Re: [Freesurfer] Cannot launch tkmedit in Ubuntu RE: Freesurfer Digest, Vol 137, Issue 10

[O'Shea,Andrew]

Looks like you just need to download x11 or xquartz to have a x-window program 
available. You can google it if you need instructions. If you are using a Mac 
they stopped including x11 as standard software on Yosemite, which I think is 
kind of stupid. 
-Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Hu, Yifan 

Sent: Thursday, July 9, 2015 3:43 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Cannot launch tkmedit in Ubuntu RE: Freesurfer 
Digest, Vol 137, Issue 10

Hi,

Thank you so much for your response! Yes, I'm at the console and am not 
remoting in. And your prediction was correct, that I can't run xclock. The 
error message is below:
No protocol specified
Error: Can't open display: :0.0

This is weird though because we had used Freesurfer half a year ago and never 
got this error. Thanks again.


Best,
Yifan

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of 
freesurfer-requ...@nmr.mgh.harvard.edu
Sent: Wednesday, July 08, 2015 11:00 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Freesurfer Digest, Vol 137, Issue 10

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Today's Topics:

   1. saving clusters in qdec (O'Shea,Andrew)
   2. Re: couple TRACULA questions (Harms, Michael)
   3. Repost: What algorithm does mri_label2label use?
  (Caspar M. Schwiedrzik)
   4. Re: Repost: What algorithm does mri_label2label use?
  (Douglas N Greve)
   5. Re: convert FS volume in scanner space (von Polier, Georg)
   6. Re: convert FS volume in scanner space (Bruce Fischl)
   7. wm- volume limitations (Krieger, Donald N.)
   8. Re: wm- volume limitations (Douglas Greve)
   9. Re: convert FS volume in scanner space (Douglas Greve)
  10. Re: longitudinal analysis (Liu Y)
  11. Re: wm- volume limitations (Krieger, Donald N.)
  12. Make liberal ROI masks (Martin Hebart)
  13. Re: convert FS volume in scanner space (von Polier, Georg)
  14. mris_fill on HCP data (Matteo Bastiani)
  15. Re: convert FS volume in scanner space (Douglas Greve)
  16. Re: convert FS volume in scanner space (von Polier, Georg)
  17. Cannot launch tkmedit in Ubuntu (Hu, Yifan)
  18. Re: mris_fill on HCP data (Bruce Fischl)
  19. Re: Cannot launch tkmedit in Ubuntu (Bruce Fischl)


--

Message: 1
Date: Tue, 7 Jul 2015 16:10:37 +
From: "O'Shea,Andrew" 
Subject: [Freesurfer] saving clusters in qdec
To: "freesurfer@nmr.mgh.harvard.edu" 
Message-ID: 
Content-Type: text/plain; charset="us-ascii"

Hello,
Is it possible to save a mask of significant clusters past a certain threshold, 
say 3.0, directly from the qdec interface? I want to save a few clusters, and 
then map them back to individual subject space. I see I can do this if I 
manually trace the cluster and save the ROI, but this not exact and takes some 
time. Is there a simple way I am missing?
-Andrew
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Message: 2
Date: Tue, 7 Jul 2015 21:00:19 +
From: "Harms, Michael" 
Subject: Re: [Freesurfer] couple TRACULA questions
To: Freesurfer support list 
Message-ID: 
Content-Type: text/plain; charset="us-ascii"


Hi Anastasia,
Will the next version of TRACULA support the use of 'topup' and 'eddy' by any 
chance?

thanks,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders Washington University 
School of Medicine Department of Psychiatry, Box 8134
660 South Euclid Ave.   Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 7/6/15 12:00 PM, "Anastasia Yendiki" 
wrote:


Forgot to reply re: merging. You have to merge them yourselves, sorry.

On Mon, 6 Jul 2015, Harms, Michael wrote:

>
> Hi Anastasia,
> We are looking at running TRACULA on some data, where we were
>attracted by the longitudinal component of TRACULA.  Is a paper on the
>longitudinal  aspect of TRACULA in the works?
>
> If we have multiple dMRI runs/series per imaging session, do we need
>to merge/concatenate those ourselves pri

Re: [Freesurfer] Cannot launch tkmedit in Ubuntu RE: Freesurfer Digest, Vol 137, Issue 10

[Hu, Yifan]

 center not 
at magnet center, which is what I need. 

Scanner Space - coordinate center at magnet isocenter, bore axis is Z, X to the 
left, Y to the ceiling. Direction cosines and P0 defined in DICOM file (note: 
this is an LPS, not RAS coordinate system)  Native - basically the same as 
scanner, but RAS.

-Urspr?ngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas Greve
Gesendet: Mittwoch, 8. Juli 2015 16:37
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] convert FS volume in scanner space

what do you mean the coords are still in RAS?

