Re: [Freesurfer] Freeview

Can you try creating a symbolic link to libpng16.so.16 in the same location and call it libpng12.so.0? Ruopeng > On Jan 6, 2018, at 5:01 AM, Samir Rekic wrote: > > Hi Ruopeng, > I have the libpng16.so.16 installed on my system > And tried to install the

Re: [Freesurfer] Freeview

Hi Ruopeng, I have the libpng16.so.16 installed on my system And tried to install the libpng12.so.0 but the apt-get install order nor Synaptics could not find anything Rekic ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Freeview

Hi Rekic, Do you know what version of libpng installed on your system? Ruopeng > On Jan 5, 2018, at 6:04 AM, Samir Rekic wrote: > > Dear FreeSurfer Team, > I just wanted to ask you a quick question about installing Freeview on a > Ubuntu 17.04, 32-Bit Computer. I

[Freesurfer] Freeview

Dear FreeSurfer Team, I just wanted to ask you a quick question about installing Freeview on a Ubuntu 17.04, 32-Bit Computer. I couldn’t find an appropriate answer in you archives so I decided to write you. I could not find an 32 bit Version of Freeview in your archiv of previous releases so I

Re: [Freesurfer] Freeview problem: ROIs showing in wrong slice when loaded with certain volumes

Hi Sara, Would it be possible to send me the files and the freeview command you ran? Best, Ruopeng > On Dec 6, 2017, at 6:16 PM, Sims, Sara A wrote: > > Hello, > I am having an issues with freeview ROIs. When I use the command line to load > the orig and the ROIs by

[Freesurfer] Freeview problem: ROIs showing in wrong slice when loaded with certain volumes

Hello, I am having an issues with freeview ROIs. When I use the command line to load the orig and the ROIs by themselves they display correctly, however when I display the orig volume and the volume versions of the ROIs- the label ROIs suddenly change to be in the wrong plane. I have done this

[Freesurfer] freeview abort

Hi experts, When I use xshell to connect our Ubuntu system??freeview aborts without any other complaint.wade@DL:/$ freeview Abort (core dumped) after dealed with suggestion on https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-September/053992.html??freeview still cannot work.

Re: [Freesurfer] Freeview Crashes!!

What is the output of: ldd `which freeview.bin` thanks, Andrew On Nov 10, 2017, at 8:52 AM, Ruopeng Wang > wrote: What version of freesurfer did you run? It looks like the issue is related to incompatible/missing libraries.

Re: [Freesurfer] Freeview display issue in Ubuntu 14/16 VM

Have you installed the latest graphics driver for the virtual machine? Is there any 3D/OpenGL settings you can play with for the virtual machine? Best, Ruopeng On 11/14/2017 11:44 AM, Nicholas Blauch wrote: Hi Freesurfer folks, I’ve recently started using an Ubuntu virtual machine on PC

[Freesurfer] Freeview display issue in Ubuntu 14/16 VM

Hi Freesurfer folks, I’ve recently started using an Ubuntu virtual machine on PC host, and have noticed a problem in both Ubuntu 14 and 16 (but not 12) with Freeview. When a freeview window is opened, the black screen for displaying volumes/surfaces is necessarily at the front of the screen

Re: [Freesurfer] Freeview Crashes!!

What version of freesurfer did you run? It looks like the issue is related to incompatible/missing libraries. Ruopeng > On Nov 10, 2017, at 7:18 AM, vin rasa wrote: > > Dear FS Experts, > > While using updated Freeview in ubuntu 16.04, I reproducibly get two > following

[Freesurfer] Freeview Crashes!!

Dear FS Experts, While using updated Freeview in ubuntu 16.04, I reproducibly get two following errors: 1st Crash (While selecting color for the volume): Volume - Colormap -Lookup Table option: 0�freeview.bin: symbol lookup error: freeview.bin: undefined symbol: _ZN6QMutex12lockInternalEv 2nd

Re: [Freesurfer] Freeview Versions

Hi Arkadiy, If you send the buildstamps for your two freesurfer distributions, I can see what the respective versions are. You can print the buildstamp by running the command “bugr” in a sourced fs environment best Andrew On Sep 19, 2017, at 2:25 PM, Maksimovskiy, Arkadiy

