Re: [Freesurfer] Tksurfer and freeview

External Email - Use Caution  The tksurfer command is deprecated and no longer supported.  You could try using freeview directly or run tksurferfv which may use some of the same options as tksurfer, but runs freeview instead.  $ tksurferfv --help This is a script that ru

Re: [Freesurfer] Tksurfer and freeview

please send the command line and the terminal output. Also, try using tksurferfv (this is a wrapper around freeview that takes tksurfer-like commands) On 1/6/2024 8:59 PM, JAEHYUN KIM wrote: External Email - Use Caution Hello, I attempted to switch tksurfer to freeview in the script

Re: [Freesurfer] Tksurfer and freeview

External Email - Use Caution  tksurfer has been deprecated and essentially replaced with tksurferfv bash shell script which runs freeview.   But whether or not you run the front-end tksurferfv bash script or the freeview command directly, I’m not aware of an option whereby you c

[Freesurfer] Tksurfer and freeview

External Email - Use Caution Hello, I attempted to switch tksurfer to freeview in the script, but it seems like I need to change arguments "tcl" to something that can be applied to freeview. Option 'tcl' not recognized. What argument could possibly be used to replace *tcl* in

Re: [Freesurfer] Tksurfer option for horizontal scale bar

tksurfer was deprecated years ago, though it's replacement (freeview) does not seem to have that capability either. On 12/12/2023 2:29 PM, Lee, Jeungchan wrote: Hi Freesurfers, I’m using TkSurfer to visualize my results and want to add a horizontal color scale bar. I used [ -colorscalebarfla

[Freesurfer] Tksurfer option for horizontal scale bar

Hi Freesurfers, I’m using TkSurfer to visualize my results and want to add a horizontal color scale bar. I used [ -colorscalebarflag 1 ] to do so, but I only got a vertical bar. Is there any way (command options) to get a horizontal color scale bar? Thanks, jeungchan ___

Re: [Freesurfer] Tksurfer tmp.tcl

External Email - Use Caution you cannot run tksurferfv with a tcl script. tksurferfv is just a frontend for freeview that will take tksurfer-like options. On 5/26/2023 9:54 AM, Robert Terziev wrote: External Email - Use Caution Hello, I am trying to run an old script

[Freesurfer] Tksurfer tmp.tcl

External Email - Use Caution Hello, I am trying to run an old script from the ENIGMA webpage, that was based on freesurfer 5.1 and uses tksurfer. Here is a code excerpt: tksurfer $sub lh pial -tcl tmp.tcl echo "labl_import_annotation \"aparc.annot\"" > tmp.tcl echo "scale_b

Re: [Freesurfer] Tksurfer Error

From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Sunday, July 10, 2022, 4:09 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tksurfer Error tksurfer is depracated. Try using tksurferfv instead On 6/29/2022 4

Re: [Freesurfer] Tksurfer Error

tksurfer is depracated. Try using tksurferfv instead On 6/29/2022 4:33 PM, Rachel Wagner wrote: External Email - Use Caution Hello, I am attempting to paint my spm functional data onto freesurfer’s anatomical image. I ran this code: tksurfer bert lh inflated -overlay updated.img -

Re: [Freesurfer] Tksurfer Error

External Email - Use Caution The tksurfer command is deprecated/no longer supported. You could try using freeview directly or run tksurferfv, which may take the same options as tksurfer but run freeview to display things. - R.. On Jun 29, 2022, at 16:33, Rachel Wagner

[Freesurfer] Tksurfer Error

External Email - Use Caution Hello, I am attempting to paint my spm functional data onto freesurfer’s anatomical image. I ran this code: tksurfer bert lh inflated -overlay updated.img -overlay-reg register.dat And got this error: Tcl_Init failed: Can't find a usable init.tcl

Re: [Freesurfer] tksurfer

*On Behalf Of *Arian Klows *Sent:* Wednesday, November 3, 2021 1:07 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] tksurfer *External Email - Use Caution * Hi experts, I recently downloaded the freesurfer and am testing it. I tried tksurfer, but the editor window is

Re: [Freesurfer] tksurfer

Hi Arian Tksurfer has been deprecated for a long time. Can you try freeview instead? Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Arian Klows Sent: Wednesday, November 3, 2021 1:07 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] tksurfer External Email

