This works, thanks Ruopeng.
BTW, Freesurfer is really a gem!
mary
On 2017-03-03 23:04, Ruopeng Wang wrote:
> Sorry, that appears to only work with 3D view. On 2D view you’ll have
> to use Cmd + arrow keys to pan. I’ll fix it in future update.
>
>> On Mar 3, 2017, at 9:58 AM, Ruopeng Wang
>> wr
Hi,
How do I pan on Freeview on a Mac please? Mine is an El Capitan, MacBook
Pro (Early 2011).
On
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewGeneralUsage/FreeviewNavigation
it reads:
You can pan across the data, which is especially useful when zoomed in.
To do so while in
Hello FS experts,
A quick question for you all. Does the FS stream produce any values for the
Prefrontal Cortex specifically?
Thanks,
Fatima
E-pos vrywaringsklousule
Hierdie e-pos mag vertroulike inligting bevat en mag regtens geprivilegeerd
wees en is sle
Hello,
I got this error while trying to generate the stats table on qdec on my own
data:
What I don't understand is for the 1st error, where it says it can't locate
aseg.stats for 240, the aseg.stats file is in subject 240's file.
But what is the reason for the 2nd error?
asegstats2table --mea
Hello,
I'm trying to run qdec on my own data and I'm trying to create fsaverage.
Following the wiki tutorial, I copied the command:
if (! -e fsaverage) ln -s $FREESURFER_HOME/subjects/fsaverage
but I got the following error:
bash: syntax error near unexpected token `ln'
Can an
Hello,
I was running the tutorial on Qdec, when I went to generate stats data, it
started running fine, and then I got the following error message:
aparcstats2table --hemi rh --parc aparc.a2005s --meas area --tablefile
/mnt/hgfs/VBM/freesurfer_EONCS/EONCS/buckner_data/tutorial_subjs/qdec/stats
/fbert-feat/fbert1.feat/.files: Directory
renamed before its status could be extracted
tar: buckner_data/tutorial_subjs/fbert-feat/fbert2.feat/.files: Directory
renamed before its status could be extracted
tar: Error exit delayed from previous errors
[root@localhost EONCS]#
Can someone please e
Thanks Daniel! That's great!
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Daniel Ferreira
Padilla
Sent: 14 September 2011 10:25
To: Ahmed, F, Me
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all
ubject: Re: [Freesurfer] Recon-all Error: _FindFacePath
Hello Khoa,
Thank you very much for your suggestion. I checked both brainmask.mgz and
wm.mgz and it saw ok for me. I have already sent my two scans to Bruce. Hope
something can be done.
Cheers!
Daniel Ferreira
2011/9/13 Khoa Nguyen
Hello Freesurfers,
I got this error on my processing and wondered what the problem may be:
Talairach Failure Detection Mon Aug 15 16:26:35 SAST 2011
/mnt/hgfs/VBM/freesurfer_EONCS/EONCS/NN117/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
ERROR: talairach_afd: Talairach Transform: tr
Sent: 15 August 2011 18:15
To: Ahmed, F, Me
Cc: freesurfer@nmr.mgh.harvard.edu; Louis Nicholas Vinke
Subject: Re: [Freesurfer] recon-all error with nu_correct
check this!!!
/bin/mv: cannot move `./tmp.mri_nu_correct.mni.26621/1/nu2_residue.mnc' to `./
tmp.mri_nu_correct.mni.26621/1/n
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Louis Nicholas
Vinke
Sent: 15 August 2011 17:59
To: Ahmed, F, Me
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all error with nu_correct
Hi Fatima,
What is the recon-all command line you are using to start the recon?
-Louis
Hello Freesurfer experts,
I am having great difficulty in trying to run the recon-all process on some
scans of mine. I have tried running it a number of times, to no avail and the
error I have gotten most recently is the nu_correct error. I have attached the
log for this recon-all and hope some
y of Aging, vol. 10,
1657-1676 and references cited herein.