Re: [Freesurfer] Freeview aborts under centos6

e case, hopefully freeview will run... or at least throw a > different error > > best > Andrew > > From: Hoopes, Andrew > Sent: Tuesday, September 19, 2017 1:56 PM > To: Freesurfer support list > Subject: Re: [Freesurfer

Re: [Freesurfer] Freeview Strange Behavior

Hi Angel, It appears you're running freeview from FS v5.3, which is over 4 years old. Anyway you can try v6.0 or the latest dev build? Best, Rubin On 09/20/2017 10:19 AM, Torrado Carvajal, Angel wrote: Good morning, We have been experiencing a weird behavior in Freeview when loading non

Re: [Freesurfer] Freeview aborts under centos6

Hi Andrew, Thank you! Here is the output of bugr > [gschwind@login1 ~]$ bugr > Cut-and-paste the following info into your FreeSurfer problem report: > - > FREESURFER_HOME: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64 >

[Freesurfer] Freeview Versions

Dear Freesurfer Experts, My apologies if I missed this information elsewhere on the website, but could not find any info. about it. There appear to be two Freeview versions, both from 2017 (released one day apart), for which the screenshots are attached. I was wondering if you could let me

Re: [Freesurfer] Freeview aborts under centos6

Hi Markus, okay - I'll directly send you a tar of the vtk library. A reinstall of vtk might work, because those shared objects that we distribute are usually sym-linked Can you also send the fs buildstamp? You can get this by running the command ‘bugr’ after sourcing freesurfer Andrew On Sep

Re: [Freesurfer] Freeview aborts under centos6

Dear Andrew, after the System admin executed your proposed commands, it stays the same, Freeview aborts. Is there anything else we could try? Thank you and best wishes, Markus 2017-09-15 20:06 GMT+02:00 Hoopes, Andrew : > Hm okay thanks - I’m curious what happens

Re: [Freesurfer] Freeview aborts under centos6

Thanks, I gave this to the system admin as I do not ave the sudo rights. I’ll come back! Best, Markus > On 15 Sep 2017, at 20:06, Hoopes, Andrew wrote: > > Hm okay thanks - I’m curious what happens when you run: > > cd $FREESURFER_HOME/lib/vtk/lib/vtk-5.6 > # backup

Re: [Freesurfer] Freeview aborts under centos6

Hm okay thanks - I’m curious what happens when you run: cd $FREESURFER_HOME/lib/vtk/lib/vtk-5.6 # backup the shared objects mv libvtkverdict.so libvtkverdict.so.bk mv libvtkverdict.so.5.6 libvtkverdict.so.5.6.bk # link them to 5.6 ln -s libvtkverdict.so.5.6.0 libvtkverdict.so ln -s

Re: [Freesurfer] Freeview aborts under centos6

Dear Andrew, The command gives this result: [gschwind@login1 ~]$ /sbin/ldconfig -N -v $(sed 's/:/ /' <<< > $LD_LIBRARY_PATH) | grep libvtkverdict.so > /sbin/ldconfig: Can't stat > /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71.x86_64/jre/lib/amd64/server: No > such file or directory > /sbin/ldconfig:

Re: [Freesurfer] Freeview aborts under centos6

Hi Markus, What is the output when you run the following: (this will list libraries you have access to) /sbin/ldconfig -N -v $(sed 's/:/ /' <<< $LD_LIBRARY_PATH) | grep libvtkverdict.so best, Andrew On Sep 15, 2017, at 3:33 AM, Markus Gschwind

[Freesurfer] Freeview aborts under centos6

Dear experts, I am installing freeusrfer on our cluster which is running Centos6. [gschwind@login1 ~]$ uname -a Linux login1.cluster 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Apr 11 17:13:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Freeview aborts without any other complaint. [gschwind@login1 ~]$

[Freesurfer] Freeview aborts under centos6

Hi experts, I am installing freeusrfer on our cluster which is running Centos6. [gschwind@login1 ~]$ uname -a Linux login1.cluster 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Apr 11 17:13:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Freeview aborts without any other complaint. [gschwind@login1 ~]$

Re: [Freesurfer] Freeview in FreeSurfer 6.0

I think this may have been fixed in the dev build. Would it possible for you to try the dev build? You can download it here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev > On Aug 21, 2017, at 1:34 AM, Wu Jianxiao (Jadecci)