[Freesurfer] tksurfer

External Email - Use Caution Hi experts, I recently downloaded the freesurfer and am testing it. I tried tksurfer, but the editor window is blank. Please see below. Can anyone please help me in resolving this issue!? [image: image.png] Is this an internal problem with my comput

Re: [Freesurfer] tksurfer question

You can also use tksurferfv, which is a frontend for freeview that takes the tksurfer options On 3/2/2021 1:41 PM, Wang, Ruopeng wrote: Hi, Tksurfer has been replaced by freeview. You can load an overlay file with the following freeview command: freeview -f lh.inflated:overlay=xxx.mgh Best

Re: [Freesurfer] tksurfer question

Hi, Tksurfer has been replaced by freeview. You can load an overlay file with the following freeview command: freeview -f lh.inflated:overlay=xxx.mgh Best, Ruopeng On Mar 1, 2021, at 2:32 PM, DS mailto:zky...@126.com>> wrote: External Email - Use Caution Dear experts, I want to use

[Freesurfer] tksurfer question

External Email - Use Caution Dear experts, I want to use the tksurfer to show the .mgh file by command line. Based on the manual, I tried tksurfer fsaverage lh inflated But, there is no room to input the overlay .mgh file. Moreover, I did not find relevant info in the -tcl scrip

Re: [Freesurfer] tksurfer 64bit update?

External Email - Use Caution My apologies, I totally read "does not". I see it now (it's a feature in the new version of freesurfer it seems, I was pointing to version 6). Thank you so much! Best, Jesse On Sep 10, 2020, at 11:10 AM, Wang, Ruopeng mailto:rwa...@mgh.harvard.

Re: [Freesurfer] tksurfer 64bit update?

I believe tksurfer will be depreciated if not already. But like I said in the previous email, freeview does support surface-based label drawing. On Sep 10, 2020, at 10:49 AM, Jesse Gomez mailto:jessego...@princeton.edu>> wrote: External Email - Use Caution Thanks Ruopeng. Is surface-b

Re: [Freesurfer] tksurfer 64bit update?

External Email - Use Caution Thanks Ruopeng. Is surface-based or tksurfer coming back? The surface-based label drawing was much more powerful than drawing slice by slice in volume space. On Sep 10, 2020, at 10:35 AM, Wang, Ruopeng mailto:rwa...@mgh.harvard.edu>> wrote: Hi

Re: [Freesurfer] tksurfer 64bit update?

Hi Jesse, Freeview does support surface-based ROI drawing. There is a Path/Custom Fill tool button on the left pane. Once it is checked, you should see a bunch of tool buttons similar to what tksurfer had for ROI drawing. Best, Ruopeng On Sep 10, 2020, at 10:27 AM, Jesse Gomez mailto:jessego.

[Freesurfer] tksurfer 64bit update?

External Email - Use Caution Hello, I noticed tksurfer disappeared in the new 7.1 version of freesurfer. While it's still present in older versions of course, it no longer runs on 64-bit only operating systems (e.g. OSX Catalina). Is tksurfer going to be updated? It seems to be

Re: [Freesurfer] tksurfer - failed to calloc

From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Nasr, Shahin,Ph.D. Sent: Wednesday, July 22, 2020 12:44 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] tksurfer - failed to calloc Hi Surfers, I get the following error when I use tksurfer for one of our subjects

[Freesurfer] tksurfer - failed to calloc

Hi Surfers, I get the following error when I use tksurfer for one of our subjects: znzTAGskip: tag=1830834290, failed to calloc 1834378240 bytes! To clarify, this error is only limited to freesurfer version 6.0 and 7. But version 5.3 works fine with the same subject. Regards __

Re: [Freesurfer] tksurfer

External Email - Use Caution Hello Amar, You will probably need to install some software in Ubuntu in order to run freeview (and other commands in the  freesurfer distribution).  I would start with installing the list of packages  with the "sudo apt-get install" command for the

Re: [Freesurfer] tksurfer

External Email - Use Caution Dear Support Team, I am starting the work in the field of capturing the anatomical features from the brain through free surfer, but still lot of issue i am facing through installing free surfer in in linux through VM ware or in windows 10 using ubuntu

Re: [Freesurfer] tksurfer

Hi Emalie tksurfer and tkmedit have been deprecated for a long time. Can you try using freeview instead? cheers Bruce On Fri, 21 Feb 2020, Emalie McMahon wrote: External Email - Use Caution Hello,  I get an error (see below) when opening tksurfer and tkmedit. Is there anywa

