Re: [Freesurfer] tkmedit does not start

Hi Francesco Tkmedit has been deprecated for a *long* time. Can you try FreeView instead? Cheers Bruce -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Francesco Lomi Sent: Monday, October 7, 2024 6:50 AM To: Freesurfer support list Subject: [Freesurfer

[Freesurfer] tkmedit does not start

External Email - Use Caution Dear all, I am writing you because I am trying to launch tkmedit on my Ubuntu computer but the program does not start. I get no errors but simply the terminal goes back to a new input line. I have Freesurfer correctly installed because I normally use fr

Re: [Freesurfer] tkmedit in FreeSurfer 7.0

after v6, please just use freeview. Best Andrew *From: * on behalf of "Dincer, Aylin" *Reply-To: *FS Help *Date: *Monday, May 11, 2020 at 3:17 PM *To: *FS Help *Subject: *[Freesurfer] tkmedit in FreeSurfer 7.0 *External Email - Use Caution * Hi FreeSurfer Experts, We

Re: [Freesurfer] tkmedit in FreeSurfer 7.0

p Subject: [Freesurfer] tkmedit in FreeSurfer 7.0 External Email - Use Caution Hi FreeSurfer Experts, We are unable to use tkmedit using FreeSurfer 7.0 (centos 7). In the .xdebug_tkmedit file, it outputs the following error: “Tcl_Init returned 1: Can't find a usable init.tcl i

[Freesurfer] tkmedit in FreeSurfer 7.0

External Email - Use Caution Hi FreeSurfer Experts, We are unable to use tkmedit using FreeSurfer 7.0 (centos 7). In the .xdebug_tkmedit file, it outputs the following error: "Tcl_Init returned 1: Can't find a usable init.tcl in the following directories: /usr/pubsw/packages/t

Re: [Freesurfer] Tkmedit gui download

Hi Victor, I don’t think you can download standalone tkmedit. But you can download standalone freeview for your Mac from here: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview FYI, tkmedit has been depreciated. You try freeview

[Freesurfer] Tkmedit gui download

Hi all, I am still trying to adapt to working from home, and I am forced to work with incredibly slow download speeds. I am trying to download FS6.0 for mac for the sole purpose of using tkmedit, rather than the entire toolbox, just so I can edit brains (I anticipate downloading FS6.0 for mac

Re: [Freesurfer] tkmedit: no tools window

Hi Gina tkmedit has been deprecated for many years. Can you try using freeview instead? cheers Bruce On Tue, 27 Mar 2018, gj wrote: > Hi, > > When I launch tkmedit, I only get the "Display" window with no "Tools" > window so I don't have any menus (I wanted to overlay a label file -- > not sur

[Freesurfer] tkmedit: no tools window

Hi, When I launch tkmedit, I only get the "Display" window with no "Tools" window so I don't have any menus (I wanted to overlay a label file -- not sure how I do that from the command line either). I don't see any errors in the terminal from where I launch tkmedit -

Re: [Freesurfer] tkmedit error

Hi Veronica if freeview works for you then you should just use it. We have deprecated tkmedit and are trying not to invest any time or energy in it any longer. cheers Bruce On Tue, 14 Mar 2017, Veronica Munoz wrote: > Dear all, > > I'm trying to use tkmedit to verify my recon-all results but

Re: [Freesurfer] tkmedit issue - image too bright in tkmedit after running gcut

Hi Fred that just means that you need to change the window levels. Note that we have deprecated the use of tksurfer and tkmedit and don't really support them any longer cheers Bruce On Wed, 20 Jul 2016, Uquillas, Federico D'Oleire wrote: > Hi fellow FreeSurfer users, > > I just did a gcut pro

Re: [Freesurfer] tkmedit

Thanks! I will use it. Best,  Kojima  - Original Message - >From: Bruce Fischl >To: kojima_masaki_m...@yahoo.co.jp; Freesurfer support list > >Date: 2016/6/15, Wed 10:32 >Subject: Re: [Freesurfer] tkmedit > >yes! >On Wed, 15 Jun 2016, kojima_masaki_m...@ya

