If FSL isn't happy with the directions, that's going to be fatal b/c
trac-all relies on bedpostx running properly. I'm going to look into this
further to try to figure out what it is about this data that's causing
the discrepancy.
On Wed, 31 Oct 2012, Fernando Ventrice wrote:
Dear Anastasia,
When I open the dtifit_V1 and dtifit_FA with Freeview the vector directions
actually are OK, but when I open them with FSLview they are similar to your
screen-shot. Here I also send a screen-shot with the comparison between the two
softwares in each monitor.
Best,
Fernando
________________________________________
From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: Tuesday, October 30, 2012 1:24 PM
To: Fernando Ventrice
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FW: TRACULA some fiber volumes being too small
See screenshot now :)
On Tue, 30 Oct 2012, Anastasia Yendiki wrote:
Hi Fernando - Thanks for uploading your data. Looking at the primary
directions from tensor fit on the data that you sent me (see screenshot),
they seem to be off by a 90 degree angle from what you'd expect them. This
means that your gradient table is probably off as well.
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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El contenido del presente mensaje y el de sus adjuntos, es confidencial,
privado y de uso exclusivo de los destinatarios a los cuales está dirigido,
pudiendo contener información legalmente protegida. Queda prohibida la
revisión, divulgación, publicación, modificación, copia, distribución o acción
en relación con esta información, por personas o entidades distintas al
destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor
tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son
exclusivas de su autor, y no representa necesariamente, la opinión de FLENI.
http://www.fleni.org.ar
El contenido del presente mensaje y el de sus adjuntos, es confidencial,
privado y de uso exclusivo de los destinatarios a los cuales está dirigido,
pudiendo contener información legalmente protegida. Queda prohibida la
revisión, divulgación, publicación, modificación, copia, distribución o acción
en relación con esta información, por personas o entidades distintas al
destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor
tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son
exclusivas de su autor, y no representa necesariamente, la opinión de FLENI.
http://www.fleni.org.ar
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