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 $CONFIG
Make sure you only include the pathway of interest in the config file; otherwise, it will re-run the analysis for all 18. That has worked for me most of the time. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Fernando Ventrice [fventrice@fleni.org.ar] Sent: Thursday, October 18, 2012 10:14 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] FW: TRACULA some fiber volumes being too small
Dear Freesurfer/Tracula users, Finally I could successfully test Tracula and I think it is amazing what it can do automatically. These are the commands I used:
export FREESURFER_HOME=${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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