Re: [Freesurfer] tkmedit

tkmedit? Regards, Kojima - Original Message - From: Bruce Fischl To: kojima_masaki_m...@yahoo.co.jp; Freesurfer support list Date: 2016/6/14, Tue 21:50 Subject: Re: [Freesurfer] tkmedit Hi Kojima tkmedit has been deprecated. Can you try using

Re: [Freesurfer] tkmedit

rom: Bruce Fischl >To: kojima_masaki_m...@yahoo.co.jp; Freesurfer support list > >Date: 2016/6/14, Tue 21:50 >Subject: Re: [Freesurfer] tkmedit > >Hi Kojima > >tkmedit has been deprecated. Can you try using freeview instead? > >cheers >Bruce >On Tue, 14 &g

Re: [Freesurfer] tkmedit

Hi Kojima tkmedit has been deprecated. Can you try using freeview instead? cheers Bruce On Tue, 14 Jun 2016, kojima_masaki_m...@yahoo.co.jp wrote: Hi.  I have this error, when I was doing tkmedit PSY1001fs/Users/MRI/Desktop/fsurfer_test_kojima/Surf_data_main/PSY1001fs/mri/brainma sk.mgz -a

Re: [Freesurfer] tkmedit

2016/6/14, Tue 17:53 >Subject: [Freesurfer] tkmedit > > >Hi.  > > >I have this error, when I was doing tkmedit PSY1001fs >/Users/MRI/Desktop/fsurfer_test_kojima/Surf_data_main/PSY1001fs/mri/brainmask.mgz > -aux >/Users/MRI/Desktop/fsurfer_test_kojima/Surf_data_main/

[Freesurfer] tkmedit

Hi.  I have this error, when I was doing tkmedit PSY1001fs /Users/MRI/Desktop/fsurfer_test_kojima/Surf_data_main/PSY1001fs/mri/brainmask.mgz -aux /Users/MRI/Desktop/fsurfer_test_kojima/Surf_data_main/PSY1001fs/mri/wm.mgz -surfs ERROR: Assertion failed: (!c->out.queue_len), function write_vec,

Re: [Freesurfer] tkmedit mac

Thanks a lot, it worked! 2015-06-08 21:23 GMT+02:00 Aaron Schultz : > You may need to reinstall XQuartz and/or fix symlinks: > > e.g.: sudo ln -s /opt/X11 /usr/X11R6 ; sudo ln -s /opt/X11 /usr/X11 > > -Aaron Schultz > > > > On Jun 8, 2015, at 9:31 AM, Bruce Fischl > wrote: > > > > Hi J

Re: [Freesurfer] tkmedit mac

You may need to reinstall XQuartz and/or fix symlinks: e.g.: sudo ln -s /opt/X11 /usr/X11R6 ; sudo ln -s /opt/X11 /usr/X11 -Aaron Schultz > On Jun 8, 2015, at 9:31 AM, Bruce Fischl wrote: > > Hi Joana > > have you added $FREESUFER_HOME/bin to your path? Have you sourced > $FREESURF

Re: [Freesurfer] tkmedit mac

Hi Joana have you added $FREESUFER_HOME/bin to your path? Have you sourced $FREESURFER_HOME/SetUpFreeSurfer.csh? cheers Bruce On Mon, 8 Jun 2015, Joana Braga Pereira wrote: > Dear all, > > I've downloaded freesurfer and installed it on mac (v 10.10.2). > > After running the recon-all pipeli

[Freesurfer] tkmedit mac

Dear all, I've downloaded freesurfer and installed it on mac (v 10.10.2). After running the recon-all pipeline on a subject, I opened tkmedit subj001 brainmask.mgz -surfs and the following message came out: -bash: tkmedit: command not found. I can open the same subject with freeview without any

Re: [Freesurfer] TKMEDIT error when SSH'ing

st Cc: freesurfer Subject: Re: [Freesurfer] TKMEDIT error when SSH'ing Have you verified that the machine you are ssh'ing into will display tkmedit even if you are not ssh'ing into it? I ask because OSX 10.6 is an end-of-life operating system and that error is usually associated with incomp

Re: [Freesurfer] TKMEDIT error when SSH'ing

Have you verified that the machine you are ssh'ing into will display tkmedit even if you are not ssh'ing into it? I ask because OSX 10.6 is an end-of-life operating system and that error is usually associated with incompatible graphics card. However, even if it did work while sitting at the host

