Hi,
I'm trying to look at 2 connectivity files (saved in SPM) at the same time
using Freeview, but how I've been doing it in the past is no longer working and
I haven’t changed anything on my end. What I had been doing:
1. cd to the folder with my connectivity files and typing the shortcut
Thanks! Unfortunately it won't help; I need specific versions with specific
compilation options etc :-(
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From:
?Hello,
I am encountering the exact same problem on Yosemite (10.10). The log file is
attached. Any ideas? I am pretty stumped.
Anthony
From: freesurfer-boun...@nmr.mgh.harvard.edu
freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Matthew Riddle
I'm sorry if this has been answered before, I have browsed the mailing and
found nothing answering this.
I need to generate three views of the T1 data superimposed with Aseg data
automatically for Quality Control without using FreeView or Tkmedit (the
server generating this has no X11)
Is it
Dear FreeSurfer experts,
I get a new message when I use mri_convert command to convert dicom to
mgz. I used to apply this command before and there was no problem. I wonder
what is the reason that I get the new message. In addition, it does not
create mgz file, and goes to infinite loop.
Hello Martin,
I did this (ran it from both the Desktop and Documents). Also tried
re-installing Freesurfer. The subjects folder also has permissions:
drwx--+ 1632 adick staff54K Nov 5 13:01 Desktop
drwx--+ 42 adick staff 1.4K Nov 5 12:48 Documents
I also set permissions
Hello Anthony,
The problem isnt with the location of the bert folder but rather with
the permissions of the bert folder itself (and the permissions within).
To run the bert case please 'cd' into the directory containing the bert
folder and type the following:
sudo chmod -R a+wr bert
-Zeke
Hi All,
I am getting a consistent error when I try to run mris_preproc - I'm baffled as
I've used all of my scripts and fsgd files before.
There are 2 groups with 3 covariates but I keep getting this error:
mris_preproc --fsgd fsgd/HRR60.fsgd --cache-in thickness.fwhm10.fsaverage
--target
Hi Nooshin
if you can upload that dataset we will take a look
cheers
Bruce
On Wed, 5 Nov 2014,
Nooshin Zadeh wrote:
Dear FreeSurfer experts,
I get a new message when I use mri_convert command to convert dicom to
mgz. I used to apply this command before and there was no problem. I wonder
Hi PPJ
I'm not sure it is. Tksurfer has an offscreen rendering option :
setenv renderoffscreen 1
used to work, and maybe still does, but I don't think we ever implemented
it in tkmedit, and I'm not sure about freeview. Ruopeng can answer that
part
On Wed, 5 Nov 2014, Pedro Paulo de
Have you tried installing 'xauth' on the server and connecting via 'ssh
-X'? That should show all graphical output on the local machine.
On 11/05/2014 05:03 PM, Bruce Fischl wrote:
Hi PPJ
I'm not sure it is. Tksurfer has an offscreen rendering option :
setenv renderoffscreen 1
used to work,
Can you run it with --debug as the first argument and send the terminal
output?
doug
On 11/05/2014 04:21 PM, Cooke, Gillian wrote:
Hi All,
I am getting a consistent error when I try to run mris_preproc - I'm
baffled as I've used all of my scripts and fsgd files before.
There are 2
Unfortunately I'm getting this error in the terminal:
bash: --debug: command not found
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: Wednesday,
run it like this
mris_preproc --debug --fsgd fsgd/HRR60.fsgd ...
doug
On 11/05/2014 05:32 PM, Cooke, Gillian wrote:
Unfortunately I'm getting this error in the terminal:
bash: --debug: command not found
From: freesurfer-boun...@nmr.mgh.harvard.edu
Thanks Doug - this is what it produces:
out mris_preproc/lh.HRR60.thickness.10.mgh
set echo = 1 ;
set debug = 1 ;
set debug = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 10 != 0 )
set flag = $argv[1] ; shift ;
set flag = --fsgd
shift
switch ( $flag )
switch ( --fsgd )
if ( $#argv
Hmm, still not sure what's up. Can you attach your fsgd file to an email?
doug
On 11/05/2014 05:48 PM, Cooke, Gillian wrote:
Thanks Doug - this is what it produces:
out mris_preproc/lh.HRR60.thickness.10.mgh
set echo = 1 ;
set debug = 1 ;
set debug = 1
breaksw
breaksw
end
end
while (
Hi Doug,
The FSGD file is attached.
Best wishes,
Gill
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: Wednesday, November 05, 2014 5:10 PM
To:
The FSGD file is not plain text. Did you make it file on a Windows
computer? Try cut and pasting it into emacs or vi or wordpad
doug
On 11/5/14 8:26 PM, Cooke, Gillian wrote:
Hi Doug,
The FSGD file is attached.
Best wishes,
Gill
From:
Hello Zeke,
I have tried giving permissions to multiple folders (freesurfer, bin,
Documents, bert etc.) using this command with no luck. Here is where it
keeps dying. Is it possibly an issue with something else other than
permissions?
#@# Talairach Wed Nov 5 23:58:06 EST 2014
Dear All,
this is very basic. I have Analyze volumes, and I was suggested to use
-notal-check to bypass the 3rd recon step. I wanted to make sure skipping
the T registration step would not have the potential to mess up the
spherical registration in autorecon3 in any way on a case by case basis. I
Dear Bruce,
My questions is just to learn and to improve my understanding.
The commands recon-all and dt-recon are routinely generating the statistics at
the end of there running and we can check the results in aseg.stats (the
output of recon-all) and fa.stats (the output of dt-recon for FA).
Dear Freesurfer Mailing list,
While running a glm anlaysis with monte carlo correction (using cluster
wise thresholds of .05 .01), I encountered the following issue:
When examining the clusters formed for each of the different cluster
wise thresholds, the .05 threshold resulted in a superior
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