[Freesurfer] Freeview in FreeSurfer 6.0

Dear FreeSurfer team, I was viewing MNI152 template from FSL in freeview using FreeSurfer 6.0, and somehow there was a shift between 1mm and 2mm template. The problem does not show in FreeSurfer 5.3. Is there an error with freeview in FS6 or did the command change? The command I used is as

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

Hello all, I installed the latest version for Linux I get this message when trying to run an example: "freeview.bin: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No such file or directory" I installed the missing library and now it is in

Re: [Freesurfer] freeview command error

...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Tuesday, July 11, 2017 6:30 PM To: Freesurfer support list Subject: Re: [Freesurfer] freeview command error Hi Idil do you know what shell you are using in the terminal that you are trying to call freeview from

Re: [Freesurfer] freeview command error

gt; From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Tuesday, July 11, 2017 6:03 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] freeview command error > > Hi Idil

Re: [Freesurfer] freeview command error

of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Tuesday, July 11, 2017 6:03 PM To: Freesurfer support list Subject: Re: [Freesurfer] freeview command error Hi Idil how do you setup freesurfer? If you are using bash (and it looks like you are) you should source the *.sh file, not the *.csh. Also

Re: [Freesurfer] freeview command error

, Idil From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Tuesday, July 11, 2017 6:03 PM To: Freesurfer support list Subject: Re: [Freesurfer] freeview command

Re: [Freesurfer] freeview command error

Hi Idil how do you setup freesurfer? If you are using bash (and it looks like you are) you should source the *.sh file, not the *.csh. Also, note that you should use T1.mgz not T1/mgz in your freeview command line cheers Bruce On Tue, 11 Jul 2017, Yagmur Ozdemir 19 wrote: Hello, I am

[Freesurfer] freeview command error

Hello, I am installing Freesurfer with my limited coding knowledge and this problem with freeview came up when I was trying to view the volumes of recon-ed subject. lab@lab-ThinkStation-E31:~/Desktop/freesurfer/subjects$ freeview -v practice/mri/T1/mgz No command 'freeview' found, did you

[Freesurfer] Freeview Application

Hello FS team, Is there any way to download FreeView as a standalone application on a Windows computer, or would I need to download freesurfer as a whole and then VPN? Thanks in advance! Panos Panagiotis Fotiadis Research Technologist II J. P. Kistler Stroke Research Center Massachusetts

Re: [Freesurfer] Freeview overlay, positive values only

;Unrecognized sub-option flag 'overlay_color'." Perhaps you have a more > recent version of freesurfer/freeview? > > I'm currently running the following: > freesurfer-x86_64-unknown-linux-gnu-stable5-20130513 with Freeview version > 1.0, Build May 13, 2013. If necessary, I'll upg

Re: [Freesurfer] Freeview overlay, positive values only

Hi Ruopeng, Thanks for the suggestion. I tried this but freesurfer complained "Unrecognized sub-option flag 'overlay_color'." Perhaps you have a more recent version of freesurfer/freeview? I'm currently running the following: freesurfer-x86_64-unknown-linux-gnu-stable5-20130513 wit

Re: [Freesurfer] Freeview overlay, positive values only

You can set truncate like this from command-line: freeview -f surface_filename:overlay=overlay_filename:overlay_color=truncate Best, Ruopeng > On Jun 3, 2017, at 1:03 AM, Rita Elena Loiotile wrote: > > Hi, > > Is there an easy command to only load positive values of an

[Freesurfer] Freeview overlay, positive values only

Hi, Is there an easy command to only load positive values of an overlay in Freeview. I know in tksurfer it's truncphaseflag. Freeview does have the "truncate" option in the surface pane of the GUI. But, I don't see a command line flag. I'm hoping there's a way that's not in the help

Re: [Freesurfer] Freeview error

The error message says it: ERROR: MRISread: file '/Users/schumman/Non-Inf_FS_5_3/0002_WIP_3DT1_SAG_SENSE_3_1.nii/surf/lh.area.pial' has many more faces than vertices! Probably trying to use a scalar data file as a surface! You were not loading a correct surface file. lh.area.pial is a scalar

