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,

[Freesurfer] Freeview recon button

Hello freesurfers, I downloaded freesurfer v5.3.0. & I am using freeview, but it doesn't have the Recon edit button. I saw that someone asked about this questions twice in the archive but was never answered. There was a note in the wiki page that reads "*Note*: Recon edit mode is only available

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

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

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

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

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. >

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:

Re: [Freesurfer] Freesurfer/Freeview help

7 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 and am not > > familiar with the to

Re: [Freesurfer] Freesurfer/Freeview help

t you 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 fin

Re: [Freesurfer] Freesurfer/Freeview help

lots of other things that you 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 ve

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 mesh

[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 tools. So far, I have only uploaded brain.mgt from the bert file that comes with the program. If I wanted to mesh

[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] 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 "

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

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:

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

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

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

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. >

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

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 >

Re: [Freesurfer] FreeView updating

Latest freeview is just what comes with the developement version of freesurfer. You can download the latest development verion from the following page: https://surfer.nmr.mgh.harvard.edu/fswiki/Download On 06/13/2016 12:44 PM, Chiu, Bryan (PHTH) wrote: Hello, I would like to download the

[Freesurfer] FreeView updating

Hello, I would like to download the latest version of FreeView so I could use the Recon Edit option. I've downloaded the latest version of FreeSurfer (v5.3), but it seems that I have an older version of FreeView (v1.0). Could someone please assist me in updating FreeView - I can't find the

[Freesurfer] Freeview error

Dear all I installed freesurfer as supposed for linux of centos 7. I have a problem with freeview error. After install was copleteted, Tying the command : "freeview" -> freeview.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory

[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 to mark only one specific area

Hi Luis you can run mri_annotation2label and just load the label you want. cheers Bruce On Fri, 12 Feb 2016, Luis Fernado Silva Castro de Araújo wrote:  Hello Freesurfer experts, I want either a 2D or 3D picture of one of my subjects image, but with only one colored area. For example, I

[Freesurfer] Freeview to mark only one specific area

Hello Freesurfer experts, I want either a 2D or 3D picture of one of my subjects image, but with only one colored area. For example, I would like to mark the lh_lateralorbitofrontal_area. It seems that the tool to visualize images in Freesurfer is freeview, however I can't find the label for

Re: [Freesurfer] freeview command line generic overlay colormap question

Dear all, I am currently trying to automatically generate Freesurfer screenshots and, to this purpose, I need to change the color scale of the surface overlay to "Color Wheel - Inverse" and with specific min and max threshold. Looking for a way to achieve this, I found this thread with

[Freesurfer] freeview on ubuntu

Dear experts, I installed FreeSurfer on Ubuntu with these commands: sudo apt-get install tcsh cd /usr/local/ sudo tar -xzvf ~/freesurfer-*.tar.gz echo "FREESURFER_HOME=/usr/local/freesurfer" >> ~/.bashrc echo 'source $FREESURFER_HOME/SetUpFreeSurfer.sh' >> ~/.bashrc sudo gedit

[Freesurfer] freeview automatization not working nicely

Hi FS experts, I have an script (screenshots.txt) that takes screenshots of freeview of several scans: It looks like this: -v scan1/mri/T1.mgz ; -v scan1/mri/aparc+aseg.mgz:colormap=lut:opacity=0.2 ; -viewport sagittal -slice 80 127 127 -ss sag1_scan1 ; -v scan2/mri/T1.mgz ; -v

Re: [Freesurfer] freeview automatization not working nicely

Hi Max, Please try putting each command as a separate line, like this: -v scan1/mri/T1.mgz -v scan1/mri/aparc+aseg.mgz:colormap=lut:opacity=0.2 etc.. Best, Ruopeng > On Dec 17, 2015, at 5:30 AM, BAUTISTA-PERPINYA Maximilià > wrote: > > Hi FS

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 PETSC Error

Hi, I downloaded and installed Freesurfer stable release 5.3 distribution linux_centos4_x86_64 on an Ubuntu 12.04 system. However freeview crashes with a PETSC error. I read the freesurfer archives and followed the instructions found on

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:

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 ->

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

Hi, Can the developmental freeview display ?h.cortex.patch.flat? I can't find answers in the mail list. If not, is there any way to convert the patch.flat to a format freeview can display? Thanks,Xiaomin___

[Freesurfer] Freeview scrolling speed?