[Freesurfer] TKMEDIT error when SSH'ing

Hi Freesurfer folks I am SSH'ing from one MAC to another. both mac's are running Mac Os 10.6.8 I am ssh'ing with -Y option when I try to run tkmedit I get the error; Thu May 21 09:54:24 cerebrum.uwm.edu tkmedit.bin[56625] : kCGErrorIllegalArgument: _CGSFindSharedWindow: WID 2763 Thu May 21

Re: [Freesurfer] tkmedit neuroscience format

no, sorry Bruce On Wed, 22 Apr 2015, Jon Alan Wieser wrote: Dear freesurfer experts. is it possible for  tkmedit to display volumes in neuroscience format (R is R) rather than radiologic format (R is L)?" Thanks Jon ___ Freesurfer mailing list F

Re: [Freesurfer] tkmedit neuroscience format

no, sorry On 04/22/2015 12:25 PM, Jon Alan Wieser wrote: > > Dear freesurfer experts. > > is it possible for tkmedit to display volumes in neuroscience format > (R is R) rather than radiologic format (R is L)?" > > Thanks > > Jon > > > > ___ > Freesurf

[Freesurfer] tkmedit neuroscience format

Dear freesurfer experts. is it possible for tkmedit to display volumes in neuroscience format (R is R) rather than radiologic format (R is L)?" Thanks Jon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mai

Re: [Freesurfer] tkmedit SetBrushShape does not enable 3d

Ok I will try freeview. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Wednesday, 15 April 2015 10:52 PM To: Freesurfer support list Subject: Re: [Freesurfer] tkmedit SetBrushShape does not

Re: [Freesurfer] tkmedit SetBrushShape does not enable 3d

Hi Chris we stopped developing tkmedit some years ago. Can you use freeview for this instead? cheers Bruce On Wed, 15 Apr 2015, Chris Adamson wrote: In tkmedit, if I use a tcl script with   SetBrushShape 3 0 1   The radius and shape are set to 3 and circular, respectively. However, the

[Freesurfer] tkmedit SetBrushShape does not enable 3d

In tkmedit, if I use a tcl script with SetBrushShape 3 0 1 The radius and shape are set to 3 and circular, respectively. However, the brush is not 3d, it only edits in the current slice. This bug is in 5.3.0 and the cvs version. Chris. Dr Chris Adamson Research Officer, Developmental Imaging,

Re: [Freesurfer] tkmedit 'no license' error

Zeke, That fixed it! Thank you. On 10/1/14, 1:05 PM, "Z K" wrote: >Hmmm... The error say: > >ERROR: FreeSurfer license file >/Users/smig9x/Applications/freesurfer//.license not found. > >And according to your screen capture I also do not see that file. But I >do see license.txt which should wor

Re: [Freesurfer] tkmedit 'no license' error

Hmmm... The error say: ERROR: FreeSurfer license file /Users/smig9x/Applications/freesurfer//.license not found. And according to your screen capture I also do not see that file. But I do see license.txt which should work. Can you try just renaming (or copying) the file "license.txt" to ".lice

Re: [Freesurfer] tkmedit 'no license' error

Zeke, Attached is a screenshot. Thanks! On 10/1/14, 11:03 AM, "Z K" wrote: >Hello Micheal, > >Can you please provide me the output when you 'cd' into the >FREESURFER_HOME directory and type the command 'ls -a' > >-Zeke > > >On 10/01/2014 08:56 AM, Smith, Michael wrote: >> Hello Freesurfer Team!

Re: [Freesurfer] tkmedit 'no license' error

Hello Micheal, Can you please provide me the output when you 'cd' into the FREESURFER_HOME directory and type the command 'ls -a' -Zeke On 10/01/2014 08:56 AM, Smith, Michael wrote: > Hello Freesurfer Team! > > I’ve been having an issue using the tkmedit function in freesurfer. I > get the fo

[Freesurfer] tkmedit 'no license' error

Hello Freesurfer Team! I’ve been having an issue using the tkmedit function in freesurfer. I get the following error: ERROR: FreeSurfer license file /Users/smig9x/Applications/freesurfer//.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.