Re: [Freesurfer] Freeview error

actually the attachment doesn't have an extension, so I can't even look at it. Can you just resend as text? cheers Bruce On Sat, 27 May 2017, Schumman Resonance wrote: Attached is the full command line; as per a screen output Freeview quits.I have not tested all surface files, but Freeview

Re: [Freesurfer] Freeview error

I'll take a look, but in the future can you just send this as text embedded in the email instead of screen shots. thanks Bruce On Sat, 27 May 2017, Schumman Resonance wrote: Attached is the full command line; as per a screen output Freeview quits.I have not tested all surface files, but

Re: [Freesurfer] Freeview error

Attached is the full command line; as per a screen output Freeview quits. I have not tested all surface files, but Freeview uploads fine pial, white, inflated, orig, and sphere. Thanks! On Sat, May 27, 2017 at 8:46 PM, Bruce Fischl wrote: > Can you send us the full

Re: [Freesurfer] Freeview error

Can you send us the full command line and screen output? Cheers Bruce > On May 27, 2017, at 11:45 PM, Schumman Resonance wrote: > > Hi, > > Newbie question. > > When I try to upload a surface to Freview I get the following error: > > > [0]PETSC ERROR: >

[Freesurfer] Freeview error

Hi, Newbie question. When I try to upload a surface to Freview I get the following error: [0]PETSC ERROR: [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job:

Re: [Freesurfer] Freeview libpng warning

: [Freesurfer] Freeview libpng warning Does freeview still run? If it does, you can just ignore the warning. Best, Ruopeng On May 4, 2017, at 12:39 PM, Kanoff, Kristen Elise <kkan...@mgh.harvard.edu<mailto:kkan...@mgh.harvard.edu>> wrote: Hello FreeSurfer community, I am hav

Re: [Freesurfer] Freeview libpng warning

Does freeview still run? If it does, you can just ignore the warning. Best, Ruopeng > On May 4, 2017, at 12:39 PM, Kanoff, Kristen Elise > wrote: > > Hello FreeSurfer community, > > I am having an issue with the icon graphics displaying properly in freeview >

[Freesurfer] Freeview libpng warning

Hello FreeSurfer community, I am having an issue with the icon graphics displaying properly in freeview (Linux virtual machine - Ubuntu). I receive the following warning when opening the application: "libpng warning: Application built with libpng-1.2.7 but running with 1.6.25" The newer

Re: [Freesurfer] Freeview GUI Display Issues

Would it be possible for you to update to Freesurfer v6.0? On my macOS Sierra + FS 6.0, freeview appears to work well. Best, Ruopeng On 05/02/2017 12:18 PM, Kevin Japardi wrote: Hello Freesurfer! I'm working with someone in our group on some Freesurfer QA, and she's having some issues with

[Freesurfer] Freeview GUI Display Issues

Hello Freesurfer! I'm working with someone in our group on some Freesurfer QA, and she's having some issues with using the freeview gui. She's using a Mac with OS Sierra, with X11 2.7.8. Some of the issues she's having are: 1) The Mac red-yellow-green 'exit/hide/extend' buttons are blackened

Re: [Freesurfer] Freeview - corrupted pixel values after saving volume (via save as) when images with mutually different geometry are simultaneously loaded

Dear Ruopeng, thank you for the feedback. Yes, the behavior is exacly like you described. I suspected that this has something to do with resampling but I was not sure. The stripes were result of nearest-neighbor interpolation. Antonin Hi Antonin, When you load two images like that, the

Re: [Freesurfer] Freeview - corrupted pixel values after saving volume (via save as) when images with mutually different geometry are simultaneously loaded

Hi Antonin, When you load two images like that, the second image will be resampled, using nearest neighbor method by default. And when you save, it will be resampled back to its original space. So there will be shifted voxels depending how oblique it is to the first image. So I think what you

[Freesurfer] Freeview - corrupted pixel values after saving volume (via save as) when images with mutually different geometry are simultaneously loaded

Dear experts, I encountered following issue with freeview: When two images with mutually different geometry are simultaneously loaded and one of them is saved (via save as), its pixel values get somewhat corrupted. There are strips in image with modified pixel values. It seems to affect only

Re: [Freesurfer] Freeview

Existing labels are the labels that the current loaded volume contains. For example, 1109 exists in the look up table. But the volume you loaded does not contain that label. So it is not possible to show that label for the volume. Ruopeng > On Apr 8, 2017, at 6:53 AM, N Saf

