Hi Fernando - Thank you for your kind words. You can indeed try the reinit
option as Christofer suggested when one of the pathways looks like a
single curve and not like a volume.
However, because some of your other pathways in the screenshots look a bit
funky too, I would also check that there was nothing wrong with the
gradient directions. An easy way to check that is by looking at the
eigenvectors from the tensor fit (dmri/dtifit_V1.nii.gz). Although tracula
itself doesn't use tensors, if there's something wrong with the gradient
directions, it'll show up in the tensor fit.
If you're not sure how to check, you can upload all tracula-related
directories of your subject here and I'll take a look:
http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
Hope this helps,
a.y
On Thu, 18 Oct 2012, Fernando Ventrice wrote:
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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