Re: [Freesurfer] tkmedit

ery > > Universityof Pittsburgh > > (412)648-9654 Office > > (412)521-4431 Cell/Text > > *From:*freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Ali Radaideh > *Sent:* Wednesday, August 20, 2014 8:17 AM > *To:* F

Re: [Freesurfer] tkmedit

Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Ali Radaideh Sent: Wednesday, August 20, 2014 8:17 AM To: Freesurfer support list Subject: Re: [Freesurfer] tkmedit Dear Don, Thanks alot for

Re: [Freesurfer] tkmedit

> (412)521-4431 Cell/Text > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto: > freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Ali Radaideh > *Sent:* Tuesday, August 19, 2014 8:06 AM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] tkmedit > > >

Re: [Freesurfer] tkmedit

Thanks ZK, I got the following message: bash: /usr/local/freesurfer/bin/tkmedit: /bin/tcsh: bad interpreter: No such file or directory On Tue, Aug 12, 2014 at 5:29 PM, Z K wrote: > Ali, > > I have not encountered this issue before. Could you please provide a > screencapture or copy/paste of th

Re: [Freesurfer] tkmedit

Ali, I have not encountered this issue before. Could you please provide a screencapture or copy/paste of the terminal output when you type: $> tkmedit -f $FREESURFER_HOME/subjects/sample-001.mgz -Zeke On 08/12/2014 06:48 AM, Ali Radaideh wrote: > Dear Zeke, > > Thanks for your email. For so

Re: [Freesurfer] tkmedit

Dear Bruce, Thanks for your email, for some reasons your email went to the spam folder. Yes, all PC are running Ubuntu. The ram is: 7.6 GiB Processor: Intel® Core™ i7-3770 CPU @ 3.40GHz × 8 The graphic card: Intel® Ivybridge Desktop *-display description: VGA compatible controller

Re: [Freesurfer] tkmedit

Dear Zeke, Thanks for your email. For some reasons your email went to the spam folder The build-stamps.txt file contents: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 >freeview does not work Thanks, Ali On Tue, Aug 5, 2014 at 11:44 PM, Z K wrote: > Just so its clear.. You have insta

Re: [Freesurfer] tkmedit

Hi Ali they are all running ubuntu? How much ram is in them? Wha version of FreeSurfer and what version of ubuntu? What graphics cards do you have? cheers Bruce On Tue, 5 Aug 2014, Ali Radaideh wrote: Dear FreeSurfer experts, I have installed FreeSurfer on multiple machines in our image

Re: [Freesurfer] tkmedit

Just so its clear.. You have installed FreeSurfer on 15 Linux machines running Ubuntu? If so, can you please provide me with the contents of the build-stamps.txt file in the FREESURFER_HOME directory? Also, could you please inform me if freeview works by simply typing the freeview command? $>

[Freesurfer] tkmedit

Dear FreeSurfer experts, I have installed FreeSurfer on multiple machines in our image processing lab (15 PC, Linux Ubuntu) and made sure that the setting are fine. However, I have tried to test if freesurfer works or not by typing the following: tkmedit bert orig.mgz Unfortunately, I have got

Re: [Freesurfer] tkmedit error

Thank you very much. I solve it using the method. Wang Kangcheng From: Z K Date: 2014-07-31 22:00 To: Freesurfer support list CC: kangchengwang0808 Subject: Re: [Freesurfer] tkmedit error The XQuartz upgrade from v2.7.5 to v2.7.6 broke some of the FreeSurfer GUIs. Please reinstall XQuartz

Re: [Freesurfer] tkmedit doesn't show lines distinguishing grey and white matter

What gets printed out to the terminal? Can you load it through the interface? On 07/31/2014 11:37 AM, Caspar M. Schwiedrzik wrote: > Hi Talia, this is a Problem with x11 forwarding. Everything works fine > if you use VNC instead. > Caspar > > On Thursday, July 31, 2014, Talia Raney

Re: [Freesurfer] tkmedit error

The XQuartz upgrade from v2.7.5 to v2.7.6 broke some of the FreeSurfer GUIs. Please reinstall XQuartz v2.7.5. It can be downloaded from this page: http://xquartz.macosforge.org/trac/wiki/Releases -Zeke On 07/30/2014 10:54 PM, wang kangcheng wrote: > Dear experts > when I use the tkedit, it re