Ed
On 8 Jul 2011, at 15:02, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
>
> Hello,
>
> I'm wondering if anyone could help me out with a question I had. For
> a study I'm working on, I'm comparing the r
Hello,
I'm wondering if anyone could help me out with a question I had. For a study
I'm working on, I'm comparing the regional brain volumes in adolescents with
and without PTSD. I ran VBM analysis and Freesurfer on my subjects and I found
some significant results on VBM (howe
Sorry for repeating myself, but I'm unsure if my first post got through
successfully. My post is detailed below:
I require values (total volume) for the prefrontal cortex. I see labels for
"G_frontal_middle" and "G_frontal_superior" in the lh.aparc.annot files - are
these correct to use? If so,
Hello,
I require values (total volume) for the prefrontal cortex. I see labels for
"G_frontal_middle" and "G_frontal_superior" in the lh.aparc.annot files - are
these correct to use? If so, could I add up the values for these to get one
total volume for the PFC?
Thank you,
Fatima
_
Yes I do see values for cc in the stats file thank you!
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Allison Stevens
Sent: 08 June 2010 12:29
To: Ahmed, F, Me
Cc: Freesurfer Mailing List; Doug Greve
Subject
I'm running version 4.3.1
-Original Message-
From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: 08 June 2010 11:01
To: Ahmed, F, Me
Cc: Freesurfer Mailing List
Subject: RE: [Freesurfer] brain regions
How did you look at it (what was your command-line)? You should load it
Thank you for that Doug, I just had a look in the aseg.mgz file, but unless I'm
blind, I can't seem to see it...could you tell me what it's labelled as please?
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.ed
Hello FS experts,
A quick question, I'm looking for specific brain regions, but I can't seem to
find them in the files once processing has been completed, I'm just wondering
if FS does processing for areas including prefrontal cortex and corpus collosum?
Thanks,
Fatima
__
Thank you, I did create more space and I reran autorecon2 and it completed
without error.
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: 30 March 2010 15:23
To: Ahmed, F, Me
Cc: Freesurfer Mailing List
Subject: RE: [Freesurfer] autorecon2 error
that
Well I did run out of space in FS a while back, but I made space, and it had
been running ok, do you think I have run out of space?
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: 30 March 2010 14:20
To: Ahmed, F, Me
Hi Bruce,
Ok, so if I wanted to run multiple recon-all jobs in parallel, how would I go
about in doing that? My one problem is that I am running FS on an emulator
(VMware). And I'm wondering if that will stop me from running multiple jobs?
And if not, how would I go about doing this o
run time will be needed more) in the multiple
command terminals.
Best regard!
Woo-Suk, Tae
Chucheon, Korea
--- Original Message ---
From : "Ahmed, F, Me "
To : "Freesurfer Mailing List"
Date : 2009/10/28 수요일 오후 4:19:02
Subject : [Freesurfer] dual boot OS
Hello,
A quick ques
Hello,
A quick question, if I wanted to run simultaneous recon-all jobs, would I have
to install Linux as a dual boot operating system as opposed to what I currently
have, which is an emulator?
Thanks,
Fatima
___
Freesurfer mailing list
Freesurfer@nm
Hello FS experts,
I have a large number of subjects to go through with running FS and I was
wondering if there is any other way that I can speed this process up? Where I
work, they have a "super computer" system where they can run parallel
processing and I was wondering if Fs is able to run on
Hello,
I'm currently converting my dicom images into the mgz format and I was
wondering, I only have one acquisition per subject, therefore do I have to run
the motion correction step before running autorecon1? Or can I just go straight
into running autorecon1? From the tutorial, I'd imagine I
ssage-
From: Rudolph Pienaar [mailto:rudolph.pien...@childrens.harvard.edu]
Sent: 20 October 2009 15:14
To: Ahmed, F, Me
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] out of space
You can also increase the size of your vmware disk image, or add
another "blank" vmware disk
Hello,
I'm trying to get my dicom images into my VMware desktop but I have run out of
space so can't continue to copy files over. I am trying desperately to make
space on the desktop and had a question regarding that.