[Freesurfer] Freeview

Dear FreeSurfer experts, I have two questions please. 1- I cannot understand the concept of "existing labels". Why few labels (such as #19) do exist in the LUT, but they cannot be overlaid on the brain? What should I do if I need to map one of those labels on the brain that disappear when I

[Freesurfer] FREEVIEW: Registration visualization

Hello everyone, I am quite new to FreeSurfer and I have a doubt for the visualization of the data on a registered surface.Is it enough to load in freeview the surface.reg with overlayed the data like in: freeview -f lh.sphere.reg:overlay=lh.sulc or  freeview -f lh.sphere.reg:annot=aparc.annot

Re: [Freesurfer] Freeview command line option for multiple screenshots

Hi Peng, You can write all your freeview commands in a text file and call “freeview -cmd cmd.txt”. In cmd.txt, just write commands like this line by line: freeview volume_files -f surface_files … (all the initial file loadings) freeview (other commands such as -cam) -ss screenshot1.jpg

[Freesurfer] Freeview command line option for multiple screenshots

Dear all, I have several different overlays on the same brain surface. When I want to run freeview in command line and take screenshots automatically, I need to restart freeview and load the surface for each screenshot. Is it possible to keep the program on and only change overlays and take

Re: [Freesurfer] Freeview default cursor

Hi Eli, There is no command-line option to change the default cursor style/color. However, if you change it from the GUI, the change will be saved when you close freeview so it will be the default one the next time you open freeview. Best, Ruopeng On 02/28/2017 11:35 AM, Rockers, Elijah D.

[Freesurfer] Freeview default cursor

Hello, I could not find any information on changing the cursor via command line. My goal is to persistently change the default cursor style/color, I was going to create an alias on my system. Thanks, Eli Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston

[Freesurfer] Freeview 3D brush

Freesurfer devs, I attempted a modification of freeview to insert a 3D brush. I have got it working. If you want to review it to put it in the main version it is there a way to submit the diff with the changes? Cheers, Chris. Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch

Re: [Freesurfer] Freeview

Thank you very much ,it was a great help . Best Regards, Nazanin On Tue, Feb 21, 2017 at 7:34 PM, Ruopeng Wang wrote: > Just open FreeSurferColorLUT.txt file in your freesurfer installation > directory, you should be able to figure the format. > > On Feb 21, 2017,

[Freesurfer] Freeview X Error: BadValue

Hi FS gurus, I am remote logging in to nmr nexlin machines from my work iMAC and I am trying to view some freesurfer results with Freeview, but I am getting the following error: llebois@nexlin9:/eris/ressler/DD_FS_160222/150305_NTD015_FS/mri/assembly$ freeview -v nu.mgz

Re: [Freesurfer] Freeview

Just open FreeSurferColorLUT.txt file in your freesurfer installation directory, you should be able to figure the format. > On Feb 21, 2017, at 10:59 AM, N Saf wrote: > > Dear Ruopeng, > > Thank you for the fast response ,where can I learn how to create my custom > lookup

Re: [Freesurfer] Freeview

Dear Ruopeng, Thank you for the fast response ,where can I learn how to create my custom lookup table step by step ? and what the format of this file is?any help will be very appreciated. Best Regards, Nazanin On Tue, Feb 21, 2017 at 6:45 PM, Ruopeng Wang wrote: >

Re: [Freesurfer] Freeview

Hi Nazanin, To change color you will need to modify the look up table, i.e., load your own look up table. There is no way to only display a few selected labels. As a workaround, you may try applying a look up table with only a few labels in it. Best, Ruopeng > On Feb 21, 2017, at 5:20 AM, N

[Freesurfer] Freeview

Dear Experts, I load the T1 and aseg file in freeveiw and select the lookup table ,and show as isosurface in 3D view for a label .Is it possible to change the color(for example label 13 is blue but I want to show it as yellow!).another question is that if I want to show multiple labels which are

Re: [Freesurfer] freeview problem with w-file overlay

sure, use save_mgh to write them to a .mgz or .mgh file cheers Bruce On Mon, 6 Feb 2017, Björn Herrmann wrote: Dear list, I would like to use freeview to display my activations patterns. I source-localized MEG data in matlab using the freesurfer standard brain as a source space. I saved