On 7/8/15 8:25 AM, von Polier, Georg wrote:
> My command line was
>
> cd $SUBJECTS_DIR//mri
> mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o 
> brain-in-rawavg.mgz --no-save-reg
>
> according to   fswiki/FsAnat-to-NativeAnat.
>
> As I mentioned, I am happy with the results but the coordinates are still RAS 
> (from my understanding) and different from the original dicom-coordinates 
> (that my manual segmentations are in). When I use mri_convert, the 
> coordinates are in dicom-space (0 in center of image/ coil; offset and z-axis 
> identical with original dicoms), but the segmentation seems different/ more 
> prone to artifacts, also when I use rt- nearest.
>
> Georg
>
> -Urspr?ngliche Nachricht-
> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas 
> Greve
> Gesendet: Mittwoch, 8. Juli 2015 04:20
> An: freesurfer@nmr.mgh.harvard.edu
> Betreff: Re: [Freesurfer] convert FS volume in scanner space
>
> what was your vol2vol command line? What wiki page were you referencing?
> What was the problem with the coordinates?
>
> On 7/7/15 8:11 PM, Bruce Fischl wrote:
>> I think you meant you want nearest neighbor interpolation, not 
>> trilinear, since you are mapping labels. Try using -rt nearest insted 
>> On Wed, 8 Jul 2015, von Polier, Georg wrote:
>>
>>> Thanks for your reply. I tried mri_convert with -rt interpolate (resulting 
>>> in trilinear interpolation), however, the results were partially prone to 
>>> artifacts and different from those I get with mir_vol2vol (but in dicom 
>>> space).
>>>
>>> Is there a way using mir_vol2vol with results in dicom space, or a second 
>>> step that gives a vox2vox from conformed/anatomical space to dicom space?
>>>
>>> I use the .mgz-output of hippo_subfields (FS_dev).
>>>
>>> Thanks again,
>>> Georg
>>>
>>>
>>>
>>>> Am 07.07.2015 um 02:34 schrieb Bruce Fischl :
>>>>
>>>> Hi Georg
>>>>
>>>> if you have a volume (like the 001.mgz) that is in scanner 
>>>> coordinates you can use the "reslice like" and "resample type" flags in 
>>>> mri_convert:
>>>>
>>>> mri_convert -rl 001.mgz -rt trilinear input.mgz output.mgz
>>>>
>>>> cheers
>>>> Bruce
>>>>
>>>> On Mon, 6 Jul 2015, von
>>>> Polier, Georg wrote:
>>>>
>>>>> Dear FreeSurfers,
>>>>>
>>>>> I need to convert an FS-volume back in scanner space (to calculate 
>>>>> overlap with manual segmentation).
>>>>> I went through the wiki-entry and converted to native space with 
>>>>> mir_vol2vol, however the coordinates are still RAS and not identical with 
>>>>> the original Scanner-coordinates. I tried mri_convert, however, the 
>>>>> results were not as good as mri_vol2vol (apparently need trilinear 
>>>>> interpolation, not available in mri_convert).
>>>>>
>>>>> Any help would be greatly appreciated,
>>>>>
>>>>> Cheers, Georg
>>>>> ___
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>
>>>>>
>>>>>
>>>> ___
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>> The information in this e-mail is intended only for the person to 
>>>> whom it is addressed. If you believe this e-mail was sent to you in 
>>>> error and the e-mail contains patient information, please contact 
>>>> the Partners C

Re: [Freesurfer] Cannot launch tkmedit in Ubuntu

[Bruce Fischl]

Hi Yifan

are you on the console of that machine or are you remotely logging in from 
somewhere else? Can you run standard x apps (like xclock)?


cheers
Bruce



On Wed, 8 Jul 2015, Hu, Yifan wrote:



Hello,

 

When trying to use tkmedit, I got the following error message:

No protocol specified

No protocol specified

GLUT: Fatal error in tkmedit.bin: could not open display: :0.0

 

In addition, when I tried to switch to freeview instead, I also got an error
message:

No protocol specified

No protocol specified

Freeview.bin: cannot connect to X server: 0.0

 

I’m running Ubuntu 12.04 LTS.

Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

Debian version: wheezy/sid

Kernel info: Linux 3.2.0-60-generic x86_64

 

Please let me know if there is other info that you need. Any suggestion is
very much appreciated.

 

Thanks,

Yifan

--

Yifan Hu

PhD Student | Social, Cognitive, Personality, and Emotional (SCoPE)
Neuroscience Laboratory

3414/2436 Beckman Institute for Advanced Science and Technology

Cognitive Neuroscience Division, Department of Psychology

University of Illinois at Urbana-Champaign

405 North Mathews Ave

Urbana, IL 61801

USA

 

Phone: +1 (217) 607-4536

Email: yifan...@illinois.edu 

Website: http://dolcoslab.beckman.illinois.edu/

 


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[Freesurfer] Cannot launch tkmedit in Ubuntu

[Hu, Yifan]

Hello,

When trying to use tkmedit, I got the following error message:
No protocol specified
No protocol specified
GLUT: Fatal error in tkmedit.bin: could not open display: :0.0

In addition, when I tried to switch to freeview instead, I also got an error 
message:
No protocol specified
No protocol specified
Freeview.bin: cannot connect to X server: 0.0

I'm running Ubuntu 12.04 LTS.
Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Debian version: wheezy/sid
Kernel info: Linux 3.2.0-60-generic x86_64

Please let me know if there is other info that you need. Any suggestion is very 
much appreciated.

Thanks,
Yifan
--
Yifan Hu
PhD Student | Social, Cognitive, Personality, and Emotional (SCoPE) 
Neuroscience Laboratory
3414/2436 Beckman Institute for Advanced Science and Technology
Cognitive Neuroscience Division, Department of Psychology
University of Illinois at Urbana-Champaign
405 North Mathews Ave
Urbana, IL 61801
USA

Phone: +1 (217) 607-4536
Email: yifan...@illinois.edu
Website: http://dolcoslab.beckman.illinois.edu/

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.