Hi Francesco - It looks like you haven't defined SUBJECTS_DIR in your
configuration file. That needs to be set to the directory where the
freesurfer recons of your subjects' T1 scans can be found. For more info,
check the example configuration file, $FREESURFER_HOME/bin/dmrirc.example,
or
Hi Anastasia,
Thank you for the help, finally I discovered the cause of the problem. The
language of the system was set to Italian which use the comma as a decimal
separator instead of the dot. So I was able to run the trac-all but I
encountered another problem. The error I'm getting is the
Hi Francesco - Please attach your trac-all.log file. There may be an error
at an earlier stage that's causing this error.
Thanks,
a.y
On Thu, 13 Feb 2014, Francesco Baldacchini wrote:
Hi Anastasia,
Thank you for the help, finally I discovered the cause of the problem. The
language of the
Ciao Francesco - Just to clarify, to be able to have your bvecs/bvals in
rows, you should have, in addition to the latest version of freesurfer,
the update that I linked to below:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates
a.y
On Tue, 11 Feb 2014, Francesco
Hi Francesco - The decimal separator should be dot, not comma. Can you
send me the bvecs/bvals that you get after you change from row to column
format? (Both the ones that you feed into trac-all and the ones that get
created under dmri/.)
Thanks,
a.y
On Tue, 11 Feb 2014, Francesco
Ciao Anastasia, I checked and I'm using the latest version of Freesurfer,
version 5.3.0. It seems like that the command trac-all path while working
on the bvecs table and doing the corrections makes some errors and you can
see it from the bvecs file I found in the dmri directory which is only 4
Hi again Anastasia,
I tried also to convert my three row bvecs file in a three column one but I
still got the same bvecs and bvals don't have the same number of entries
error. I then tried also to change the dot to comma as the decimal
separator but still nothing
Francesco Baldacchini
Hi Francesco - Which version of tracula are you running? To be able to use
bvecs files that are in 3 rows instead of 3 columns, you need to make sure
that you have the latest update to tracula, see here:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates
This option was not
Hi,
Sorry Anastasia, I'm seeing that my question was not so clear. The files I
sent you in the first mail are the bvecs and bvals saved by trac-all -prep
in the dmri directory. The original files are in attachment in this mail,
Francesco Baldacchini
2014/1/13 Anastasia Yendiki
