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] tkm

Re: [Freesurfer] tkmedit in FreeSurfer 7.0

There is a script called tkmeditfv which runs freeview with tkmedit-style arguments. Most of the time, this is much easier On 5/12/2020 3:30 PM, Hoopes, Andrew wrote: Hi Aylin, You can add this to your SetUpFreeSurfer script in $FREESURFER_HOME, but in general tkmedit is no longer supported

Re: [Freesurfer] tkmedit in FreeSurfer 7.0

Hi Aylin, You can add this to your SetUpFreeSurfer script in $FREESURFER_HOME, but in general tkmedit is no longer supported 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: [Free

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

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

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

Thank you for quick reply. I finished preprocessing and tried to check imagies, but tkmedit does not work. Please let me know how to do. Kojima - Original Message - >From: "kojima_masaki_m...@yahoo.co.jp" >To: "freesurfer@nmr.mgh.harvard.edu" >Date: 2016/6/14, Tue 17:53 >Subject: [Fr

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

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

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

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

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

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? $>

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

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

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

Re: [Freesurfer] tkmedit contrast

s? >>> >>> Thanks, >>> Mia >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia >>> Sent: Friday, March 14, 2014 1:17 PM >

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

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

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

Ok, lots of problems! First, is the tktools directory empty? Run: ls -l /usr/local/freesurfer/tktools if there is nothing there, you will need to download and install them. Second: you are getting the warning "WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!". Can you ask your

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

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

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

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

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

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

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

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

Re: [Freesurfer] Tkmedit question

Hi Antonella it's hard for us to know without seeing your data, but certainly setting them both to 0 will show you everything Bruce On Wed, 21 Mar 2012, Antonella Kis wrote: Dear All, I am trying to understand what should be my -fthresh and -fmax or -fmin and -fmax values  while visualizin

Re: [Freesurfer] tkmedit

what is your command line? On Wed, 21 Mar 2012, Richter, Julia wrote: > Hi freesurfer experts, > > I am trying to correct the pial surfaces for my cortical thickness analysis. > I assume that I have to load my pial surface into tkmedit and that I have to > specify the subject image_type and the

Re: [Freesurfer] Tkmedit Talairach coordinates

Those are 305 coordinates transformed to "talaiarch" through Matthew Brett's transform. doug Tanner,Jared J wrote: > Hi, > > I just wanted to verify what the Talaiarch coordinates reported in > tkmedit actually are. Are they based on Matthew Brett's 10/8/98 > non-linear transform from MNI305 sp

Re: [Freesurfer] Tkmedit Talairach coordinates

the Talairach coords reported in tkmedit are the 'Brett' corrected coordinates. the mni305 are also available, but off by default, if you select View->Information->MNI Coordinates. n. On Tue, 2011-11-22 at 14:42 -0500, Tanner,Jared J wrote: > Hi, > > > I just wanted to verify what the Talaiar

Re: [Freesurfer] tkmedit window size

Hi, I don't think the order of zooming and dragging matters, it appears that the result is the same: I cannot drag the window independently of the image, this will change in size as well... Thanks, Torsten On Tue, 2011-10-04 at 09:50 -0400, Bruce Fischl wrote: > no, sorry. Why not zoom first,

Re: [Freesurfer] tkmedit window size

no, sorry. Why not zoom first, then drag to make it bigger? On Tue, 4 Oct 2011, Torsten Ruest wrote: > Hi there, > > I was wondering whether there is better option to resize the tkmedit > window: when I drag it bigger, it appears that the same change in aspect > ratio is applied to the image I am

Re: [Freesurfer] tkmedit window size

Hi Torsten, I believe we have this on our to do list for tkmedit fixes. Allison On Tue, 4 Oct 2011, Torsten Ruest wrote: > Hi there, > > I was wondering whether there is better option to resize the tkmedit > window: when I drag it bigger, it appears that the same change in aspect > ratio is app

Re: [Freesurfer] tkmedit bus error

Hi Carolina: Is it possible, but in my case when the hard disk is full at the moment of the processing, I got a fatal error from recon-all command... Sincerely, Gonzalo Rojas Costa El 19-09-2011 9:53, Carolina Valencia escribió: > Thanks for the answers. > I think the problem was the

Re: [Freesurfer] tkmedit bus error

C_vol01 rh pial > > Sincerely, > > > Gonzalo Rojas Costa > Department of Radiology > Clinica Las Condes > Santiago > Chile > > > > Message: 4 > > Date: Sun, 18 Sep 2011 10:25:26 -0400 (EDT) > > From: Bruce Fischl > > Subject: Re: [Freesurfer] tkme

Re: [Freesurfer] tkmedit bus error

Subject: Re: [Freesurfer] tkmedit bus error > To: Carolina Valencia > Cc: Freesurfer Mailing List > > Hi Carolina, > > does this happen every time? Can you run freeview on the volumes and see > if it can display them properly? > > cheers > Bruce > On Thu, 15 Sep 201

Re: [Freesurfer] tkmedit bus error

Hi Carolina, does this happen every time? Can you run freeview on the volumes and see if it can display them properly? cheers Bruce On Thu, 15 Sep 2011, Carolina Valencia wrote: > Hi FSusers > > I run recon-all in a patient without problems, but when I tried to view it in > tkmedit, an error