[Freesurfer] tkmedit error

Dear experts when I use the tkedit, it report the error (in the following). How could I solve it? tkmedit started: Thu Jul 31 10:41:56 2014 /Applications/freesurfer/tktools/tkmedit.bin patient_con_sub126 brainmask.tight.mgz -aux T1.mgz $Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $

Re: [Freesurfer] tkmedit doesn't show lines distinguishing grey and white matter

Hi Talia we need more information to help you. Have you looked at the wm.mgz? Is it accurate? What about the ?h.orig and ?h.orig.nofix surfaces? You need to track down where in the pipeline things started going wrong. cheers Bruce On Mon, 28 Jul 2014, Talia Raney wrote: > Hi,I'm having issu

[Freesurfer] tkmedit doesn't show lines distinguishing grey and white matter

Hi, I'm having issues with tkmedit. I'm doing visual inspection and I checked tkregister to be sure that the white matter is outlined in the functional image. However, when I open tkmedit for surface and cortical segmentation, it doesn't show up the red and green lines that distinguish the boundari

Re: [Freesurfer] tkmedit coronal view - y coordinate issue

The slice is displayed in native (scanner) coordinates so the talairach y can change. This is probably the case even for fsaverage since that is in MNI305 space doug On 06/30/2014 01:09 PM, DeCross, Stephanie N. wrote: > Hi, > > In FreeSurfer 5.3, when I click around in a coronal view slice, t

[Freesurfer] tkmedit coronal view - y coordinate issue

Hi, In FreeSurfer 5.3, when I click around in a coronal view slice, the Talairach y coordinate changes (in both the cursor column and the mouse column). This doesn’t make sense - it’s the same coronal slice, so shouldn’t anywhere on that same plane still have the same y coordinate? When I take

Re: [Freesurfer] tkmedit contrast

March 19, 2014 7:16 PM >> To: Freesurfer support list >> Cc: Douglas N Greve >> Subject: Re: [Freesurfer] tkmedit contrast >> >> does it work in freeview? >> On Wed, 19 Mar 2014, Borzello, Mia wrote: >> >>> Was there any solution for thi

Re: [Freesurfer] tkmedit contrast

lf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Thursday, March 20, 2014 12:39 PM To: Freesurfer support list Subject: Re: [Freesurfer] tkmedit contrast what kind of points? Almost certainly yes, but it will also be interesting debugging information for us to see whether it works or not On Th

Re: [Freesurfer] tkmedit contrast

___ > 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 20, 2014 12:39 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] tkmedit contrast > > wha

Re: [Freesurfer] tkmedit contrast

7:16 PM To: Freesurfer support list Cc: Douglas N Greve Subject: Re: [Freesurfer] tkmedit contrast does it work in freeview? On Wed, 19 Mar 2014, Borzello, Mia wrote: > Was there any solution for this? > > Thanks, > Mia > >

Re: [Freesurfer] tkmedit contrast

freeview? > > 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 19, 2014 7:16 PM > To: Freesurfer support list > Cc: Douglas N Greve > Subject: R

Re: [Freesurfer] tkmedit contrast

o, Mia > Sent: Friday, March 14, 2014 1:17 PM > To: Douglas N Greve; freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] tkmedit contrast > > no it doesn't help at all. > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [fr

Re: [Freesurfer] tkmedit contrast

: Re: [Freesurfer] tkmedit contrast no it doesn't help at all. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, March 14, 2014 1:11

Re: [Freesurfer] tkmedit edit voxel tcl script

This topic has been discussed previously without a conclusive answer. After some www inquests I realized that it is easily possible to process nii-images using spm functions for matlab. The functions for loading and saving images are: V = spm_vol(angio_corrected_marked);

Re: [Freesurfer] tkmedit contrast

t: Re: [Freesurfer] tkmedit contrast does the brightness/contrast window you display not work? On 03/14/2014 12:59 PM, Borzello, Mia wrote: > Hi Freesurfers, > > I recently coregisered a patient and am trying to visualize the > electrodes in tkmedit now, but I'm unable to see them