[Freesurfer] tksurfer

External Email - Use Caution Hello, I get an error (see below) when opening tksurfer and tkmedit. Is there anyway to resolve this? tksurfer s001 lh inflated /Applications/freesurfer/tktools/tksurfer.bin: Bad CPU type in executable. Freesurfer Details: freesurfer-i386-apple-d

Re: [Freesurfer] Tksurfer and qdec: error sourcing and floating exception

tksurfer has some instabilities in it. It is obsolete and no longer being supported. Have you tried freeview? You can use tksurferfv which runs freeview with tksurfer options. On 6/12/2019 6:54 PM, Wafaa Sweidan wrote: External Email - Use Caution Hello all, I have been using freesurf

Re: [Freesurfer] Tksurfer and qdec: error sourcing and floating exception

External Email - Use Caution Hello Wafaa, I believe qdec runs as a 32 bit application.  You may see Mac OS 10.14 put up a window warning that an application is not optimized for the system and needs to be re-compiled by its developer; that means it is a 32 bit app.  While ma

[Freesurfer] Tksurfer and qdec: error sourcing and floating exception

External Email - Use Caution Hello all, I have been using freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c on macos high sierra, then I updated to mojave 10.14. freeusrfer was working all good for a while. BUT, for unknown reasons, I am no longer able to overlay the significance

Re: [Freesurfer] tksurfer-sess frame time course question

External Email - Use Caution Dear Doug, Thank you very much for your response. >> (1) why did I get Frame (0-8) for my data that should have 12 frames? > When you use -rmprestim, it subtracts the mean of the prestim baseline > AND removes the prestim time points (-4 -2 and 0) so

Re: [Freesurfer] tksurfer-sess frame time course question

answwers below On 09/27/2018 05:44 AM, 伊藤匠吾 wrote: > > > Hello, > > I am new to FreeSurfer. > > I conducted an experiment with event-related design. > There were eight non-fixation conditions. In every trial, a simple > stimulus was presented for about 1.5 sec, and the subject made a > button pr

[Freesurfer] tksurfer-sess frame time course question

External Email - Use Caution Hello, I am new to FreeSurfer. I conducted an experiment with event-related design. There were eight non-fixation conditions. In every trial, a simple stimulus was presented for about 1.5 sec, and the subject made a button press. I did the following

Re: [Freesurfer] tksurfer/freeview vertex coordinates difference?

> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Thursday, March 01, 2018 5:46 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] tksurfer/freeview vertex coordinates difference? > > Hi Idil > > we keep track of

Re: [Freesurfer] tksurfer/freeview vertex coordinates difference?

Thank you! Best 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: Thursday, March 01, 2018 5:46 PM To: Freesurfer support list Subject: Re: [Freesurfer

Re: [Freesurfer] tksurfer/freeview vertex coordinates difference?

Hi Idil we keep track of different kinds of RAS coordinates, which may not be the same (surface ras, scanner ras, etc...). cheers Bruce On Thu, 1 Mar 2018, Yagmur Ozdemir 19 wrote: > Hello FS experts, > > I am wondering if anyone knows why the same vertices' coordinates are shown > slightly d

[Freesurfer] tksurfer/freeview vertex coordinates difference?

Hello FS experts, I am wondering if anyone knows why the same vertices' coordinates are shown slightly different when opened in freesurfer and tksurfer. I was checking some annotation files for each subject across the two on inflated surface, and noticed slight coordinate differences in RAS. ex

[Freesurfer] tksurfer- configure overlay display

Hi, I'm trying to show an overlay (.mgh file) I have created. I'm using tksurfer to view the file. I intend to change the color scale using view/configure/overlay. However, the *configure overlay display* window is clipped and I can not see the apply button. *Tksurferguide* says that it may happen

Re: [Freesurfer] tksurfer vertex location

Dear Doug, Thank you for the repy but may be couple of things. One, when I used the above command it said segmentation volume is missing , so I added the segmentation volume as in the command below and it worked and I also got the out.dat but not as I wanted. With this command : mri_segstats --se