Hi all, With Freesurfer 5.3 installed on a OS X 10.10.5 mac (MacBook Air 1.6Ghz i5, 4GB ram), I find that scrolling through slices in Freeview is VERY slow compared to tkmedit when surfaces are loading in addition to 1-2 volumes (e.g., when editing pial/WM segmentations). Any tricks/tips/help to

Re: [Freesurfer] freeview crash with emutls_get_address but work from command line on MacOS X 10.10.5

Yes, it does. However, I am able to start Freeview whiteout any argument from matlab 2015b on Mac X 10.10.5. If I use this commandsystem('freeview -f /Applications/freesurfer/subjects/fsaverage/surf/lh.white’); in matlab ferview crash, but I use this command system(‘freeview’) I am able to

Re: [Freesurfer] freeview crash with emutls_get_address but work from command line on MacOS X 10.10.5

Starting Freeview from MATLAB is an odd thing to do. What happens if you just start freeview normally? hth D On Tue, Sep 15, 2015 at 12:21 PM, Knut Jørgen Bjuland wrote: > When I load Freeview developmental version from Freesurver developmental > version from Matlab

Re: [Freesurfer] freeview crash with emutls_get_address but work from command line on MacOS X 10.10.5

It works from the terminal windows. I start from within Matlab, to get FDR correction as Freeview do not have it. And I use an FDR correction that uses data from both hemisphere. I have managed to get it working under Ubuntu 14.04.3. > On 15 Sep 2015, at 18:49, dgw

Re: [Freesurfer] freeview crash with emutls_get_address but work from command line on MacOS X 10.10.5

Does it work from the terminal window when using the full commandLine that matlab is trying to execute, including the -f flag and all the arguments? -Zeke > On Tue, Sep 15, 2015 at 12:58 PM, Knut Jørgen Bjuland > wrote: >> It works from the terminal windows. I start

[Freesurfer] freeview crash with emutls_get_address but work from command line on MacOS X 10.10.5

When I load Freeview developmental version from Freesurver developmental version from Matlab 2015b. I used this command to load freeview. fdrthresh=sprintf('%s,%s',num2str(lowerfdr),num2str(upperfdr)); commandline=sprintf('freeview -f

Re: [Freesurfer] freeview crash with emutls_get_address but work from command line on MacOS X 10.10.5

But don't you just save the FDR correction to a file then load that in freeview? I imagine the problem has to do with MATLAB changing the way it works on OSX. It doesn't use X11 anymore, unlike on linux (this is supposition). I would say the best bet would be to do the FDR correction in MATLAB,

[Freesurfer] freeview read error

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 loads is the aseg.  I am not able to load the T1, wm, or brainmask mgz’s . either from the terminal or through

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

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

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 fis...@nmr.mgh.harvard.edu wrote: they are empty (zero size). Maybe your disk filled up? On

Re: [Freesurfer] freeview read error

no, seems to be plenty left.. 240 TB On Wednesday, August 26, 2015 12:23 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu 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...

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

Re: [Freesurfer] Freeview

@nmr.mgh.harvard.edu Sent: Wednesday, August 19, 2015 6:16:13 PM Subject: [Freesurfer] Freeview Hi Freesurfers, I can’t change the current slice in freeview using the Up or Down key as described in the Freesurfer wiki. Instead the Up/Down key are moving the current slice up or down and not changing

Re: [Freesurfer] Freeview

To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freeview Page up / page down should work Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message

[Freesurfer] Freeview

Hi Freesurfers, I can't change the current slice in freeview using the Up or Down key as described in the Freesurfer wiki. Instead the Up/Down key are moving the current slice up or down and not changing the current slice. Is there any shortcut that can change the current slice instead of the

Re: [Freesurfer] Freeview

: [Freesurfer] Freeview Weird! The up and down arrows should move the current slice up and down, whereas page up/down should change the slice... You can also click on the other views to change the current slice. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com

Re: [Freesurfer] Freeview

disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Mohamad J. Alshikho malshi...@mgh.harvard.edu To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, August 19, 2015 6:23:28 PM Subject: Re: [Freesurfer] Freeview Page up / down

[Freesurfer] Freeview crash if started with argument from Matlab 2015a on Mac os 11.10.5

Dear FreeSurfer experts I have downloaded the FreeSurfer tutorials. When I try to load Freeview in Matlab with the argument that I found in the group tutorial Freeview will crash on Mac OS X 10.10.5, but it worked on Fedora 22. I am using Matlab because Freeview do not have FDR. Fdr