Re: [Freesurfer] tkmedit contrast

sure. It's under view->configure->brightness/contrast I believe On Fri, 14 Mar 2014, Borzello, Mia wrote: Hi Freesurfers,  I recently coregisered a patient and am trying to visualize the electrodes in tkmedit now, but I'm unable to see them very clearly. The CT has 1mm slices, so I don't think

Re: [Freesurfer] tkmedit contrast

does the brightness/contrast window you display not work? On 03/14/2014 12:59 PM, Borzello, Mia wrote: > Hi Freesurfers, > > I recently coregisered a patient and am trying to visualize the > electrodes in tkmedit now, but I'm unable to see them very clearly. > The CT has 1mm slices, so I don't th

Re: [Freesurfer] tkmedit edit voxel tcl script

Hi Pfannmoe, I don't believe it is possible to edit a voxel via tcl scripts. If so the command would be listed on this page: https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditReference/TkMeditScripting -Louis On Wed, 5 Mar 2014, Joerg Pfannmoeller wrote: > Hello, > > if I have sel

Re: [Freesurfer] TkmEdit Scripting SetBrushInfo Error

Allright, it works if I use those commands: UpdateBrushInfo { inBrush inLow inHigh inNewValue inMode inCloneSource } SetEditBrushConfiguration ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fr

[Freesurfer] tkmedit edit voxel tcl script

Hello, if I have selected a voxel in a volume with tkmedit with a tcl script, how can I set the voxel value to 0. Sincerely yours pfannmoe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fr

[Freesurfer] TkmEdit Scripting SetBrushInfo Error

Hi, I am getting tzhe following an error if I use the following command in a tcl-script: SetBrushInfo 3 1 2000 1 The error is: "Error: Parsing script file This error was encountered while running the script specified with the -tcl option. " What is wrong? Sincerely yours pfannmoe

Re: [Freesurfer] tkmedit and masking

Sorry, no. You can use mri_mask from the command-line though doug On 2/14/14 11:19 AM, Joerg Pfannmoeller wrote: > Hello, > > I am using tkmedit to display functional data as an overlay on anatomical > data. I am asking myself if there is a feature in tkmedit which allows to > apply a mask to t

[Freesurfer] tkmedit and masking

Hello, I am using tkmedit to display functional data as an overlay on anatomical data. I am asking myself if there is a feature in tkmedit which allows to apply a mask to the functional. Ideally would be a cortex mask to remove all non-cortex voxels. Regards Joerg -- Joerg Pfannmoeller

Re: [Freesurfer] tkmedit is not working

Hi again, you could try: wget -c ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Linux-centos4-stable-pub-v5.3.0.tar.gz which in theory is restartable and should resume a download if interrupted. Also I would like to recommend that you test whether your operating system is

Re: [Freesurfer] tkmedit is not working

I have downloaded in morning only. But seems there is some problem while downloading. While unzipping it is saying : *gzip: stdin: unexpected end of file freesurfer/trctrain/trc007/dlabel/cvs/rh.ilf_AS_roi1.flt.nii.gztar: Unexpected EOF in archivetar: Unexpected EOF in archivetar: Error is n

Re: [Freesurfer] tkmedit is not working

yes, particularly since 5.2 was deprecated. Thanks for pointing this out Sebastian Bruce On Tue, 4 Feb 2014, Sebastian Moeller wrote: > Hi again, > > On Feb 4, 2014, at 14:44 , Saurabh Thakur wrote: > >> >> On Tue, Feb 4, 2014 at 6:56 PM, Bruce Fischl >> wrote: >> ls -l /usr/local/freesurfer

Re: [Freesurfer] tkmedit is not working

Hi again, On Feb 4, 2014, at 14:44 , Saurabh Thakur wrote: > > On Tue, Feb 4, 2014 at 6:56 PM, Bruce Fischl > wrote: > ls -l /usr/local/freesurfer/tktools > > Hi Bruce, > > I m sending you some result : > > //==/// > freesurfer-Linux

Re: [Freesurfer] tkmedit is not working

On Tue, Feb 4, 2014 at 6:56 PM, Bruce Fischl wrote: > ls -l /usr/local/freesurfer/tktools Hi Bruce, I m sending you some result : //==/// *freesurfer-Linux-centos4-stable-pub-v5.2.0 Setting up environment for FreeSurfer/FS-