Re: [Freesurfer] tksurfer vertex location

btw, in tksurfer you can type the vertex no you want into the vertex field. If you want to extract it programatically, then you can run something like mri_segstats --vox vertexno 0 0 --id 1 --i yoursurfacemap.mgh --avgwf out.dat On 01/23/2017 05:29 AM, Nabin Koirala wrote: > Dear Bruce, > > T

Re: [Freesurfer] tksurfer vertex location

Dear Bruce, Thank you for the reply but as you mentioned that tksurfer is deprecated, is it possible to do the same from QDEC ? i.e Can I get all the values from the plot (or save the plot) which we get in QDEC for significant cluster ? Thank you. Regards, Nabin On Fri, Jan 20, 2017 at 4:06 PM,

Re: [Freesurfer] tksurfer vertex location

Hi Nabin note that tksurfer is deprecated - we are not developing it anymore. That said, I thing you can type: select_vertex_by_vno at the tcl prompt, where is the number of the vertex you want to select cheers Bruce On Fri, 20 Jan 2017, Nabin Koirala wrote: Dear freesurfer team,  I wa

[Freesurfer] tksurfer vertex location

Dear freesurfer team, I was trying to obtain the values at a vertex in tksurfer and this is what is written in tksurfer manual. *At first, an empty plot will be displayed in a separate window. To generate a plot for a particular vertex, select a point by clicking on the parametric map at that

[Freesurfer] tksurfer viewing issues

Hi Bruce, I'm analyzing phase encoded retinotopy, and it is not clear to me how to load complex overlays in freeview. Perhaps I am missing something? Best, Paige Hi Paige we have stopped development and most support of tksurfer. Can you use freeview instead or is there still some functionalit

Re: [Freesurfer] tksurfer viewing issues

Hi Paige we have stopped development and most support of tksurfer. Can you use freeview instead or is there still some functionality that you need that is unique to tksurfer? cheers Bruce On Thu, 29 Sep 2016, Paige Scalf wrote: > Hello, > > I too am having trouble with tksurfer displaying the

[Freesurfer] tksurfer viewing issues

Hello, I too am having trouble with tksurfer displaying the surfaces upside down and back to front, but believing that they are correctly oriented (i.e. Talairach coordinates change in the wrong direction wrt to the surface but in the correct direction wrt the display window). I"m also running a C

Re: [Freesurfer] tksurfer scale bar

d.edu Subject: Re: [Freesurfer] tksurfer scale bar you can also try tksurferfv. this is a frontend for freeview that takes tksurfer-style arguments On 04/01/2016 09:57 AM, Bruce Fischl wrote: > > freeview -f lh.inflated:overlay=lh.pet_data.mgz > > would be a good place to start. Ther

Re: [Freesurfer] tksurfer scale bar

--- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Michael Asghar Sent: 01 April 2016 14:59 To: Freesurfer support list Subject: Re: [Freesurfer] tksurfer scale bar Thanks -Original Message- From: freesurfer-boun...@nmr.mgh.harvar

Re: [Freesurfer] tksurfer scale bar

- any simple commands to >> load up a surface, overlay some statistical data? >> >> Thanks! >> Michael >> >> -Original Message- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce &

Re: [Freesurfer] tksurfer scale bar

ael Asghar Sent: 01 April 2016 14:59 To: Freesurfer support list Subject: Re: [Freesurfer] tksurfer scale bar Thanks -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: 01 April 2016 14:58 To: Freesu

Re: [Freesurfer] tksurfer scale bar

Thanks -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: 01 April 2016 14:58 To: Freesurfer support list Subject: Re: [Freesurfer] tksurfer scale bar freeview -f lh.inflated:overlay

Re: [Freesurfer] tksurfer scale bar

ruce Fischl Sent: 01 April 2016 14:44 To: Freesurfer support list Subject: Re: [Freesurfer] tksurfer scale bar Hi Michael tksurfer is deprecated - have you tried this in freeview? cheers Bruce On Fri, 1 Apr 2016, Michael Asghar wrote: Hi Freesurfer   I’m struggling with trying to edit the s

Re: [Freesurfer] tksurfer scale bar

ssage- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: 01 April 2016 14:44 To: Freesurfer support list Subject: Re: [Freesurfer] tksurfer scale bar Hi Michael tksurfer is deprecated - have you tried this in freeview?