Re: [Freesurfer] Freeview Recon Edit Tool Unavailable

You need to install development version of freeview. Instructions can be found on this page in the Freeview dev version section: https://surfer.nmr.mgh.harvard.edu/fswiki/Download -Zeke On 07/23/2015 12:57 PM, Gomar, Jesus wrote: Hi Freesurfers, We are trying to use the Recon Edit tool in

[Freesurfer] Freeview surface misaligned with T1 - volume geometry missing

version of mris_convert was only available for linux-centos6. Is there a new version of mris_convert for Mac that correctly saves volume geometry? (2) The latest freeview (ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/lion/Freeview.zip) does not work for me and crashes when I try

Re: [Freesurfer] [FreeSurfer] Freeview Crash PETSC ERROR

Sorry that is an archive zip that i also downloaded The one installed is Freesurfer -Darwin -lion -stabel -pub-v5.3.0.dmg On Thu, Jun 25, 2015 at 10:36 AM, joseph veliz josephveli...@gmail.com wrote: Positive we downloaded Freesurfer -Darwin - lion -dev.tar.gz On Thu, Jun 25, 2015 at 9:04

Re: [Freesurfer] [FreeSurfer] Freeview Crash PETSC ERROR

On 06/23/2015 04:52 PM, joseph veliz wrote: Hello, We are having issues installing Freeview on Macbook pro (2015) 2.2 GHz, 16GB DDR3, OSX 10.9.4, Integrated 1.5 GB intel iris pro graphic processing. Installing lastest Freesurfer and Freeview downloads of Darwin lion v5.3.0. After

Re: [Freesurfer] [FreeSurfer] Freeview Crash PETSC ERROR

Positive we downloaded Freesurfer -Darwin - lion -dev.tar.gz On Thu, Jun 25, 2015 at 9:04 AM, Z K zkauf...@nmr.mgh.harvard.edu wrote: On 06/23/2015 04:52 PM, joseph veliz wrote: Hello, We are having issues installing Freeview on Macbook pro (2015) 2.2 GHz, 16GB DDR3, OSX 10.9.4,

Re: [Freesurfer] [FreeSurfer] Freeview Crash PETSC ERROR

://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/lion/Freeview.zip ), Double click it, and replace you $FREESURFER_HOME/Freeview file with the one in the zip file. -Zeke On 06/25/2015 01:39 PM, joseph veliz wrote: Sorry that is an archive zip that i also downloaded The one

Re: [Freesurfer] [FreeSurfer] Freeview Crash PETSC ERROR

(ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/lion/Freeview.zip), Double click it, and replace you $FREESURFER_HOME/Freeview file with the one in the zip file. -Zeke On 06/25/2015 01:39 PM, joseph veliz wrote: Sorry that is an archive zip that i also downloaded The one

Re: [Freesurfer] [FreeSurfer] Freeview Crash PETSC ERROR

completely removing the current installation and re-install? making absolutely sure you are using freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg Once that is complete you can update to the newst freeview. Download the following link (ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview

[Freesurfer] [FreeSurfer] Freeview Crash PETSC ERROR

Hello, We are having issues installing Freeview on Macbook pro (2015) 2.2 GHz, 16GB DDR3, OSX 10.9.4, Integrated 1.5 GB intel iris pro graphic processing. Installing lastest Freesurfer and Freeview downloads of Darwin lion v5.3.0. After installing Freesurfer , license and environment setup,

Re: [Freesurfer] Freeview Update

On 06/19/2015 09:33 PM, joseph veliz wrote: Thanks Zeke, Could you please help me understand if there would be any inconsistencies or variation between data sets edited by Freeview on a newer macbook pro vs data sets edited by Freeview on a older iMac? This should not be an issue. Editing

Re: [Freesurfer] Freeview Update

Thanks Zeke, Could you please help me understand if there would be any inconsistencies or variation between data sets edited by Freeview on a newer macbook pro vs data sets edited by Freeview on a older iMac? I want to make corrections using latest Freeview update on a new macbook pro. Is

Re: [Freesurfer] Freeview Update

The instructions for updating freeview only work when updating from the most recent freesurfer release (i.e. version 5.3). It won't work if updating from version 5.1 If you want to use the latest development version of freeview you will have to update to the most recent version of freesurfer,

[Freesurfer] Freeview Update

Hello, I am running freesurfer darwin leopard i686 v5.1.0 and am trying to update to the latest freeview. Following the download/installation instructions by deleting the freeview.app file from the application folder and replacing it with the new freeview.app file, does not seem to work.