I have 2 freesurfer folders; 1 is on my desktop and 1 is located in /usr/loca
, Me ; Freesurfer Mailing List; Abe, Sumiko
Subject: Re: [Freesurfer] tksurfer
I have another suggestion. When I am logged to my machine locally,
tksurfer works but only if I enable auto-redraw AND the color scale
bar. However, when I log in remotely (via FreeNX), I get the same
sliver problem
Please disregard my last email, my computer restarted and after this, VMware
loaded up normally.
-Original Message-
From: Ahmed, F, Me
Sent: 01 October 2009 09:24
To: 'Nick Schmansky'; Abe, Sumiko
Cc: Freesurfer Mailing List
Subject: RE: [Freesurfer] tksurfer
Hello,
I seem
Hello,
I seem to have a slight problem. I tried to update the Nvidia graphics driver,
as I do have this, however, when I typed in:
su root
/sbin/init 3
It closed my terminal, closed the desktop and seemed to be restarting VMware,
it went to the start up page for VMware, and asked me for
Hello,
I'm trying to view and check the smoothing and inflation surfaces, the white
and pial surfaces for "bert" using tksurfer as I'm trying to get used to using
Freesurfer, but I'm a little confused to what I'm seeing. When I type in:
"tksurfer bert lh inflated" for example, I only see a very
Ahmed, F, Me
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] autorecon2 error
The error in the log says 'cannot restore segment prot after reloc:
Permission denied', which has been appearing lately with the newest
CentOS releases.
Try typing this prior to running recon-all:
/usr/
Nick,
I tried running '/usr/sbin/setenforce 0' as root and it worked. Qdec opened.
Thank you!
-Original Message-
From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu]
Sent: 10 September 2009 17:50
To: Ahmed, F, Me
Cc: Freesurfer Mailing List
Subject: RE: [Freesu
, Me
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] qdec permission denied
This seems to be a very new problem, associated with recent OSs. Some
googling of the error message:
Error: cannot restore segment prot after reloc: Permission denied
turns-up these results:
http
Hello,
I have managed to get FS installed onto my Centos virtual machine and I'm
currently trying to carry out the testing of my installation. I got to the qdec
part and got the following:
[...@localhost freesurfer]$ qdec
qdec.bin: error while loading shared libraries:
/usr/local/freesurfer/li
know. So thanks once again.
Fatima
-Original Message-
From: Rudolph Pienaar [mailto:rudo...@nmr.mgh.harvard.edu]
Sent: 25 August 2009 16:01
To: Ahmed, F, Me
Cc: Nick Schmansky; Freesurfer Mailing List
Subject: Re: [Freesurfer] installing on ubuntu
Hi Fatima --
Ahmed, F, Me wrote:
Hi Nick,
You probably don't recall but you were trying to help me sort out a few
problems with my FS a while back. You told me to uninstall and then reinstall
to hopefully see if the problem fixes itself. The problems I face now are with
the installation, I followed the commands on the
@nmr.mgh.harvard.edu] On Behalf Of Ahmed, F, Me
Sent: Monday, August 24, 2009 5:21 AM
To: Freesurfer Mailing List
Subject: [Freesurfer] installing on ubuntu
Hello.
I am going to attempt to install FS on Ubuntu, but just had a quick question
before I start. On the Download page on the wiki site,
Hello.
I am going to attempt to install FS on Ubuntu, but just had a quick question
before I start. On the Download page on the wiki site, it states the following:
On Ubuntu, you will need to do the following:
cd /usr/lib
ln -s libtiff.so.4 libtiff.so.3
When exactly does this need to be done?
4.3.1-full.tar.gz': Permission
denied
[...@localhost Desktop]$
Can someone please explain to me why it says permission denied?
Thank you,
Fatima
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailma
y have no idea how to run this program!
Sigh, thank you for trying to help.