Re: [Freesurfer] freeview problem with w-file overlay

You can write it out as a curv (write_curv.m), or you can use mri_surf2surf to convert from w (aka paint) to curv or mgh format On 02/06/2017 01:33 PM, Björn Herrmann wrote: > Dear list, > > I would like to use freeview to display my activations patterns. I > source-localized MEG data in matlab

[Freesurfer] freeview problem with w-file overlay

Dear list, I would like to use freeview to display my activations patterns. I source-localized MEG data in matlab using the freesurfer standard brain as a source space. I saved the source localization as a w-file, that is, as an overlay. I used to display the overlay in tksurfer, but I cannot

Re: [Freesurfer] freeview command line options

Thanks for the advice, bruce. On Fri, Jan 27, 2017 at 4:17 PM, Bruce Fischl wrote: > probably you should just smooth the volume and save it as a new volume > before running freeview > > cheers > Bruce > On Fri, 27 Jan 2017, Ruopeng Wang wrote: > >> Hi Peng, >> >> No,

Re: [Freesurfer] freeview command line options

Dear Ruopeng, Thank you for the information. best Peng On Fri, Jan 27, 2017 at 4:10 PM, Ruopeng Wang wrote: > Hi Peng, > > No, there is no command-line option for that. I will add it in future update. > > Best, > Ruopeng > >> On Jan 27, 2017, at 9:49 AM, peng

Re: [Freesurfer] freeview command line options

probably you should just smooth the volume and save it as a new volume before running freeview cheers Bruce On Fri, 27 Jan 2017, Ruopeng Wang wrote: > Hi Peng, > > No, there is no command-line option for that. I will add it in future update. > > Best, > Ruopeng > >> On Jan 27, 2017, at 9:49 AM,

Re: [Freesurfer] freeview command line options

Hi Peng, No, there is no command-line option for that. I will add it in future update. Best, Ruopeng > On Jan 27, 2017, at 9:49 AM, peng wrote: > > Dear Freesurfer experts, > > When I use Freeview GUI to show overlays on a surface, I can click on > the button "Configure",

Re: [Freesurfer] Freeview v6.0 Draw ROI Bug - Only Brush Size of 1 Saved?

Hi Doug, We will investigate and fix it asap. Best, Ruopeng > On Jan 25, 2017, at 4:13 PM, Douglas Merkitch > wrote: > > Hello, > > I think I have encountered a bug in freeview on > freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c. When I attempt to draw and >

Re: [Freesurfer] Freeview in 6.0 - editing labels

thanks! I will give this a shot. best Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Wed, Jan 25, 2017 at 12:41 PM, Ruopeng Wang wrote: > Hi Trisanna, > > There is no straight-forward way to let you edit surface

Re: [Freesurfer] Freeview in 6.0 - editing labels

Hi Trisanna, There is no straight-forward way to let you edit surface labels but you can try these steps: 1. Load a volume and a surface. 2. Load the label you want to edit as volume label (ROI). 3. Select the ROI in the layer list to bring up ROI property panel. Click on “Map to Surface”

[Freesurfer] Freeview in 6.0 - editing labels

Hi there Does the 6.0 version of Freeview have a way to edit labels on surfaces similar to how tksurfer allowed us to do this? Thanks! Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology ___ Freesurfer mailing

[Freesurfer] freeview error (libpng12.so.0) on Ubuntu

Hello all! I know there are issues with freeview use on Ubuntu, but I hit a wall in fixing them. I am currently getting this error when typing "freeview" into the command prompt: "freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file

[Freesurfer] freeview V6beta - reposition surface option

Dear experts, I have several questions regarding "reposition surface" tool in freeview (V6beta): 1. Are here any documentation how to use "reposition surface" tool? I would especially velcome the explanation of significance of "sigma", "size" and "gradient direction" parameter. I tried to

Re: [Freesurfer] Freeview -dti Display as Vectors Discrepancy

] on behalf of Douglas Merkitch [douglas_merki...@rush.edu] Sent: Wednesday, November 23, 2016 12:37 PM To: Freesurfer support list Subject: [Freesurfer] Freeview -dti Display as Vectors Discrepancy Hello experts, I have come across what I think could be an inconsistency with how freeview