Re: [Freesurfer] freeview data checking for longitudinal

Hi Bryan, what issues are you running into? Just open the images from all time points on top of each other. Make sure to load the ones from the .long.base dirs. The same can be done for surfaces. freeview tp1.long.base/mri/norm.mgz tp2.long.base/mri/norm.mgz ... Martin On 05/15/2015 03:03

[Freesurfer] freeview data checking for longitudinal

Hi, I am trying to create a command line for data checking the same participant over multiple longitudinal timepoints in freeview. However at the moment I am running into issues. Can someone provide me an example of a freeview command to be used if I wanted to overlay the scans? Any help is

[Freesurfer] Freeview mountain lion

Hi there,I recently tried to update the Freeview version so I can have the recon edit button. I managed to copy the file over but now I get the following error:dyld: Library not loaded: @executable_path/../Frameworks/QtScriptTools.framework/Versions/4/QtScriptTools Referenced from:

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 htmlheadmeta http-equiv=Content-Type

Re: [Freesurfer] Freeview

Can you please provide me with the contents of your $FREESURFER_HOME/build-stamp.txt file? -Zeke On 05/11/2015 07:33 PM, Isabelle Deschamps wrote: Dear Freesurfer Users, I am trying to update the freeview file. However, I cannot find the folder

[Freesurfer] Freeview

Dear Freesurfer Users,I am trying to update the freeview file. However, I cannot find the folder$FREESURFER_HOME/Freeview.app/Contents/MacOS/FreeviewWhen I go into my Freesurfer folder, I cannot find Freeview.app.Any help would be greatly appreciated.Thanks,Isabelle

[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

Re: [Freesurfer] freeview registration

Date: Sun, 1 Mar 2015 13:57:52 -0500 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] freeview registration I think that freeview does not correctly generate the registration file

Re: [Freesurfer] freeview registration

freesurfer release. Xiaomin Date: Sun, 1 Mar 2015 13:57:52 -0500 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] freeview registration I think that freeview does not correctly generate the registration file. You can use

Re: [Freesurfer] freeview registration

...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] freeview registration I think that freeview does not correctly generate the registration file. You can use it to check the regsitration, but us tkregister if you need to edit it. doug On 2/27/15 10:18

Re: [Freesurfer] freeview registration

I think that freeview does not correctly generate the registration file. You can use it to check the regsitration, but us tkregister if you need to edit it. doug On 2/27/15 10:18 AM, Xiaomin Yue wrote: Hi All, After using freeview to manually adjust the registration between a

[Freesurfer] freeview registration

Hi All, After using freeview to manually adjust the registration between a functional and T1.mgz generated by bbregister, I saved the registration file in freeview as lta format, which seems the only option. However, the registration file has same file name for source and target volume. So,

Re: [Freesurfer] Freeview colorbar with command line white background?

Hi Ruopeng, Thank you very much for the verification. That is no problem at all. I was asking because I thought I did something wrong. :-) It is quite easy for myself to only save the positive part. Thank you very much! Best regards, Xiuming On Feb 7, 2015, at 10:14 PM, Ruopeng Wang

Re: [Freesurfer] Freeview colorbar with command line white background?

Hi Xiuming, I think the color scale always display the full scale which includes the inverted part. I understand it is not ideal in this case. I will improve it. Best, Ruopeng On Feb 6, 2015, at 8:26 PM, Xiuming Zhang (Ming) ericzhangxium...@gmail.com wrote: Hi Ruopeng, Thanks a lot for

Re: [Freesurfer] Freeview colorbar with command line white background?

Hi Ruopeng, Thanks a lot for helping clarify this! May I ask a follow-up question? Why am I getting a symmetric-around-0 colorbar (please see the attachment)? I only have values from 3.99e-6 to 1.2e-5. Thank you very much! Best regards, Xiuming

Re: [Freesurfer] Freeview colorbar with command line white background?

Hi Xiuming, You can’t change color scale or change the background color from the command-line. You can change the background color from the GUI: Edit - Preferences. I will add these options in the command-line. Best, Ruopeng On Feb 6, 2015, at 11:52 AM, Xiuming Zhang

[Freesurfer] Freeview colorbar with command line white background?