From: Pedro Paulo de Magalhães Oliveira Junior [mailto:p...@netfilter.com.br]
Sent: 14 August 2009 15:14
To: Ahmed, F, Me
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] installation problems
I think you should gra
The same error occurred after typing that in
From: Pedro Paulo de Magalhães Oliveira Junior [mailto:p...@netfilter.com.br]
Sent: 14 August 2009 15:08
To: Ahmed, F, Me
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] installation problems
You can copy you tgz to /usr/local or in the
Ok, how do I get it in there?
From: Pedro Paulo de Magalhães Oliveira Junior [mailto:p...@netfilter.com.br]
Sent: 14 August 2009 15:01
To: Ahmed, F, Me
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] installation problems
My guess is: your tgz is not in /usr/local
: freesurfer-Linux-centos4-stable-pub-v4.3.1-full.tar: Cannot open: No such
file or directory
tar: Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error exit delayed from previous errors
Please can you advise me on how to correct this?
Thank you kindly
Fatima
Hello,
I just have a quick question, when reinstalling FS, is it ok to use the
license that I initially received when first installing it? Or must I register
for a new license?
Thank you and Kind regards,
Fatima
___
Freesurfer mailing list
Freesurfe
Thank you Martin, you were correct, my Freesurfer was not installed in that
directory, but I managed to uninstall it...now I have to reinstall. But I'm
wondering how I'm going to avoid the same problems I faced when installing it
before. Are there any tips you (or anyone) can give
lo de
Magalhães Oliveira Junior
Sent: 11 August 2009 15:21
To: Ahmed, F, Me
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] reinstalling freesurfer
You can simply execute:
rm -rf /usr/local/freesurfer
If your freesurfer installation is in another directory, change the command
above accord
Oliveira Junior
Sent: 11 August 2009 15:21
To: Ahmed, F, Me
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] reinstalling freesurfer
You can simply execute:
rm -rf /usr/local/freesurfer
If your freesurfer installation is in another directory, change the command
above accordingly
Hello Experts,
I apologise for the stupidity of this question, but I am not used to using
Linux at all, but I need to uninstall my Freesurfer and then reinstall it,
however, I have no idea how to uninstall in Linux. Can someone possibly assist
me in this problem? I'd be extremely gra
COR/mgz
Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT
2007 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Tue Jun 30 09:43:14 BST 2009
Can anyone please tell me what this means and if I can correct it?
Thanks,
Fatima
autorecon1_Bert_errors.docx
Nick,
There is no output, I typed that in and got nothing.
[...@localhost freesurfer]$ env | grep PERL
[...@localhost freesurfer]$
Fatima
-Original Message-
From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu]
Sent: 22 June 2009 14:41
To: Ahmed, F, Me
Cc: Sita Kakunoori
Nick,
I tried running fixup_mni_paths and got the following output (see attached).
Fatima
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky
Sent: 19 June 2009 23:24
To: Ahmed, F, Me
Cc: Sita
Sorry, according to the thread that you provided me, nu_correct uses perl, so
make sure that perl is found at:
/usr/bin/perl
"perl" is found at /usr/bin/perl, so it is in the correct place and
theoretically, it should be working. But it isn't. Is there any reason why that
cou
7;s just
not working. Please help!
Thank you.
Fatima
-Original Message-
From: Sita Kakunoori [mailto:s...@nmr.mgh.harvard.edu]
Sent: 18 June 2009 18:29
To: Ahmed, F, Me
Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] error message
're-run with force' me
rd.edu]
Sent: 17 June 2009 17:12
To: Ahmed, F, Me
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] error message
Hi Fatima,
You probably would find it easier easier to just point recon-all directly
at the dicoms with -i. It saves the conversion step. If you do the
conversion and put
urfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Pedro Paulo de
Magalhães Oliveira Junior
Sent: 17 June 2009 15:14
To: Ahmed, F, Me
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] error message
Fatima,
Try this simple procedure to get started.
orecon1 -s CON_ADAMS_MONIQUE
ERROR: cannot find CON_ADAMS_MONIQUE/orig.mgz
Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT
2007 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Wed Jun 17 08:59:47 BST 2009
Please can you advise me on what the problem is and how to
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