Glad to hear it worked!
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Salar Dini, Elaheh
Sent: Tuesday, December 21, 2021 6:54 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] trac-all -prep error
External Email - Use
d.edu
on behalf of Salar Dini, Elaheh
Sent: Tuesday, December 21, 2021 1:46 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] trac-all -prep error
External Email - Use Caution
Dear Anastasia,
I just wanted to follow-up on my previous message with having this in mind:
the inde
2:05 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] trac-all -prep error
Hi Ela - Do you know what phase-encode direction your DWIs were collected with
(e.g. AP, PA, LR, etc.)? Then add it to the config file like this: "set pedir =
(AP)"
Otherwise, if your data are stor
.
Thank you as always.
Kindly,
Ela
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Yendiki, Anastasia
Sent: Thursday, December 9, 2021 2:05 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] trac-all -prep error
Hi Ela - Do you know what phase
freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] trac-all -prep error
External Email - Use Caution
Dear freesurfer developers and Dr. Yendiki,
I am trying to run trac-all -prep -c dmriEla, dmriEla being my config file. I
am attaching the config file here. If I perform registration-based
External Email - Use Caution
Dear freesurfer developers and Dr. Yendiki,
I am trying to run trac-all -prep -c dmriEla, dmriEla being my config file. I
am attaching the config file here. If I perform registration-based correction
with eddy_correct, doeddy=1, things start to run.
You're running the old version, you should install 7.2
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Arman Avesta
Sent: Wednesday, December 1, 2021 10:35 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] trac-all -prep error
External Email - Use Caution
Hello Arman,
The first error indicates there is a file missing from under fsl/bin,
/usr/local/fsl/bin/eddy_correct: line 95: /usr/local/fsl/bin/imglob: No such
file or directory
- which makes me think something may not be correct with how fsl is
of Zeng, Qi
Sent: Wednesday, May 13, 2020 7:36 PM
To: Freesurfer support list
Subject: [Freesurfer] trac-all prep error
External Email - Use Caution
Hi,
I have an error message when processing trac-all prep. attached the log file.
error:
"terminate called after throwing an instance of
From: Eileen Moore eimo...@mail.sdsu.edu
Subject: Re: [Freesurfer] trac-all -prep error field map error
To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Message-ID:
CA++dajQo_2EF=
lvufckbs+_061v7dctfc5t11pn0k4g9d-c...@mail.gmail.com
Content-Type: text/plain; charset=utf
-0400 (EDT)
From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] trac-all -prep error field map error
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Message-ID:
alpine.lrh.2.03.140717040.12...@nmr.mgh.harvard.edu
Content
am still getting an
error. (See attached log file).
Thanks,
Eileen.
--
Message: 10
Date: Thu, 17 Jul 2014 04:14:16 -0400 (EDT)
From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] trac-all -prep error field map error
To: Freesurfer
for me to do epidewarp manually and then follow through with the
remaining steps using trac-all?
Thanks,
Eileen.
Date: Mon, 14 Jul 2014 11:23:47 -0400 (EDT)
From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] trac-all -prep error field map error
dicom images.
Is there a way for me to do epidewarp manually and then follow through with
the remaining steps using trac-all?
Thanks,
Eileen.
Date: Mon, 14 Jul 2014 11:23:47 -0400 (EDT)
From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] trac-all -prep error field map
Hi Eileen - That step is run with the program epidewarp.fsl, which you can
run on the command line to see the available options. The input phase map
volume is expected to have either 2 frames (2 separate phase maps) or 1
frame (the difference phase map). This error from trac-all means that it
Hi Verena - Which version of freesurfer are you using? In the public
release of 5.1 the CVS registration option in trac-all is disabled.
a.y
On Tue, 23 Oct 2012, Verena Gramse wrote:
From: Verena Gramse
Sent:
...@nmr.mgh.harvard.edu]
Sent: Tuesday, October 23, 2012 12:00 PM
To: Verena Gramse
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] trac-all -prep error during inter-subject
registration with mri_cvs_register
Hi Verena - Which version of freesurfer are you using? In the public
release of 5.1 the CVS
From: Verena Gramse
Sent: Monday, October 22, 2012 8:19 PM
To: freesur...@nmr.mgh.harvard
Subject: trac-all -prep error during inter-subject registration with
mri_cvs_register
Dear Tracula Team,
I have been running into problems during Inter-subject
Hi Sarina - You'll have to specify the list of gradient directions
(bvecfile) and b-values (bvalfile), see here for more info:
http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc
Please send email to the freesurfer list and not to me directly. Emails
sent to the freesurfer list are saved
quando avvio il trac-all (relase FS5.1) mi crea questo errore:
/opt/freesurfer/bin/trac-preproc
#-
#@# Image corrections Tue Mar 27 11:17:27 CEST 2012
mri_convert
Ciao Sarina - The problem is here fslorient: Command not found. You have
to make sure that FSL is properly installed and the FSL executables are in
your path, as trac-all calls a few of them.
Hope this helps,
a.y
On Tue, 27 Mar 2012, Sarina Sacco wrote:
quando avvio il trac-all (relase
Hello, in running trac-all -prep, I get an error saying that it can't
open lowb.nii.gz.hdr:
fslroi
/raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/dwi.nii.gz
/raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz
0 1
fslmaths
Hey Chris - That is strange. The FSLOUTPUTTYPE would've been my first
guess, too. Does this lowb.nii.gz actually exist? Anything looks strange
when you run mri_info/freeview/fslview on it?
a.y
On Wed, 15 Feb 2012, Chris Watson wrote:
Hello, in running trac-all -prep, I get an error saying
Here's output from mri_info:
[freesurfer@occipital dmri]$ mri_info lowb.nii.gz
Volume information for lowb.nii.gz
type: nii
dimensions: 96 x 96 x 56
voxel sizes: 2.5000, 2.5000, 2.5000
type: FLOAT (3)
fov: 240.000
dof: 0
xstart: -120.0,
When you run that bet command line outside of trac-all, does it give you
the same error?
On Wed, 15 Feb 2012, Chris Watson wrote:
Here's output from mri_info:
[freesurfer@occipital dmri]$ mri_info lowb.nii.gz
Volume information for lowb.nii.gz
type: nii
dimensions: 96 x 96 x 56
Yes, the same error.
Chris
Anastasia Yendiki wrote:
When you run that bet command line outside of trac-all, does it give
you the same error?
On Wed, 15 Feb 2012, Chris Watson wrote:
Here's output from mri_info:
[freesurfer@occipital dmri]$ mri_info lowb.nii.gz
Volume information for
Actually, it now works when I re-source my .bash_profile and .bashrc
files. Not sure why that would be.
Chris
Chris Watson wrote:
Yes, the same error.
Chris
Anastasia Yendiki wrote:
When you run that bet command line outside of trac-all, does it give
you the same error?
On Wed, 15
Weird. Glad it got fixed, let us know if you have any more trouble.
On Wed, 15 Feb 2012, Chris Watson wrote:
Actually, it now works when I re-source my .bash_profile and .bashrc files.
Not sure why that would be.
Chris
Chris Watson wrote:
Yes, the same error.
Chris
Anastasia
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