Re: [Freesurfer] tksurfer scale bar

Hi Michael tksurfer is deprecated - have you tried this in freeview? cheers Bruce On Fri, 1 Apr 2016, Michael Asghar wrote: Hi Freesurfer   I’m struggling with trying to edit the scale bar in tksurfer. Commands like ‘set scalebar_bright 240’ work, but draw_scalebar gives an invalid comman

[Freesurfer] tksurfer scale bar

Hi Freesurfer I'm struggling with trying to edit the scale bar in tksurfer. Commands like 'set scalebar_bright 240' work, but draw_scalebar gives an invalid command error. I've tried redrawing, but it doesn't help. Basically, I want the black background to become white (can do it via convert -

Re: [Freesurfer] tksurfer

it looks like the cluster is covering most of the brain, including precentral gyrus. The precentral gyrus ROI in the table file indicates that is where the peak of the cluster is and does not mean that the cluster is confined to that ROI On 3/16/16 9:43 AM, John Anderson wrote: Dear experts,

Re: [Freesurfer] tksurfer

Thank you doug, Please what do you suggesst me to do? Is this related to something wrong in the analysis?   Bests, John   Sent: Wednesday, March 16, 2016 at 10:42 AM From: "Douglas Greve" To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tksurfer it looks like the

Re: [Freesurfer] tksurfer

Hi John I do not know anything about the error that you are getting but I was also having some problems with tksurfer and was told by Dr. Fischl that this viewer is no longer being updated and that it would be best to try freeview. Did you give this a go? best wishes Trisanna -- Ph.D. Candidate

Re: [Freesurfer] tksurfer

? Bests, John *Sent:* Wednesday, March 16, 2016 at 10:42 AM *From:* "Douglas Greve" *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] tksurfer it looks like the cluster is covering most of the brain, including precentral gyrus. The precentral gyrus ROI in the table file indic

Re: [Freesurfer] Tksurfer and Tkregister2 in Ubuntu 14.04

Hi Zeke, I am wondering if you had a chance to look at this. Thanks, Reza Hello Reza, > > > I wasn't able to replicate on Ubuntu 12 but it's entirely possible this but > exists only in Ubuntu 14. It's tough because we don't have test machines with > every Linux distro that people post to the li

Re: [Freesurfer] tksurfer

On 06/17/2015 04:19 PM, isabel martinez tejada wrote: > I cannot put a "." in the file name because Mac doesn't allow it. It > says that a file that starts with a dot is an invisible file and there > is no way I can do it, its only for special files of the system. > > Thanks, > > Isabel I'm gue

Re: [Freesurfer] tksurfer

03 -1000 > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] tksurfer > > > Dear Isabel, > > the “.” is part of the name of the file, that is why the system cannot > find it. > > Hope this helps, > > Rodolphe. > > `·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯

Re: [Freesurfer] tksurfer

:58:03 -1000 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tksurfer Dear Isabel, the “.” is part of the name of the file, that is why the system cannot find it. Hope this helps, Rodolphe. `·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯`

Re: [Freesurfer] tksurfer

try renaming it to .license On Wed, 17 Jun 2015, isabel martinez tejada wrote: Dear experts, I am using a Mac that runs bash shell. I have performed a group analysis and would like to visualize the results. When using tksurfer I come up with a license error.  The lines of commands I am runn

Re: [Freesurfer] tksurfer

Dear Isabel, the “.” is part of the name of the file, that is why the system cannot find it. Hope this helps, Rodolphe. `·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.· Rodolphe Nenert, Ph.D. Department of Neurology 312 Civitan Internat

[Freesurfer] tksurfer

Dear experts, I am using a Mac that runs bash shell. I have performed a group analysis and would like to visualize the results. When using tksurfer I come up with a license error. The lines of commands I am running are: export FREESURFER_HOME=/Applications/freesurfer source $FR

Re: [Freesurfer] Tksurfer and Tkregister2 in Ubuntu 14.04

Thanks Doug! What is the estimated time for the release of Freesurfer/FS-FAST stable version 6, including a documentation to use it with freeview? Reza The new version of fsfast will use freeview for tksurfer/tkmedit/tkregister. In 5.3, you can use tkmeditfv and/or add -freeview to the tkmedit-s

Re: [Freesurfer] Tksurfer and Tkregister2 in Ubuntu 14.04

Thanks Zeke! I have replicated this problem in at least three machines running Ubuntu 14.04. Reza Hello Reza, I wasn't able to replicate on Ubuntu 12 but it's entirely possible this but exists only in Ubuntu 14. It's tough because we don't have test machines with every Linux distro that peop

