:
[Freesurfer] From
bedpostX and
recon-all to
tracula
After
removing
Subject:
Re:
[Freesurfer] From
bedpostX and
recon-all to
tracula
:
[Freesurfer]
From
bedpostX and
recon-all to
tracula
support
list
Subject: Re:
[Freesurfer] From
bedpostX and
recon-all to tracula
After removing this I
have a new
Subject:
Re:
[Freesurfer] From
bedpostX and
recon-all to
tracula
Cc: Freesurfer support list
Subject: Re: [Freesurfer] From bedpostX and recon-all to tracula
After removing this I have a new (possibly unrelated error):
mv -f /media/Sokol/Subj/041/dmri/bvecs /media/Sokol/Subj/041/dmri/
bvecs.norot
xfmrot /media/Sokol/Subj/041/dmri
, 2014 5:29 PM
To: Anastasia Yendiki
Cc: Freesurfer support list
Subject: Re: [Freesurfer] From bedpostX and
recon-all to tracula
After removing this I have a new (possibly
unrelated error
]
Sent: Monday, December 15, 2014
5:29 PM
To: Anastasia Yendiki
Cc: Freesurfer support list
Subject: Re: [Freesurfer] From
bedpostX
...@nmr.mgh.harvard.edu] on behalf of
Katherine Damme [katherine.da...@gmail.com
mailto:katherine.da...@gmail.com]
Sent: Monday, December 15, 2014 5:29 PM
To: Anastasia Yendiki
Cc: Freesurfer support list
Subject: Re: [Freesurfer] From bedpostX and recon-all to tracula
After
[katherine.da...@gmail.com]
Sent: Monday, December 15, 2014 5:29 PM
To: Anastasia Yendiki
Cc: Freesurfer support list
Subject: Re: [Freesurfer] From bedpostX and recon-all to tracula
After removing this I have a new (possibly unrelated error):
mv -f /media
Where would I be specifying a directory as an input/output?
I used the following cmd: /usr/local/freesurfer/bin/trac-all -prep -c
dmri.fy
On Sun, Dec 14, 2014 at 7:12 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
Hi Katerine
the COR-* format is an old one that we don't use anymore. If
It's hard to tell what's causing the error without seeing the entire
trac-all.log. However, by glancing at your config file you seem to still
have B0 inhomogeneity correction turned on (dob0 = 1) but without
specifying any field map dicoms. I'd turn it off and see if that fixes it.
On Mon,
, December 15, 2014 5:29 PM
To: Anastasia Yendiki
Cc: Freesurfer support list
Subject: Re: [Freesurfer] From bedpostX and recon-all to tracula
After removing this I have a new (possibly unrelated error):
mv -f /media/Sokol/Subj/041/dmri/bvecs /media/Sokol/Subj/041/dmri/bvecs.norot
xfmrot /media/Sokol/Subj
, Christopher
[christopher.wat...@childrens.harvard.edu]
Sent: Monday, December 15, 2014 8:42 PM
To: Freesurfer support list; Anastasia Yendiki
Subject: Re: [Freesurfer] From bedpostX and recon-all to tracula
I think certain filesystems don't support sym linking (e.g. FAT32). So that
might
At what point is the COR-*.info file made?
I got the following error:
corRead(): can't open file /media/Sokol/Subj/COR-.info
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /media/Sokol/Subj/...
Linux kate.ad.wcas.northwestern.edu 2.6.32-431.3.1.el6.x86_64 #1 SMP
Hi Katerine
the COR-* format is an old one that we don't use anymore. If you specify
a directory as an input/output we will assume that it contains COR files,
which is probably what you are seeing.
cheers
Bruce
On Sun, 14 Dec 2014, Katherine Damme wrote:
At what point is the COR-*.info
Hi Kate - The screenshot looks more like a low-b image from a diffusion
scan than a field map. In case this helps, the phase map data will have
either 2 volumes (2 phase maps acquired at different echo times) or 1
volume (the difference of 2 such phase maps).
Best,
a.y
On Thu, 11 Dec 2014,
I am sorry, I am a bit confused. What am I supposed to be specifying under
the b0mlist and b0plist?
I thought that it was the B0 low-b image from diffusion.
Thank you!
On Thu, Dec 11, 2014 at 2:25 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Kate - The screenshot looks more
No, those are field maps used to correct for inhomogeneities in the main
magnetic field (which in MRI lingo is referred to as the B0 field, not to
be confused with the b=0 images). You can skip that correction (you have
to skip it if you don't have field maps).
On Thu, 11 Dec 2014,
Hi Kate - The -prep, -bedp, and -path steps need to be run separately, in
that order. You can't run them all at once unfortunately. See:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula
a.y
On Wed, 29 Oct 2014, Katherine Damme wrote:
Sorry for the delay. I signed
Can you please attach the trac-all.log file, which has the entire output
from beginning to end? Ofter something goes wrong earlier that causes the
program to fail later in the process.
Also, we'll need your original configuration file. Thanks!
On Mon, 8 Sep 2014, Katherine Damme wrote:
Hello Freesurfer Community!
Thank you Anastasia and Christopher, I am still getting ending with errors
and the log file gives no clue that I have been able to detect, see
attached.
Any help would be appreciated!
On Thu, Sep 4, 2014 at 4:29 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu
If you sym link the already finished bedpostx directory to
$SUBJECT/dmri.bedpostX, you should be able to run trac-all -prep and
trac-all -path without any issues (adjusting the config that comes with
tracula)
On 09/03/2014 05:04 PM, Katherine Damme wrote:
Hello Freesurfer Community!
I have
Hi Kate - There is an example configuration file for tracula in your
freesurfer distribution ($FREESURFER_HOME/bin/dmrirc.example). The same
file is also here:
http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc
If you attach your configuration file and the log file
(scripts/trac-all.log), we can
Hello Freesurfer Community!
I have sucessfully completed diffusion preprocessing in FSL and the
recon-all of the structural image and would like to use tracula for the
tract reconstruction. I keep having trouble with my configuration file.
Does anyone have a bedpostX tracula config file they
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