Re: [Freesurfer] tkmedit: Extending white matter and pial surfaces

Hi Michelle you have to identify the cause of the underestimation. Is there missed white matter? If so, is it darker than 110? In that case adding control points would be the right thing to do. cheers Bruce On Fri, 26 Aug 2011, Michelle Umali wrote: > Hi Freesurfers, > When looking at the sur

Re: [Freesurfer] tkmedit protrusion and hyperintense splotches

Hi Michelle, those aren't necessarily problems. We see this in lower quality scans where you get little 1d protruberances that have very small radius of curvature. Have you checked the ?h.white surface in those locations? At the end of the day, that's what you really care about. If you don't li

Re: [Freesurfer] tkmedit

Hi Michelle Can you send us an image with arrows to point out what you think are problems? Cheers Bruce On May 9, 2011, at 11:51 PM, Michelle Umali wrote: > Dear Freesurfers, > I've noticed some problems in some inflated brains with the curvature > displayed that I know will require manual inte

Re: [Freesurfer] tkmedit and tkregister2 permission or ? problems

Hi Jim, I think for --s you just want heinrick cheers, Bruce On Wed, 20 Apr 2011, jim kroger wrote: > Hello, I am having trouble running tkmedit and tkregister2. > > With tkregister2, I issue the command > > tkregister2 --mgz --s heinrick/mri/transforms/talairach.xfm --fstal > (and sometimes I

Re: [Freesurfer] tkmedit undo volume?

Stevens [astev...@nmr.mgh.harvard.edu] Sent: Tuesday, March 22, 2011 9:21 AM To: Nugent, Allison C. (NIH/NIMH) [E] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tkmedit undo volume? Hi Allison, Can you send me the link to the wiki page that says that? To my knowledge, you can only undo the very las

Re: [Freesurfer] tkmedit undo volume?

Hi Allison, Can you send me the link to the wiki page that says that? To my knowledge, you can only undo the very last edit you made in tkmedit and that is by going to Edit > undo. With freeview, you can select undo as many times as you'd like. Allison On Wed, 16 Mar 2011, Nugent, Allison C. (N

Re: [Freesurfer] tkmedit and intensity normalisation

Hi Ali: Q 1: I believe this has to do with your NVIDIA driver/ X windows. If you are using Linux, open a terminal and type 'glxgears'. If you see a window pop-up with 3 colored gears running, then your graphics driver is working within X windows. If you do not see this, then you need to goto the i

Re: [Freesurfer] tkmedit and intensity normalisation

I don't know about the 1st question, but on the 2nd question, you do not have to rerun recon-all twice if you fix both of them at the same time. doug Ali Radaideh wrote: > > Dear FreeSurfer experts, > > I have two question for you please, > > First, I started recently to get the following messag

Re: [Freesurfer] tkmedit scripting question

Hi Krish, thanks a lot. Unfortunately that only sets the values for the dialog but does not actually activate them. I will try my luck, now that you showed me how to set more involved tcl structures :). I will report back (once our computer system works again). Best Sebastian On Jul

Re: [Freesurfer] tkmedit scripting question

Hi Sebastian I was able to manipulate the dialogue like this %set gEditBrush(1,cloneSource) 1 %set gEditBrush(1,mode) 1 Try a combination of 0 or 1 for the last argument. And spaces ( or lack of them ) are absolutely important. Don't leave any space in gEditBrush(1,mode) The first argument

Re: [Freesurfer] tkmedit buttons grayed out

Hi Reza, what anatomical volume are you using? I think that either happens if you (1) don't have write permission to the subject's tmp/edit.dat file, or (2) the volume you loaded isn't "conformed" (i.e. not one of our standard anatomical volumes such as orig.mgz, norm.mgz...). cheers Bruce On

Re: [Freesurfer] tkmedit and tksurfer volume display problem in Ubuntu 9.04

Thanks Bruce + Daniel. I get no error messages in the terminal when running tkmedit/tkmsurfer. Drivers are enabled and up-to-date, and other similar software is working OK (for instance, fslview). However, I have installed freesurfer in another computer with an nvidia video card and tkmedit looks

Re: [Freesurfer] tkmedit and tksurfer volume display problem in Ubuntu 9.04

Hi Miguel, As Bruce said, the best thing to do is to make sure you have enabled "Hardware Drivers" for your video card and make sure they are up-to-date. However, if you do not have a video card with the appropriate level of OpenGL support for an application (e.g., if you are running in a VM)

Re: [Freesurfer] tkmedit and tksurfer volume display problem in Ubuntu 9.04

Hi Miguel, make sure your video driver is up to date. Are there any error messages in the console? Bruce On Wed, 13 Jan 2010, Miguel Burgaleta wrote: > Hi again, > > I am experiencing some problems when testing my freesurfer installation in > Ubuntu 9.04. When I run tkmedit and tkmsurfer the int

Re: [Freesurfer] tkmedit : Functional RAS to Functional index

It uses the "vox2ras" matrix. You can get this with mri_info --vox2ras-tkr f.nii Take the inverse of this matrix and multiply it by the CRS Oya, Hiroyuki wrote: > Hello Experts, > > Transformation from Volume RAS to Functional RAS is done with > anat2exf.reg.dat. > But how does tkmedit calcul

  1   2   >