There were recently a few messages on the list regarding this.
What you should do is include "set reinit=1" in your config file, and then run
trac-all -priors -c $CONFIG
trac-all -path -c $CONFIG
Make sure you only include the pathway of interest in the config file;
otherwise, it will re-run the analysis for all 18.
That has worked for me most of the time.
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fernando Ventrice
[fventr...@fleni.org.ar]
Sent: Thursday, October 18, 2012 10:14 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] FW: TRACULA some fiber volumes being too small
Dear Freesurfer/Tracula users,
Finally I could successfully test Tracula and I think it is amazing what it can
do automatically. These are the commands I used:
export FREESURFER_HOME=${HOME}/Programs/freesurfer_510 && source
$FREESURFER_HOME/SetUpFreeSurfer.sh
source /etc/fsl/fsl.sh
export FSLPARALLEL=condor
trac-all -prep -c
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice
trac-all -bedp -c
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice
# "trac-all -bedp" gave some errors so I used bedpostx directly:
bedpostx
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dmri
trac-all -path -c
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice
freeview -tv
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dpath/merged_avg33_mni_flt.mgz
-v
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dmri/dtifit_FA.nii.gz
&
All finished without errors, but there seems to be a problem with CC Forceps
Mayor volume, which gave very small values. Is this OK or I made some mistake?
First I tested with some patient and other fiber tracks also gave very small
volumes. I attached some pictures and the dmrirc and trac-all log files.
Best,
Fernando Ventrice
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