Re: [Freesurfer] tkmedit is not working

Tue, 4 Feb 2014, Saurabh Thakur wrote: Hi Everyone, Terminal output is: /// --// saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ tkmedit /usr/local/freesurfer/tktools/tkmedit.bin: C

[Freesurfer] tkmedit is not working

Hi Everyone, Terminal output is: ///--// saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$* tkmedit* /usr/local/freesurfer/tktools*/tkmedit.bin: Command not found.* saurabh@saurabh

[Freesurfer] tkmedit - display reconstruction toolbar by default

All, Is there any configuration file/source code file that can be edited to display the reconstruction toolbar by default in tkmedit? Thank you. Chris. Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch Childrens Research Institute Murdoch Childrens Research Institute Royal Chil

Re: [Freesurfer] tkmedit error message

Hi Elissa has tkmedit ever worked? This looks like an internal mac problem. For example, a google search turns up: https://discussions.apple.com/message/12614494#12614494 does freeview work? As far as the invalid messages go, you'll need to send us the details for us to comment. And yes, upda

[Freesurfer] tkmedit error message

Hello, I am a new freesurfer user. I tried to view subject data with tkmedit for the first time after the recon-all process finished without errors. Here is what I typed and the message I got: [ariana:~/Desktop/ELISSA_ THESIS/ATO] cmurphy% tkmedit ATO brainmask.mgz -aux T1.mgz -surfs -aseg Wed Oc

Re: [Freesurfer] tkmedit font size on scalebar

Hi Joerg sorry, there doesn't seem to be any way to do this other than recompiling the code. I could build you a version with a specific font if that would help, assuming glut supports it cheers Bruce On Mon, 2 Sep 2013, Jörg Pfannmöller wrote: Dear FreeSurfer experts, how can I increase t

[Freesurfer] tkmedit font size on scalebar

Dear FreeSurfer experts, how can I increase the font size on the tkmedit scale bar? Cheers Joerg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this

Re: [Freesurfer] tkmedit and freeview show different control points

Hi Sebastian can you email us the first couple of lines of the control.dat file? thanks Bruce On Fri, 5 Jul 2013, Sebastian Urchs wrote: > Hi, > > I am trying to migrate to freeview from tkmedit and started comparing edits > in both programs. I found that when I set control points in tkmedit a

Re: [Freesurfer] tkmedit on ssh remote machine error

yes, I have ForwardX11Trusted yes in ssh_config and I do ssh -Y Jon - Original Message - From: "R Edgar" To: "Jon Wieser" Cc: "Z K" , "freesurfer" Sent: Thursday, May 30, 2013 3:26:05 PM Subject: Re: [Freesurfer] tkmedit on ssh remote machin

Re: [Freesurfer] tkmedit on ssh remote machine error

On Thu, May 30, 2013 at 2:37 PM, Jon Wieser wrote: > both machines have Mac OS X 10.6.8 > > the tkmedit works fine when not logged in remotely > there is no error and the brain image is there Did you do "ssh -Y" or have "ForwardX11Trusted yes" in your ssh.config? Richard

Re: [Freesurfer] tkmedit on ssh remote machine error

both machines have Mac OS X 10.6.8 the tkmedit works fine when not logged in remotely there is no error and the brain image is there Jon - Original Message - From: "Z K" To: "Jon Wieser" Cc: "freesurfer" Sent: Thursday, May 30, 2013 12:16:55 PM Subject: R

Re: [Freesurfer] tkmedit on ssh remote machine error

Jon, I have not seen or heard of this error before... are both machines Mac OSX 10.6.8? Also, will the same command will produce a brain image when not logged in remotely? -Zeke On 05/30/2013 12:43 PM, Jon Wieser wrote: > > hi freesurfer folks > > I'm ssh'ing to from one MAc to another > X11

[Freesurfer] tkmedit on ssh remote machine error

hi freesurfer folks I'm ssh'ing to from one MAc to another X11 is on both machines MAC OS X 10.6.8 When I start TKmedit with: (freesurfer files are in the freesurfer directory) tkmedit freesurfer brainmask.mgz -aux T1.mgz I get the errors: Thu May 30 11:34:50 cerebrum.uwm.edu tkmedit.bin[