Re: [Freesurfer] Tksurfer and Tkregister2 in Ubuntu 14.04

Hello Reza, I wasn't able to replicate on Ubuntu 12 but it's entirely possible this but exists only in Ubuntu 14. It's tough because we don't have test machines with every Linux distro that people post to the list about in order to attempt replicate. But I'll install Ubuntu 14 on a laptop afte

Re: [Freesurfer] Tksurfer and Tkregister2 in Ubuntu 14.04

The new version of fsfast will use freeview for tksurfer/tkmedit/tkregister. In 5.3, you can use tkmeditfv and/or add -freeview to the tkmedit-sess command line. I've put the 6.0 versions of tksurferfv and tksurfer-sess here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/tksurferf

Re: [Freesurfer] Tksurfer and Tkregister2 in Ubuntu 14.04

Hi Bruce, I guess I will eventually move to freeview - though I am not quite sure if it is easy to use with FS-FAST. For now, all features of tksurfer/tkmedit/tkregister2 work fine for me, except the one described below. So it would be great if this bug, that is specific for ubuntu, is resolved

Re: [Freesurfer] Tksurfer and Tkregister2 in Ubuntu 14.04

Hi Reza can you use freeview for what you want instead? tksurfer and tkmedit are deprecated cheers Bruce On Thu, 11 Jun 2015, Reza Rajimehr wrote: Hi, Is there any plan by the Freesurfer team to address this well-known bug? http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35

[Freesurfer] Tksurfer and Tkregister2 in Ubuntu 14.04

Hi, Is there any plan by the Freesurfer team to address this well-known bug? http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35938.html http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg36193.html For now the only workaround is to enter values through command-line.

Re: [Freesurfer] tksurfer crash when loading surfaces

Hi Jesse the thickness files are scalar fields over the surface, not surfaces themselves. Load it as an overlay, not as a surface cheers Bruce On Fri, 22 May 2015, Jesse Bledsoe wrote: Hi everyone, I searched the wiki and old posts but couldn't find a solution to this issue. I had no prob

[Freesurfer] tksurfer crash when loading surfaces

Hi everyone, I searched the wiki and old posts but couldn't find a solution to this issue. I had no problems with the full recon-all script though got hung up trying to load surfaces in tksurfer. The surface files are there but the buttons in tksurfer aren't bright so I tried to load them manuall

Re: [Freesurfer] tksurfer batch mode without GUI

Hi Jonathan you can try: setenv renderoffscreen 1 before running tksurfer. This worked many years ago, but given that tksurfer is mostly deprecated I'm not sure it will work now (bitrot is powerful). cheers Bruce On Sun, 12 Apr 2015, jonathan oron wrote: > Hi experts,I've created many

[Freesurfer] tksurfer batch mode without GUI

Hi experts, I've created many batch files that I would like to run in parallel using tksurfer -tcl scriptname.tcl Is there a way to ask tksurfer to run the script and process the graphical information (i.e. output tiff files I render using the tcl script) without physically showing the graphic

Re: [Freesurfer] tksurfer overlay threshold

.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Wednesday, March 04, 2015 4:42 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] tksurfer overlay threshold > > you need it to be: > > % sclv_set_current_threshold_from_percentile .7 .8 .9 > > or someth

Re: [Freesurfer] tksurfer overlay threshold

: [Freesurfer] tksurfer overlay threshold you need it to be: % sclv_set_current_threshold_from_percentile .7 .8 .9 or something like taht On Wed, 4 Mar 2015, Hirsch, Gabriella wrote: > OK, I tried that, and it does load however I get this message in the terminal: > > tksurfer: run t

Re: [Freesurfer] tksurfer overlay threshold

rvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Wednesday, March 04, 2015 4:07 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] tksurfer overlay threshold > > try: > > sclv_set_current_threshold_from_percentile > > > cheers &

Re: [Freesurfer] tksurfer overlay threshold

From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, March 04, 2015 4:07 PM To: Freesurfer support list Subject: Re: [Freesurfer] tksurfer overlay threshold try

Re: [Freesurfer] tksurfer overlay threshold

t; > Any thoughts would be greatly appreciated! > > Thank you. > > Gabriella > > > > > > From: Z K [zkauf...@nmr.mgh.harvard.edu] > Sent: Wednesday, March 04, 2015 2:32 PM > To: Hirsch, Gabriella > Subject: Re: [Freesurfer] tksu

