running freeview via some kind of X Terminal Emulator on Windows? What if you load a volume? Ruopeng > On Jun 28, 2018, at 7:33 PM, Mark Wagshul > wrote: > > Hi. > > I’m a newbie to Freeview, hoping that this is a simple problem. When I open >

[Freesurfer] Freeview not showing images

External Email - Use Caution Hi. I'm a newbie to Freeview, hoping that this is a simple problem. When I open it (specifying the lh.pial surface), I get this view: [cid:image001.jpg@01D40F16.EC48FB10] Anyone have an idea what's going on here, is it an issue with the screen

Re: [Freesurfer] Freeview surface annotation outline line thickness

Hi Kayle, There is no such option. I'll put it on my list for future improvement. Best, Ruopeng On 05/04/2018 01:09 PM, Kayle Sawyer wrote: The freeview flag "annot_outline=1" is great for viewing results for significant clusters from mri_glmfit-sim. Is there a way to make the outlines

[Freesurfer] Freeview surface annotation outline line thickness

External Email - Use Caution The freeview flag "annot_outline=1" is great for viewing results for significant clusters from mri_glmfit-sim. Is there a way to make the outlines thicker? With the default thickness, the outlines are difficult to make out in a multipanel figure. (The

Re: [Freesurfer] [Freesurfer/Freeview cutting]

Hi, There is no surface cutting function in freeview. But I’m going to add it. Will let you know when I have it ready for testing. Best, Ruopeng > On Mar 7, 2018, at 11:16 PM, Dave Yas wrote: > > Hello, > > Can we cut the surface (for flatting later) in freeview? if

[Freesurfer] [Freesurfer/Freeview cutting]

Hello, Can we cut the surface (for flatting later) in freeview? if yes, how? I cant find a tutorial online for that. tksurfer is not working, it crashes by it self. If i cant use freeview to cut, do you suggest another alternative? thank you ___

Re: [Freesurfer] freeview. crash with undefined symbol: _ZN6QMutex12lockInternalEv when I choose colormap lookup table

d.so.1 (0x7f78aeca2000) libXau.so.6 => /lib64/libXau.so.6 (0x7f78aea9e000) I have Fedora 27. Knut Jørgen From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Knut J Bjuland <knutjor...@outlook.com>

[Freesurfer] freeview. crash with undefined symbol: _ZN6QMutex12lockInternalEv when I choose colormap lookup table

Dear Freesurfer export, When I chose colormap to lookup table with bert/mri/aseg.mgz freeview crash with the following message. [New Thread 0x7fffce7f4700 (LWP 78012)] /usr/local/freesurfer60/bin/freeview.bin: symbol lookup error: /usr/local/freesurfer60/bin/freeview.bin: undefined

Re: [Freesurfer] freeview for FS-FAST results

Thanks. My question is only for visualization purpose, not for statistics. I would like to exclude from maps the clusters < 5 voxels. Stefano > > Il 5 marzo 2018 alle 21.42 Douglas N Greve ha > scritto: > > Set --cwp 1. This will keep all clusters

Re: [Freesurfer] freeview for FS-FAST results

Thanks, what's meaning FYI? What do you advise? > > Il 5 marzo 2018 alle 21.42 Douglas N Greve ha > scritto: > > Set --cwp 1. This will keep all clusters regardless of size. Then look > in the summary table and see where the cluster-wise p-value is for

Re: [Freesurfer] freeview for FS-FAST results

Set --cwp 1. This will keep all clusters regardless of size. Then look in the summary table and see where the cluster-wise p-value  is for 5 voxels or less, then rerun with that cwp. FYI, this is not a good way to correct for multple comparisson On 03/05/2018 03:35 PM, std...@virgilio.it

[Freesurfer] freeview for FS-FAST results

Hi list, is it possible to avoid the clusters < 5 voxels using freeview for FS-FAST results (mni.305) obtained after running mri_glmfit-sim --glmdir my-glm.wls --grf? Thanks Kind regards Stefano___ Freesurfer mailing list

Re: [Freesurfer] Freeview update on Mac

Hi Sarah, I updated the wiki page. We actually just put up a standalone, dev freeview app today. best Andrew On February 27, 2018 at 11:38:57 AM, Sarah Cole (coleashle...@gmail.com) wrote: Hi Doug/Zeke, Could you please update the page for freeview update on

[Freesurfer] Freeview update on Mac

Hi Doug/Zeke, Could you please update the page for freeview update on Mac- if it is available. https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview Thanks, S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Freeview mac OSX firewall setting

Dear all, Has anyone using mac OSX experienced constant popping-up of a window asking firewall setting every time when you open FreeView although you have already set it? It's not critical but kind of annoying... so hope you one of you already solved it. Best, -- Seung-Goo ("SG") KIM, Ph.D.

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