[Freesurfer] Freeview -dti Display as Vectors Discrepancy

Hello experts, I have come across what I think could be an inconsistency with how freeview interprets and/or displays dti data as vectors. Specifically, the x component seems to be inverted in freeview from freesurfer-Darwin-lion-stable-pub-v5.3.0 as compared to fslview (version 509) AND

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 >

[Freesurfer] Freeview display problems

I am running Freeview Version 1.0 Build May 26 2016 remotely from my Mac OS 10.11.6 with X11 forwarding. I have been using this setup for years. However, within the last wee I encountered a problem with the FreeView display. Everything works fine except that the image panes are no longer

Re: [Freesurfer] FreeView questions

Hi Anders, Try turn off/on color bar or change the overlay thresholds to see if it updates. I believe this is fixed in v6.0. As to rotate the 3D view by certain degrees, there is no GUI for that. You can do that in the command-line via "-cam" options. Run "freeview -h" for more info on how

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

[Freesurfer] Freeview Loading Volumes

I use Freeview on a daily basis as my primary image viewer. I like it a lot and found it to be tremendously useful. I am usually interested in opening images in the current directory where I launched Freeview from the command line. I know you can load multiple images at once from the command

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

Re: [Freesurfer] Freeview error: Surface does not contain valid volume geometry information

Hi Claudia you need to send us your full command line and the various other information we ask for when reporting issues (operating system, etc..) thanks Bruce On Tue, 20 Sep 2016, Claudia Dacquino wrote: Hi all, after doing GLM analysis I'm trying to run freeview to see results, but I

[Freesurfer] Freeview error: Surface does not contain valid volume geometry information

Hi all, after doing GLM analysis I'm trying to run freeview to see results, but I get this warning: Surface does not contain valid volume geometry information. It may not align with volumes and other surfaces. What's wrong? I'm using 5.1 version. Thanks to all. Claudia -- Dott.ssa Claudia

[Freesurfer] freeview error:

Hi FreeSurfer Team, I am trying to edit longitudinal data using FreeView. The original timepoints were processed and edited using FreeSurfer 5.1. The longitudinal data was also ran using FreeSurfer 5.1. I am currently trying to edit the longitudinal data using FreeView, however FreeView

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

[Freesurfer] Freeview quits unexpectedly

Hello FreeSurfer developers, I am trying to load a thickness file (ex: lh.long.thickness-avg.fwhm10.mgh) in freeview, but as soon as I click the file or press enter after the command line, the program quits unexpectedly. I can load T1, orig.mgz, .pial files, etc. without problem. But when it

Re: [Freesurfer] Freeview question

Yes, that worked Thank you. > Have you tried rebooting your computer? > > Best, > Ruopeng > >> On Jul 12, 2016, at 3:14 PM, pfot...@nmr.mgh.harvard.edu wrote: >> >> Hello FS Community, >> Lately, whenever I am trying to use freeview I get the following error >> message: >> >> freeview.bin:

Re: [Freesurfer] Freeview question

Have you tried rebooting your computer? Best, Ruopeng > On Jul 12, 2016, at 3:14 PM, pfot...@nmr.mgh.harvard.edu wrote: > > Hello FS Community, > Lately, whenever I am trying to use freeview I get the following error > message: > > freeview.bin: error while loading shared libraries:

[Freesurfer] Freeview question

Hello FS Community, Lately, whenever I am trying to use freeview I get the following error message: freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6: cannot open shared object file: No such file or directory Exit 127 The error started showing up after the cluster went

[Freesurfer] Freeview: how to change spline color bar

Dear Freesurfers, How would I be able to use a different colormap under point sets please? I can only find "solid color" and "heatmap" but a blue to red colorbar would suit my needs more. Any assistance is greatly appreciated. Thank you, Best wishes, Barbara

Re: [Freesurfer] Freesurfer/Freeview help

>       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

Re: [Freesurfer] Freesurfer/Freeview help

r the pial surface. We supply voxel >> > segmentations of lots of other things that you could mesh, but >> > we don't >> > by default. >> > >> > cheers >> > Bruce >> > On Mon, 27 Jun 2016, Abbie McNulty wr

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

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