Dear freesurfer experts, I have two quick questions regarding freeview. (1) The color bar is still from 0 to 1 even if I am overlying a super small-valued (1e-6) map on lh.inflated. Here is what I did: freeview -f lh.inflated:overlay=lh.map:overlay_method=linear:edgethickness=0 -viewport 3d

Re: [Freesurfer] freeview shared library fault with fix after update to Fedora 21

Thank you for reporting this information. On 02/02/2015 11:53 AM, Krieger, Donald N. wrote: Dear freesurfer team: I just updated to Fedora 21 and freeview failed with errors finding libpng12.so.0 and libXss.so.1 . I copied these from an earlier version of Fedora into /usr/lib64 and

[Freesurfer] freeview shared library fault with fix after update to Fedora 21

Dear freesurfer team: I just updated to Fedora 21 and freeview failed with errors finding libpng12.so.0 and libXss.so.1 . I copied these from an earlier version of Fedora into /usr/lib64 and freeview now works. I'm running recon-all under this new release and will post back if there are

Re: [Freesurfer] Freeview question: using line profile

I think you need to create 2 sets of way points as iso-lines. You can do that from File - New Point Set and select 'way point'. Then you should be able to use the line profile tool. On 01/14/2015 04:55 PM, Albrecht, Daniel S. wrote: Hello, I'm having trouble using the line profile tool in

Re: [Freesurfer] Freeview question: using line profile

Hi Dan, for the line profile you'd select a few points along one curve (e.g. along the pial surface in a slice) , then along the opposite curve (e.g. along the wm surface) and you can then compute line profiles connecting the two curves (via solution of a poisson equation). the tool samples

[Freesurfer] Freeview question: using line profile

Hello, I'm having trouble using the line profile tool in FreeView. I have a PET image overlaid on an MR image, and would like to view a line profile of a rectangular ROI on the PET image. I assumed that the line profile selection in Tools would be able to do this, but I haven't been able to

Re: [Freesurfer] Freeview question: using line profile

To: Freesurfer support list Subject: Re: [Freesurfer] Freeview question: using line profile I think you need to create 2 sets of way points as iso-lines. You can do that from File - New Point Set and select 'way point'. Then you should be able to use the line profile tool. On 01/14/2015 04:55 PM

[Freesurfer] freeview errors

Hello, I sent in a message yesterday but to no avail. I thought I would add a little more info about the error message I'm receiving. I am trying to view surfaces in 3D using Freeview on my own subject data via this script from the Freesurfer website (replacing the subject name); freeview -f

Re: [Freesurfer] freeview errors

Can you try just loading one surface? Such as: freeview -f /media/seagate_external/subject/surf/lh.inflated Does it load? What if: mris_info /media/seagate_external/subject/surf/lh.inflated or even just: ls -l /media/seagate_external/subject/surf/lh.inflated Does it show any error? On

Re: [Freesurfer] freeview error

What if you just load one surface: freeview -f good_output/surf/lh.pial Does it load? Best, Ruopeng On 01/06/2015 03:23 PM, Hirsch, Gabriella wrote: Hi, I am trying to view surfaces in 3D using Freeview on my own subject data via this command (replacing the subject name); freeview -f

[Freesurfer] Freeview - Vector and Spline information for Sufaces

Dear all, I'm currently trying to view face and/or vertex normals in freeview (of an existing surface). I've seen the option to load vector display data, but I do not know the format of such a file. Can someone help me with that issue? Regards, Daniel Universitätsklinikum Jena - Bachstrasse

[Freesurfer] Freeview in a VM (Debian)

Hi all, I am running FS in a VM (Debian, wheezy) and I would like to create a 3D reconstruction of the hippocampus in .png. For that, I executed the following code lines: mri_extract_label aseg.mgz 17 lh.nii mri_extract_label aseg.mgz 53 rh.nii freeview -slice 500 500 500 -v

Re: [Freesurfer] freeview fault: PETSC Error ... PERSISTENT

[mailto:freesurfer- boun...@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky, MGH Sent: Tuesday, November 04, 2014 11:59 PM To: Freesurfer support list Subject: Re: [Freesurfer] freeview fault: PETSC Error ... you can try downloading our nightly 'dev' build of freeview, from here: https

[Freesurfer] Freeview-stable4 error?

Hi, I'm trying to look at 2 connectivity files (saved in SPM) at the same time using Freeview, but how I've been doing it in the past is no longer working and I haven’t changed anything on my end. What I had been doing: 1. cd to the folder with my connectivity files and typing the shortcut

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