Re: [Freesurfer] tkmedit BUS error

Hi Amber, See the following wikipage which I created to troubleshoot various GUI issues. Specifically the second issue down which addresses the "Bus Error". https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_GUIs_troubleshooting -Zeke On 05/24/2013 03:26 PM, Amber M Gregory wrote: > I am ha

[Freesurfer] tkmedit BUS error

I am having a problem using tkmedit and tksurfer with Freesurfer. Freeview is working. Below is the tkmedit error and relevant specs. Any suggestions are welcome. General Specs Apple OS 10.6.8 Processor: 2x 2.26 Ghz Quad-core Intel Xeon 16 GB DDR3 Freesurfer Ver 5.3.0 Chipset Model:NVIDIA Ge

Re: [Freesurfer] tkmedit segmentation color offset

Using mri_label2vol will work a little better than mri_vol2vol. doug On 3/5/13 8:41 PM, Bruce Fischl wrote: you'll have to look at the help. It's pretty extensive since Doug wrote it :) Then you can use freeview to visualize the transformed intensity and aseg volumes cheers Bruce On Tue, 5 M

Re: [Freesurfer] tkmedit segmentation color offset

you'll have to look at the help. It's pretty extensive since Doug wrote it :) Then you can use freeview to visualize the transformed intensity and aseg volumes cheers Bruce On Tue, 5 Mar 2013, Natalie Han wrote: Thanks for the quick reply. Can you elaborate a little bit how to use mri_vol2vol

Re: [Freesurfer] tkmedit segmentation color offset

Thanks for the quick reply. Can you elaborate a little bit how to use mri_vol2vol to get what I want? what would be the final scipt for tkmedit then? On Tue, Mar 5, 2013 at 5:31 PM, Bruce Fischl wrote: > Hi Natalie > > sorry, tkmedit won't do what you want. It's old and we are not developing > i

Re: [Freesurfer] tkmedit segmentation color offset

Hi Natalie sorry, tkmedit won't do what you want. It's old and we are not developing it anymore. You can apply the transform using mri_vol2vol, just make sure to use nearest nbr interp for the aseg. cheers Bruce On Tue, 5 Mar 2013, Natalie Han wrote: Hi, all,  I have a tkmedit display iss

[Freesurfer] tkmedit segmentation color offset

Hi, all, I have a tkmedit display issue when I try to add transformation to the main volume, but the segmentation volume won't conform to Talairach domain accordingly. Here is the commandline tkmedit subject norm.mgz -main-transform talairach.xfm -seg aseg.mgz really appreciate any feedback on

Re: [Freesurfer] tkmedit error

Hi Ehsan what is the command you ran? And what is your SUBJECTS_DIR env variable set to when you run it? cheers Bruce On Mon, 25 Feb 2013, Ehsan Tadayon wrote: Hello I'm new to freesurfer, I have some .nii images that i converted to  .mgz via mri_converter in freesurfer and run recon-all on

[Freesurfer] tkmedit error

Hello I'm new to freesurfer, I have some .nii images that i converted to .mgz via mri_converter in freesurfer and run recon-all on them! it seems everything is fine and i've got stats in m subjects folders. but when I try to do tkmedit to visualize images it gives me an error: Tkmedit couldn't

Re: [Freesurfer] tkmedit background color

No, sorry, black is the only choice. doug On 11/30/2012 07:13 AM, Righart, Ruthger Dr. wrote: > Dear Freesurfer experts, > > I am trying to find out how to change the background color of tkmedit. > > Is there a possibility to change the background color from black to white, > just for display p

[Freesurfer] tkmedit background color

Dear Freesurfer experts, I am trying to find out how to change the background color of tkmedit. Is there a possibility to change the background color from black to white, just for display purposes? (to avoid laborious photoshop work). Best Regards, Ruthger Righart _

Re: [Freesurfer] TKMedit editing aux. volume - can't remove voxels from volume

Hi Rosa, tkmedit indicates voxels that have been turned "off" by setting them to 1, not 0. This is so we can keep track of the editing and preserve it during surface recon. If you want more general-purpose volume editing, you should probably use freeview instead. cheers Bruce On Sun, 21 Oc

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