Re: [Freesurfer] tksurfer overlay threshold

ubject: Re: [Freesurfer] tksurfer overlay threshold Yeah I figured that would be the case. Your best bet in this situation is to respond to Bruce's last email on the Freesurfer list and say that Zeke provided you with the most recent version of tksurfer but the command still does not work. You m

Re: [Freesurfer] tksurfer overlay threshold

ednesday, March 04, 2015 11:53 AM To: Z K Cc: Freesurfer support list Subject: Re: [Freesurfer] tksurfer overlay threshold oh, thanks Zeke for catching that Bruce On Wed, 4 Mar 2015, Z K wrote: > Hi Gabriela, > > You might have a typo. Its "set_current_t

Re: [Freesurfer] tksurfer overlay threshold

> >> > Do I have to add values to the tcl command as well? >> > >> > From: freesurfer-boun...@nmr.mgh.harvard.edu >> > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> > [fis...@nmr

Re: [Freesurfer] tksurfer overlay threshold

eesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...@nmr.mgh.harvard.edu] >> Sent: Wednesday, March 04, 2015 10:26 AM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] tksurfer overlay threshold >> >> Hi Gabriela >> >

Re: [Freesurfer] tksurfer overlay threshold

f of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, March 04, 2015 11:07 AM To: Freesurfer support list Subject: Re: [Freesurfer] tksurfer overlay threshold you would need to include parameters, but that doesn't explain your error. What version of tksurfer are you using? It is proba

Re: [Freesurfer] tksurfer overlay threshold

d.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Wednesday, March 04, 2015 10:26 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] tksurfer overlay threshold > > Hi Gabriela > > they set the t

Re: [Freesurfer] tksurfer overlay threshold

nd as well? From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, March 04, 2015 10:26 AM To: Freesurfer support list Subject: Re: [Freesurfer] tksurfer overlay threshold Hi Gabriela th

Re: [Freesurfer] tksurfer overlay threshold

esurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Tuesday, March 03, 2015 5:48 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] tksurfer overlay threshold > > > I'm not sure what yo

Re: [Freesurfer] tksurfer overlay threshold

...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Tuesday, March 03, 2015 7:05 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] tksurfer overlay threshold > > you can use the command: > > set_current_threshold_from_p

Re: [Freesurfer] tksurfer overlay threshold

From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, March 03, 2015 7:05 PM To: Freesurfer support list Subject: Re: [Freesurfer] tksurfer overlay threshold you can use the command: set_current_threshold_from_percentil

Re: [Freesurfer] tksurfer overlay threshold

-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, March 03, 2015 5:48 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tksurfer overlay threshold I'm not sure what you mean. optimal in what sense? doug On 03/03/201

Re: [Freesurfer] tksurfer overlay threshold

you can use the command: set_current_threshold_from_percentile(min, mid,max) which will compute the thresholds based on the histogram of values On Tue, 3 Mar 2015, Douglas N Greve wrote: > > I'm not sure what you mean. optimal in what sense? > doug > > On 03/03/2015 03:21 PM, Hirsch, Gabriella

Re: [Freesurfer] tksurfer overlay threshold

I'm not sure what you mean. optimal in what sense? doug On 03/03/2015 03:21 PM, Hirsch, Gabriella wrote: > Hi Fs experts, > > I had a quick question about settings thresholds of surface overlays > in Tksurfer. I am currently generating images of the thickness, volume > and surface area of indiv

Re: [Freesurfer] tksurfer

you know what I'm doing wrong? > > Thanks > Andre > > *Von:* freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve > [gr...@nmr.mgh.harvard.edu] > *Gesendet:* Dienstag, 3. Februar

Re: [Freesurfer] tksurfer

know what I'm doing wrong? Thanks Andre Von: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve [gr...@nmr.mgh.harvard.edu] Gesendet: Dienstag, 3. Februar 2015 20:39 An: freesurfer@nmr.

Re: [Freesurfer] tksurfer

Is it world readable? You might also change its name to license.txt On 2/3/15 12:13 PM, André Schmidt wrote: Dear experts, I like to see the obtained annotation files using tksurfer. However, I already got the following error message if I use tksurfer HC001 lh inflated in the terminal: Fr

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